PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies
items: Study of marsh wetland landscape pattern evolution on the Zoigê Plateau due to natural/human dual-effects
items: A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma
items: Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis
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

Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies
type: item
type: AcademicArticle
description: Background The blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system. Methods By reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages. Results While the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our m…
format: application/pdf
format: text/html
creator: Jennifer Enciso
creator: Luis Mendoza
creator: Elena R. Álvarez-Buylla
creator: Rosana Pelayo
subject: Computational Biology
subject: Hematology
subject: Immunology
description: doi:10.7717/peerj.9902
publisher: PeerJ Inc.
rights: © 2020 Enciso et al.
abstract: Background The blockage at the early B lymphoid cell development pathway within the bone marrow is tightly associated with hematopoietic and immune diseases, where the disruption of basal regulatory networks prevents the continuous replenishment of functional B cells. Dynamic computational models may be instrumental for the comprehensive understanding of mechanisms underlying complex differentiation processes and provide novel prediction/intervention platforms to reinvigorate the system. Methods By reconstructing a three-module regulatory network including genetic transcription, intracellular transduction, and microenvironment communication, we have investigated the early B lineage cell fate decisions in normal and pathological settings. The early B cell differentiation network was simulated as a Boolean model and then transformed, using fuzzy logic, to a continuous model. We tested null and overexpression mutants to analyze the emergent behavior of the network. Due to its importance in inflammation, we investigated the effect of NFkB induction at different early B cell differentiation stages. Results While the exhaustive synchronous and asynchronous simulation of the early B cell regulatory network (eBCRN) reproduced the configurations of the hematopoietic progenitors and early B lymphoid precursors of the pathway, its simulation as a continuous model with fuzzy logics suggested a transient IL-7R+ ProB-to-Pre-B subset expressing pre-BCR and a series of dominant B-cell transcriptional factors. This conspicuous differentiating cell population up-regulated CXCR7 and reduced CXCR4 and FoxO1 expression levels. Strikingly, constant but intermediate NFkB signaling at specific B cell differentiation stages allowed stabilization of an aberrant CXCR7+ pre-B like phenotype with apparent affinity to proliferative signals, while under constitutive overactivation of NFkB, such cell phenotype was aberrantly exacerbated from the earliest stage of common lymphoid progenitors. Our m…
bibliographic citation: Enciso et al. (2020) Dynamical modeling predicts an inflammation-inducible CXCR7+ B cell precursor with potential implications in lymphoid blockage pathologies. PeerJ 8:e9902 https://doi.org/10.7717/peerj.9902
date submitted: 2020-03-24
date accepted: 2020-08-18
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Enciso
  given name: Jennifer
author list: Agent
  family name: Mendoza
  given name: Luis
author list: Agent
  family name: Álvarez-Buylla
  given name: Elena R.
author list: Agent
  family name: Pelayo
  given name: Rosana
doi: 10.7717/peerj.9902
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Enciso et al.
attribution name: Enciso et al.

Study of marsh wetland landscape pattern evolution on the Zoigê Plateau due to natural/human dual-effects
type: item
type: AcademicArticle
description: Zoigê Plateau, China’s largest plateau marsh wetland, has experienced large-scale degradation of the marsh wetland and evolution of the wetland landscape pattern over the past 40 years due to climate warming and human activities. How exactly do the wetland landscape pattern characteristics change? How do climatic change and human activities affect the wetland evolution? These questions are yet to be systematically investigated. In order to investigate changes to the marsh wetland on the Zoigê Plateau, field investigations, spatial and statistical analysis were undertaken. Findings from our study indicate that from 1977–2016, the area of marsh wetland on the Plateau reduced by 56.54%, approximately 66,700 hm2 of marsh wetland has been lost. The centroids of both marsh and marshy meadow migrated and the landscape centroid migration behaviors were also correlated with the distribution and variation of the marsh wetland on different slopes. In addition, the number of marsh landscape patches initially increased before decreasing; the number of marshy meadow landscape patches also recorded an initial increase, followed by a decline before a final increase. As the effects of human activities weakened, the aggregation degrees of both marsh and marshy meadow increased. Overall, the fragmentation degree, diversity and fractal dimension of the marsh wetland all declined. An investigation into the driving factors affecting the Plateau area shows that the increase of annual average temperature was the natural factor while trenching and overgrazing were the main human factors resulting in wetland degradation. Results from this study provide basic data and theoretical foundation for the protection and restoration of marsh wetland in alpine regions.
format: application/pdf
format: text/html
creator: Liqin Dong
creator: Wen Yang
creator: Kun Zhang
creator: Shuo Zhen
creator: Xiping Cheng
creator: Lihua Wu
subject: Ecosystem Science
subject: Ecohydrology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9904
publisher: PeerJ Inc.
rights: © 2020 Dong et al.
abstract: Zoigê Plateau, China’s largest plateau marsh wetland, has experienced large-scale degradation of the marsh wetland and evolution of the wetland landscape pattern over the past 40 years due to climate warming and human activities. How exactly do the wetland landscape pattern characteristics change? How do climatic change and human activities affect the wetland evolution? These questions are yet to be systematically investigated. In order to investigate changes to the marsh wetland on the Zoigê Plateau, field investigations, spatial and statistical analysis were undertaken. Findings from our study indicate that from 1977–2016, the area of marsh wetland on the Plateau reduced by 56.54%, approximately 66,700 hm2 of marsh wetland has been lost. The centroids of both marsh and marshy meadow migrated and the landscape centroid migration behaviors were also correlated with the distribution and variation of the marsh wetland on different slopes. In addition, the number of marsh landscape patches initially increased before decreasing; the number of marshy meadow landscape patches also recorded an initial increase, followed by a decline before a final increase. As the effects of human activities weakened, the aggregation degrees of both marsh and marshy meadow increased. Overall, the fragmentation degree, diversity and fractal dimension of the marsh wetland all declined. An investigation into the driving factors affecting the Plateau area shows that the increase of annual average temperature was the natural factor while trenching and overgrazing were the main human factors resulting in wetland degradation. Results from this study provide basic data and theoretical foundation for the protection and restoration of marsh wetland in alpine regions.
bibliographic citation: Dong et al. (2020) Study of marsh wetland landscape pattern evolution on the Zoigê Plateau due to natural/human dual-effects. PeerJ 8:e9904 https://doi.org/10.7717/peerj.9904
date submitted: 2020-03-10
date accepted: 2020-08-18
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Dong
  given name: Liqin
author list: Agent
  family name: Yang
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Kun
author list: Agent
  family name: Zhen
  given name: Shuo
author list: Agent
  family name: Cheng
  given name: Xiping
author list: Agent
  family name: Wu
  given name: Lihua
doi: 10.7717/peerj.9904
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Dong et al.
attribution name: Dong et al.

A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC. Methods Based on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets. Results Seventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets. Conclusion The seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC.
format: application/pdf
format: text/html
creator: Weige Zhou
creator: Shijing Zhang
creator: Zheyou Cai
creator: Fei Gao
creator: Wenhui Deng
creator: Yi Wen
creator: Zhen-wen Qiu
creator: Zheng-kun Hou
creator: Xin-Lin Chen
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.9944
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: Background Hepatocellular carcinoma (HCC) is one of the most universal malignant liver tumors worldwide. However, there were no systematic studies to establish glycolysis‑related gene pairs (GRGPs) signatures for the patients with HCC. Therefore, the study aimed to establish novel GRGPs signatures to better predict the prognosis of HCC. Methods Based on the data from Gene Expression Omnibus, The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium databases, glycolysis-related mRNAs were used to construct GRGPs. Cox regression was applied to establish a seventeen GRGPs signature in TCGA dataset, which was verified in two validation (European and American, and Asian) datasets. Results Seventeen prognostic GRGPs (HMMR_PFKFB1, CHST1_GYS2, MERTK_GYS2, GPC1_GYS2, LDHA_GOT2, IDUA_GNPDA1, IDUA_ME2, IDUA_G6PD, IDUA_GPC1, MPI_GPC1, SDC2_LDHA, PRPS1_PLOD2, GALK1_IER3, MET_PLOD2, GUSB_IGFBP3, IL13RA1_IGFBP3 and CYB5A_IGFBP3) were identified to be significantly progressive factors for the patients with HCC in the TCGA dataset, which constituted a GRGPs signature. The patients with HCC were classified into low-risk group and high-risk group based on the GRGPs signature. The GRGPs signature was a significantly independent prognostic indicator for the patients with HCC in TCGA (log-rank P = 2.898e−14). Consistent with the TCGA dataset, the patients in low-risk group had a longer OS in two validation datasets (European and American: P = 1.143e−02, and Asian: P = 6.342e−08). Additionally, the GRGPs signature was also validated as a significantly independent prognostic indicator in two validation datasets. Conclusion The seventeen GRGPs and their signature might be molecular biomarkers and therapeutic targets for the patients with HCC.
bibliographic citation: Zhou et al. (2020) A glycolysis-related gene pairs signature predicts prognosis in patients with hepatocellular carcinoma. PeerJ 8:e9944 https://doi.org/10.7717/peerj.9944
date submitted: 2020-05-07
date accepted: 2020-08-24
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Weige
author list: Agent
  family name: Zhang
  given name: Shijing
author list: Agent
  family name: Cai
  given name: Zheyou
author list: Agent
  family name: Gao
  given name: Fei
author list: Agent
  family name: Deng
  given name: Wenhui
author list: Agent
  family name: Wen
  given name: Yi
author list: Agent
  family name: Qiu
  given name: Zhen-wen
author list: Agent
  family name: Hou
  given name: Zheng-kun
author list: Agent
  family name: Chen
  given name: Xin-Lin
doi: 10.7717/peerj.9944
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: © 2020 Zhou et al.
attribution name: Zhou et al.

Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis
type: item
type: AcademicArticle
description: Breast cancer is one of the most common malignant tumors among women worldwide and has a high morbidity and mortality. This research aimed to identify hub genes and small molecule drugs for breast cancer by integrated bioinformatics analysis. After downloading multiple gene expression datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, 283 overlapping differentially expressed genes (DEGs) significantly enriched in different cancer-related functions and pathways were obtained using LIMMA, VennDiagram and ClusterProfiler packages of R. We then analyzed the topology of protein–protein interaction (PPI) network with overlapping DEGs and further obtained six hub genes (RRM2, CDC20, CCNB2, BUB1B, CDK1, and CCNA2) from the network via STRING and Cytoscape. Subsequently, we conducted genes expression verification, genetic alterations evaluation, immune infiltration prediction, clinicopathological parameters analysis, identification of transcriptional and post-transcriptional regulatory molecules, and survival analysis for these hub genes. Meanwhile, 29 possible drug candidates (e.g., Cladribine, Gallium nitrate, Alvocidib, 1β-hydroxyalantolactone, Berberine hydrochloride, Nitidine chloride) were identified from the DGIdb database and the GSE85871 dataset. In addition, some transcription factors and miRNAs (e.g., E2F1, PTTG1, TP53, ZBTB16, hsa-miR-130a-3p, hsa-miR-204-5p) targeting hub genes were identified as key regulators in the progression of breast cancer. In conclusion, our study identified six hub genes and 29 potential drug candidates for breast cancer. These findings may advance understanding regarding the diagnosis, prognosis and treatment of breast cancer.
format: application/pdf
format: text/html
creator: Mingqian Hao
creator: Wencong Liu
creator: Chuanbo Ding
creator: Xiaojuan Peng
creator: Yue Zhang
creator: Huiying Chen
creator: Ling Dong
creator: Xinglong Liu
creator: Yingchun Zhao
creator: Xueyan Chen
creator: Sadia Khatoon
creator: Yinan Zheng
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.9946
publisher: PeerJ Inc.
rights: © 2020 Hao et al.
abstract: Breast cancer is one of the most common malignant tumors among women worldwide and has a high morbidity and mortality. This research aimed to identify hub genes and small molecule drugs for breast cancer by integrated bioinformatics analysis. After downloading multiple gene expression datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, 283 overlapping differentially expressed genes (DEGs) significantly enriched in different cancer-related functions and pathways were obtained using LIMMA, VennDiagram and ClusterProfiler packages of R. We then analyzed the topology of protein–protein interaction (PPI) network with overlapping DEGs and further obtained six hub genes (RRM2, CDC20, CCNB2, BUB1B, CDK1, and CCNA2) from the network via STRING and Cytoscape. Subsequently, we conducted genes expression verification, genetic alterations evaluation, immune infiltration prediction, clinicopathological parameters analysis, identification of transcriptional and post-transcriptional regulatory molecules, and survival analysis for these hub genes. Meanwhile, 29 possible drug candidates (e.g., Cladribine, Gallium nitrate, Alvocidib, 1β-hydroxyalantolactone, Berberine hydrochloride, Nitidine chloride) were identified from the DGIdb database and the GSE85871 dataset. In addition, some transcription factors and miRNAs (e.g., E2F1, PTTG1, TP53, ZBTB16, hsa-miR-130a-3p, hsa-miR-204-5p) targeting hub genes were identified as key regulators in the progression of breast cancer. In conclusion, our study identified six hub genes and 29 potential drug candidates for breast cancer. These findings may advance understanding regarding the diagnosis, prognosis and treatment of breast cancer.
bibliographic citation: Hao et al. (2020) Identification of hub genes and small molecule therapeutic drugs related to breast cancer with comprehensive bioinformatics analysis. PeerJ 8:e9946 https://doi.org/10.7717/peerj.9946
date submitted: 2020-06-11
date accepted: 2020-08-25
issued: 2020-09-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Mingqian
author list: Agent
  family name: Liu
  given name: Wencong
author list: Agent
  family name: Ding
  given name: Chuanbo
author list: Agent
  family name: Peng
  given name: Xiaojuan
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Chen
  given name: Huiying
author list: Agent
  family name: Dong
  given name: Ling
author list: Agent
  family name: Liu
  given name: Xinglong
author list: Agent
  family name: Zhao
  given name: Yingchun
author list: Agent
  family name: Chen
  given name: Xueyan
author list: Agent
  family name: Khatoon
  given name: Sadia
author list: Agent
  family name: Zheng
  given name: Yinan
doi: 10.7717/peerj.9946
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-09-29
copyright: ©2020 Hao et al.
attribution name: Hao et al.

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.
format: application/pdf
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.
format: application/pdf
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

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