PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Hellebrigenin anti-pancreatic cancer effects based on apoptosis and autophage
items: Characteristics of the soil microbial community in the forestland of Camellia oleifera
items: Impact of electrocardiographic morphology on clinical outcomes in patients with non-ST elevation myocardial infarction receiving coronary angiography and intervention: a retrospective study
items: Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets
items: Association of heart rate trajectories with the risk of adverse outcomes in a community-based cohort in Taiwan
items: Understanding PM2.5 concentration and removal efficiency variation in urban forest park—Observation at human breathing height
items: Tetrandrine alleviates cerebral ischemia/reperfusion injury by suppressing NLRP3 inflammasome activation via Sirt-1
items: Public perspectives and media reporting of wolf reintroduction in Colorado
items: Resampling-based methods for biologists
items: Evaluation of a novel syndromic surveillance system for the detection of the 2007 melamine-related nephrotoxicosis foodborne outbreak in dogs and cats in the United States

Hellebrigenin anti-pancreatic cancer effects based on apoptosis and autophage
type: item
type: AcademicArticle
description: Hellebrigenin is a natural product found in the toad skin secretions and plants of Urginea, including Hellebores and Kalanchoe genera. It has been shown to be active against Leishmania chagasi promastigotes and Trypanosoma cruzi trypomastigotes and also reported to play an anti-tumor effect on several cancer cell lines in vitro, including pancreatic cancer. This study is aimed to investigate the effects of Hellebrigenin on pancreatic carcinoma cells, SW1990 and BxPC-3 in vitro and its molecular mechanism involved in antitumor activities. Our results showed that Hellebrigenin effectively inhibited the proliferation of SW1990 and BxPC-3 cells in dose- and time-dependent manner. Flow cytometry results showed that Hellebrigenin induced the G0/G1 arrest in both of SW1990 and BxPC-3 cells and promoted cell early apoptosis and autophagy according to morphological observation. Immunofluorescence staining results further confirmed that cell apoptosis and autophagy also increased upon the Hellebrigenin treatment. Moreover, higher dose of Hellebrigenin further increased the cell apoptosis rate while decrease the mitochondrial membrane potential 24 h after treatment. The autophagy rate increased 48 h after treatment with significant difference (P < 0.05). Western blot analysis showed that the expression of caspase 3, 7, cleaved caspase 7, Atg 12, LC3 proteins were increased in SW1990 cell after treatment with Hellebrigenin. In addition, increasing expression of caspase 3, 7, 9, PARP, cleaved caspase 3, 7, 9, PARP, the sub basic protein of the PI3K family, Beclin-1, LC 3, Atg 3, 5, 12, 16 L were also observed after BxPC-3 cells treated with Hellebrigenin. In summary, this study reported for the first time that Hellebrigenin effectively induced autophagy and apoptosis especially the early apoptosis in SW1990 and BxPC-3 cells.
format: application/pdf
format: text/html
creator: Xiaolu Wei
creator: Jing He
creator: Bo Gao
creator: Lingyu Han
creator: Yingqiu Mao
creator: Haiyu Zhao
creator: Nan Si
creator: Hongjie Wang
creator: Jian Yang
creator: Baolin Bian
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.9011
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: Hellebrigenin is a natural product found in the toad skin secretions and plants of Urginea, including Hellebores and Kalanchoe genera. It has been shown to be active against Leishmania chagasi promastigotes and Trypanosoma cruzi trypomastigotes and also reported to play an anti-tumor effect on several cancer cell lines in vitro, including pancreatic cancer. This study is aimed to investigate the effects of Hellebrigenin on pancreatic carcinoma cells, SW1990 and BxPC-3 in vitro and its molecular mechanism involved in antitumor activities. Our results showed that Hellebrigenin effectively inhibited the proliferation of SW1990 and BxPC-3 cells in dose- and time-dependent manner. Flow cytometry results showed that Hellebrigenin induced the G0/G1 arrest in both of SW1990 and BxPC-3 cells and promoted cell early apoptosis and autophagy according to morphological observation. Immunofluorescence staining results further confirmed that cell apoptosis and autophagy also increased upon the Hellebrigenin treatment. Moreover, higher dose of Hellebrigenin further increased the cell apoptosis rate while decrease the mitochondrial membrane potential 24 h after treatment. The autophagy rate increased 48 h after treatment with significant difference (P < 0.05). Western blot analysis showed that the expression of caspase 3, 7, cleaved caspase 7, Atg 12, LC3 proteins were increased in SW1990 cell after treatment with Hellebrigenin. In addition, increasing expression of caspase 3, 7, 9, PARP, cleaved caspase 3, 7, 9, PARP, the sub basic protein of the PI3K family, Beclin-1, LC 3, Atg 3, 5, 12, 16 L were also observed after BxPC-3 cells treated with Hellebrigenin. In summary, this study reported for the first time that Hellebrigenin effectively induced autophagy and apoptosis especially the early apoptosis in SW1990 and BxPC-3 cells.
bibliographic citation: Wei et al. (2020) Hellebrigenin anti-pancreatic cancer effects based on apoptosis and autophage. PeerJ 8:e9011 https://doi.org/10.7717/peerj.9011
date submitted: 2019-11-07
date accepted: 2020-03-27
issued: 2020-05-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Xiaolu
author list: Agent
  family name: He
  given name: Jing
author list: Agent
  family name: Gao
  given name: Bo
author list: Agent
  family name: Han
  given name: Lingyu
author list: Agent
  family name: Mao
  given name: Yingqiu
author list: Agent
  family name: Zhao
  given name: Haiyu
author list: Agent
  family name: Si
  given name: Nan
author list: Agent
  family name: Wang
  given name: Hongjie
author list: Agent
  family name: Yang
  given name: Jian
author list: Agent
  family name: Bian
  given name: Baolin
doi: 10.7717/peerj.9011
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-08
copyright: © 2020 Wei et al.
attribution name: Wei et al.

Characteristics of the soil microbial community in the forestland of Camellia oleifera
type: item
type: AcademicArticle
description: Characterizing soil microbial community is important for forest ecosystem management and microbial utilization. The microbial community in the soil beneath Camellia oleifera, an important woody edible oil tree in China, has not been reported before. Here, we used Illumina sequencing of 16S and ITS rRNA genes to study the species diversity of microorganisms in C. oleifera forest land in South China. The results showed that the rhizosphere soil had higher physicochemical properties, enzyme activities and microbial biomass than did the non-rhizosphere soil. The rhizosphere soil microorganisms had a higher carbon source utilization capacity than the non-rhizosphere soil microorganisms, and attained the highest utilization capacity in summer. The soil microbial community of C. oleifera was characterized by rich ester and amino acid carbon sources that played major roles in the principal functional components of the community. In summer, soil microbes were abundant in species richness and very active in community function. Rhizosphere microorganisms were more diverse than non-root systems in species diversity, which was associated with soil pH, Available phosphorous (AP) and Urease (URE). These results indicated that microbial resources were rich in rhizosphere soil. A priority should be given to the rhizosphere microorganisms in the growing season in developing and utilizing soil microorganisms in C. oleifera plantation. It is possible to promote the growth of C. oleifera by changing soil microbial community, including carbon source species, pH, AP, and URE. Our findings provide valuable information to guide microbial isolation and culturing to manage C. oleifera land.
format: application/pdf
format: text/html
creator: Peng Zhang
creator: Zhiyi Cui
creator: Mengqing Guo
creator: Ruchun Xi
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.9117
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Characterizing soil microbial community is important for forest ecosystem management and microbial utilization. The microbial community in the soil beneath Camellia oleifera, an important woody edible oil tree in China, has not been reported before. Here, we used Illumina sequencing of 16S and ITS rRNA genes to study the species diversity of microorganisms in C. oleifera forest land in South China. The results showed that the rhizosphere soil had higher physicochemical properties, enzyme activities and microbial biomass than did the non-rhizosphere soil. The rhizosphere soil microorganisms had a higher carbon source utilization capacity than the non-rhizosphere soil microorganisms, and attained the highest utilization capacity in summer. The soil microbial community of C. oleifera was characterized by rich ester and amino acid carbon sources that played major roles in the principal functional components of the community. In summer, soil microbes were abundant in species richness and very active in community function. Rhizosphere microorganisms were more diverse than non-root systems in species diversity, which was associated with soil pH, Available phosphorous (AP) and Urease (URE). These results indicated that microbial resources were rich in rhizosphere soil. A priority should be given to the rhizosphere microorganisms in the growing season in developing and utilizing soil microorganisms in C. oleifera plantation. It is possible to promote the growth of C. oleifera by changing soil microbial community, including carbon source species, pH, AP, and URE. Our findings provide valuable information to guide microbial isolation and culturing to manage C. oleifera land.
bibliographic citation: Zhang et al. (2020) Characteristics of the soil microbial community in the forestland of Camellia oleifera. PeerJ 8:e9117 https://doi.org/10.7717/peerj.9117
date submitted: 2019-09-25
date accepted: 2020-04-12
issued: 2020-05-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Peng
author list: Agent
  family name: Cui
  given name: Zhiyi
author list: Agent
  family name: Guo
  given name: Mengqing
author list: Agent
  family name: Xi
  given name: Ruchun
doi: 10.7717/peerj.9117
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-08
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Impact of electrocardiographic morphology on clinical outcomes in patients with non-ST elevation myocardial infarction receiving coronary angiography and intervention: a retrospective study
type: item
type: AcademicArticle
description: Background The impact of electrocardiography (ECG) morphology on clinical outcomes in patients with non-ST segment elevation myocardial infarction (NSTEMI) receiving percutaneous coronary intervention (PCI) is unknown. This study investigated whether different ST morphologies had different clinical outcomes in patients with NSTEMI receiving PCI. Methods This retrospective study analyzed record-linked data of 362 patients who had received PCI for NSTEMI between January 2008 and December 2010. ECG revealed ST depression in 67 patients, inverted T wave in 91 patients, and no significant ST-T changes in 204 patients. The primary endpoint was long-term all-cause mortality. The secondary endpoint was long-term cardiac death and non-fatal major adverse cardiac events. Results Compared to those patients whose ECG showed an inverted T wave and non-specific ST-T changes, patients whose ECG showed ST depression had more diabetes mellitus, advanced chronic kidney disease (CKD) and left main artery disease, as well as more in-hospital mortality, cardiac death and pulmonary edema during hospitalization. Patients with ST depression had a significantly higher rate of long-term total mortality and cardiac death. Finally, multiple stepwise Cox regression analysis showed that an advanced Killip score, age, advanced CKD, prior percutaneous transluminal coronary angioplasty and ST depression were independent predictors of the primary endpoint. Conclusions Among NSTEMI patients undergoing coronary angiography, those with ST depression had more in-hospital mortality and cardiac death. Long-term follow-up of patients with ST depression consistently reveals poor outcomes.
format: application/pdf
format: text/html
creator: Chiung-Jen Wu
creator: Kuo-Ho Yeh
creator: Hui-Ting Wang
creator: Wen-Hao Liu
creator: Huang-Chung Chen
creator: Han-Tan Chai
creator: Wen-Jung Chung
creator: Shukai Hsueh
creator: Chien-Jen Chen
creator: Hsiu-Yu Fang
creator: Yung-Lung Chen
subject: Cardiology
subject: Epidemiology
subject: Internal Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.8796
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Background The impact of electrocardiography (ECG) morphology on clinical outcomes in patients with non-ST segment elevation myocardial infarction (NSTEMI) receiving percutaneous coronary intervention (PCI) is unknown. This study investigated whether different ST morphologies had different clinical outcomes in patients with NSTEMI receiving PCI. Methods This retrospective study analyzed record-linked data of 362 patients who had received PCI for NSTEMI between January 2008 and December 2010. ECG revealed ST depression in 67 patients, inverted T wave in 91 patients, and no significant ST-T changes in 204 patients. The primary endpoint was long-term all-cause mortality. The secondary endpoint was long-term cardiac death and non-fatal major adverse cardiac events. Results Compared to those patients whose ECG showed an inverted T wave and non-specific ST-T changes, patients whose ECG showed ST depression had more diabetes mellitus, advanced chronic kidney disease (CKD) and left main artery disease, as well as more in-hospital mortality, cardiac death and pulmonary edema during hospitalization. Patients with ST depression had a significantly higher rate of long-term total mortality and cardiac death. Finally, multiple stepwise Cox regression analysis showed that an advanced Killip score, age, advanced CKD, prior percutaneous transluminal coronary angioplasty and ST depression were independent predictors of the primary endpoint. Conclusions Among NSTEMI patients undergoing coronary angiography, those with ST depression had more in-hospital mortality and cardiac death. Long-term follow-up of patients with ST depression consistently reveals poor outcomes.
bibliographic citation: Wu et al. (2020) Impact of electrocardiographic morphology on clinical outcomes in patients with non-ST elevation myocardial infarction receiving coronary angiography and intervention: a retrospective study. PeerJ 8:e8796 https://doi.org/10.7717/peerj.8796
date submitted: 2019-10-21
date accepted: 2020-02-25
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Chiung-Jen
author list: Agent
  family name: Yeh
  given name: Kuo-Ho
author list: Agent
  family name: Wang
  given name: Hui-Ting
author list: Agent
  family name: Liu
  given name: Wen-Hao
author list: Agent
  family name: Chen
  given name: Huang-Chung
author list: Agent
  family name: Chai
  given name: Han-Tan
author list: Agent
  family name: Chung
  given name: Wen-Jung
author list: Agent
  family name: Hsueh
  given name: Shukai
author list: Agent
  family name: Chen
  given name: Chien-Jen
author list: Agent
  family name: Fang
  given name: Hsiu-Yu
author list: Agent
  family name: Chen
  given name: Yung-Lung
doi: 10.7717/peerj.8796
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: ©2020 Wu et al.
attribution name: Wu et al.

Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets
type: item
type: AcademicArticle
description: Background Abnormal expression of long non-coding RNAs (lncRNA) play a significant role in the incidence and progression of high-grade serous ovarian cancer (HGSOC), which is a leading cause of mortality among gynecologic malignant tumor patients. In this study, our aim is to identify lncRNA-associated competing endogenous RNA (ceRNA ) axes that could define more reliable prognostic parameters of HGSOC, and to investigate the lncRNAs’ potential mechanism of in lymphocyte infiltration. Methods The RNA-seq and miRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database; while for obtaining the differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs), we used edgeR, limma and DESeq2. After validating the RNA, miRNA and gene expressions, using integrated three RNA expression profiles (GSE18520, GSE27651, GSE54388) and miRNA profile (GSE47841) from the Gene Expression Omnibus (GEO) database, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analyses through ClusterProfiler. The prognostic value of these genes was determined with Kaplan–Meier survival analysis and Cox regression analysis. The ceRNA network was constructed using Cytoscape. The correlation between lncRNAs in ceRNA network and immune infiltrating cells was analyzed by using Tumor IMmune Estimation Resource (TIMER), and gene markers of tumor-infiltrating immune cells were identified using Spearman’s correlation after removing the influence of tumor purity. Results A total of 33 DELs (25 upregulated and eight downregulated), 134 DEMs (76 upregulated and 58 downregulated), and 1,612 DEGs (949 upregulated and 663 downregulated) were detected that could be positively correlated with overall survival (OS) of HGSOC. With the 1,612 analyzed genes, we constructed a ceRNA network, which indicated a pre-dominant involvement of the immune-related pathways. Furthermore, our data revealed that LINC00…
format: application/pdf
format: text/html
creator: Meijing Wu
creator: Xiaobin Shang
creator: Yue Sun
creator: Jing Wu
creator: Guoyan Liu
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.8961
publisher: PeerJ Inc.
rights: © 2020 Wu et al.
abstract: Background Abnormal expression of long non-coding RNAs (lncRNA) play a significant role in the incidence and progression of high-grade serous ovarian cancer (HGSOC), which is a leading cause of mortality among gynecologic malignant tumor patients. In this study, our aim is to identify lncRNA-associated competing endogenous RNA (ceRNA ) axes that could define more reliable prognostic parameters of HGSOC, and to investigate the lncRNAs’ potential mechanism of in lymphocyte infiltration. Methods The RNA-seq and miRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database; while for obtaining the differentially expressed lncRNAs (DELs), miRNAs (DEMs), and genes (DEGs), we used edgeR, limma and DESeq2. After validating the RNA, miRNA and gene expressions, using integrated three RNA expression profiles (GSE18520, GSE27651, GSE54388) and miRNA profile (GSE47841) from the Gene Expression Omnibus (GEO) database, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analyses through ClusterProfiler. The prognostic value of these genes was determined with Kaplan–Meier survival analysis and Cox regression analysis. The ceRNA network was constructed using Cytoscape. The correlation between lncRNAs in ceRNA network and immune infiltrating cells was analyzed by using Tumor IMmune Estimation Resource (TIMER), and gene markers of tumor-infiltrating immune cells were identified using Spearman’s correlation after removing the influence of tumor purity. Results A total of 33 DELs (25 upregulated and eight downregulated), 134 DEMs (76 upregulated and 58 downregulated), and 1,612 DEGs (949 upregulated and 663 downregulated) were detected that could be positively correlated with overall survival (OS) of HGSOC. With the 1,612 analyzed genes, we constructed a ceRNA network, which indicated a pre-dominant involvement of the immune-related pathways. Furthermore, our data revealed that LINC00…
bibliographic citation: Wu et al. (2020) Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets. PeerJ 8:e8961 https://doi.org/10.7717/peerj.8961
date submitted: 2019-12-30
date accepted: 2020-03-23
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Meijing
author list: Agent
  family name: Shang
  given name: Xiaobin
author list: Agent
  family name: Sun
  given name: Yue
author list: Agent
  family name: Wu
  given name: Jing
author list: Agent
  family name: Liu
  given name: Guoyan
doi: 10.7717/peerj.8961
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: ©2020 Wu et al.
attribution name: Wu et al.

Association of heart rate trajectories with the risk of adverse outcomes in a community-based cohort in Taiwan
type: item
type: AcademicArticle
description: Heart rate trajectory patterns integrate information regarding multiple heart rate measurements and their changes with time. Different heart rate patterns may exist in one population, and these are associated with different outcomes. Our study investigated the association of adverse outcomes with heart rate trajectory patterns. This was a prospective cohort study based on the Chin-Shan Community Cardiovascular Cohort in Taiwan. A total of 3,015 Chinese community residents aged > 35 years were enrolled in a prospective investigation of cardiovascular risk factors and outcomes from 1990 to 2013.The primary outcome was all-cause mortality, and the secondary outcome was a composite of coronary artery disease and cerebrovascular accidents. The following trajectory patterns were identified: stable, 61%; decreased, 5%; mildly increased, 32%; and markedly increased, 2%. During follow-up (median, 13.9 years), 557 participants died and 217 experienced secondary outcomes. The adjusted hazard ratios of primary and secondary outcomes for participants with a markedly increased trajectory pattern were 1.80 (95% CI [1.18–2.76]) and 1.45 (95% CI [0.67–3.12]), respectively, compared to those for participants with a stable trajectory pattern. A markedly increased heart rate trajectory pattern may be associated with all-cause mortality risks. Heart rate trajectory patterns demonstrated the utility of repeated heart rate measurements for risk assessment.
format: application/pdf
format: text/html
creator: Cheng-Chun Wei
creator: Pei-Chun Chen
creator: Hsiu-Ching Hsu
creator: Ta-Chen Su
creator: Hung-Ju Lin
creator: Ming-Fong Chen
creator: Yuan-Teh Lee
creator: Kuo-Liong Chien
subject: Cardiology
subject: Public Health
description: doi:10.7717/peerj.8987
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: Heart rate trajectory patterns integrate information regarding multiple heart rate measurements and their changes with time. Different heart rate patterns may exist in one population, and these are associated with different outcomes. Our study investigated the association of adverse outcomes with heart rate trajectory patterns. This was a prospective cohort study based on the Chin-Shan Community Cardiovascular Cohort in Taiwan. A total of 3,015 Chinese community residents aged > 35 years were enrolled in a prospective investigation of cardiovascular risk factors and outcomes from 1990 to 2013.The primary outcome was all-cause mortality, and the secondary outcome was a composite of coronary artery disease and cerebrovascular accidents. The following trajectory patterns were identified: stable, 61%; decreased, 5%; mildly increased, 32%; and markedly increased, 2%. During follow-up (median, 13.9 years), 557 participants died and 217 experienced secondary outcomes. The adjusted hazard ratios of primary and secondary outcomes for participants with a markedly increased trajectory pattern were 1.80 (95% CI [1.18–2.76]) and 1.45 (95% CI [0.67–3.12]), respectively, compared to those for participants with a stable trajectory pattern. A markedly increased heart rate trajectory pattern may be associated with all-cause mortality risks. Heart rate trajectory patterns demonstrated the utility of repeated heart rate measurements for risk assessment.
bibliographic citation: Wei et al. (2020) Association of heart rate trajectories with the risk of adverse outcomes in a community-based cohort in Taiwan. PeerJ 8:e8987 https://doi.org/10.7717/peerj.8987
date submitted: 2019-11-01
date accepted: 2020-03-25
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Cheng-Chun
author list: Agent
  family name: Chen
  given name: Pei-Chun
author list: Agent
  family name: Hsu
  given name: Hsiu-Ching
author list: Agent
  family name: Su
  given name: Ta-Chen
author list: Agent
  family name: Lin
  given name: Hung-Ju
author list: Agent
  family name: Chen
  given name: Ming-Fong
author list: Agent
  family name: Lee
  given name: Yuan-Teh
author list: Agent
  family name: Chien
  given name: Kuo-Liong
doi: 10.7717/peerj.8987
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: ©2020 Wei et al.
attribution name: Wei et al.

Understanding PM2.5 concentration and removal efficiency variation in urban forest park—Observation at human breathing height
type: item
type: AcademicArticle
description: To increase our knowledge of PM2.5 concentrations near the surface in a forest park in Beijing, an observational study measured the concentration and composition of PM2.5 in Beijing Olympic Forest Park from 2014 to 2015. This study analyzed the meteorological factors and removal efficiency at 1.5 m above the ground (human breathing height) over the day in the forest. The results showed that the average concentrations of PM2.5 near the surface peaked at 07:00–09:30 and reached their lowest at 12:00–15:00. Besides, the results showed that the annual concentration of PM2.5 in the forest was highest during winter, followed by spring and fall, and was lowest during summer. The main chemical components of PM2.5 near the surface in the forest were SO42− and NO3−, which accounted for 68.72% of all water-soluble ions that we observed. The concentration of PM2.5 in the forest had a significant positive correlation with relative humidity and a significant negative correlation with temperature. The removal efficiency near the surface showed no significant variation through the day or year. In the forest, the highest removal efficiency occurred between 07:00 and 09:30 in summer, while the lowest occurred between 09:30 and 12:00 in winter.
format: application/pdf
format: text/html
creator: Guoxin Yan
creator: Zibo Yu
creator: Yanan Wu
creator: Jiakai Liu
creator: Yu Wang
creator: Jiexiu Zhai
creator: Ling Cong
creator: Zhenming Zhang
subject: Atmospheric Chemistry
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.8988
publisher: PeerJ Inc.
rights: © 2020 Yan et al.
abstract: To increase our knowledge of PM2.5 concentrations near the surface in a forest park in Beijing, an observational study measured the concentration and composition of PM2.5 in Beijing Olympic Forest Park from 2014 to 2015. This study analyzed the meteorological factors and removal efficiency at 1.5 m above the ground (human breathing height) over the day in the forest. The results showed that the average concentrations of PM2.5 near the surface peaked at 07:00–09:30 and reached their lowest at 12:00–15:00. Besides, the results showed that the annual concentration of PM2.5 in the forest was highest during winter, followed by spring and fall, and was lowest during summer. The main chemical components of PM2.5 near the surface in the forest were SO42− and NO3−, which accounted for 68.72% of all water-soluble ions that we observed. The concentration of PM2.5 in the forest had a significant positive correlation with relative humidity and a significant negative correlation with temperature. The removal efficiency near the surface showed no significant variation through the day or year. In the forest, the highest removal efficiency occurred between 07:00 and 09:30 in summer, while the lowest occurred between 09:30 and 12:00 in winter.
bibliographic citation: Yan et al. (2020) Understanding PM2.5 concentration and removal efficiency variation in urban forest park—Observation at human breathing height. PeerJ 8:e8988 https://doi.org/10.7717/peerj.8988
date submitted: 2019-07-08
date accepted: 2020-03-25
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Guoxin
author list: Agent
  family name: Yu
  given name: Zibo
author list: Agent
  family name: Wu
  given name: Yanan
author list: Agent
  family name: Liu
  given name: Jiakai
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Zhai
  given name: Jiexiu
author list: Agent
  family name: Cong
  given name: Ling
author list: Agent
  family name: Zhang
  given name: Zhenming
doi: 10.7717/peerj.8988
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: ©2020 Yan et al.
attribution name: Yan et al.

Tetrandrine alleviates cerebral ischemia/reperfusion injury by suppressing NLRP3 inflammasome activation via Sirt-1
type: item
type: AcademicArticle
description: Background & Aims Tetrandrine (Tet) has been reported to have anti-inflammatory effects and protect from the ischemic strokes. The NLRP3 inflammasome plays a key role in cerebral ischemia/reperfusion (I/R)-induced inflammatory lesions. However, the molecular mechanisms of Tet related to the progression of cerebral ischemia are still unclear. Therefore, the aim of this study was to investigate the possible effects of Tet on cerebral ischemia and the related mechanisms involved in NLRP3 inflammasome. Methods C57BL/6J mice used as a cerebral I/R injury model underwent middle cerebral artery occlusion (MCAO) for 2 h following reperfusion for 24 h. Tet (30 mg/kg/day, i.p.) was administered for seven days and 30 min before and after MCAO. Their brain tissues were evaluated for NLRP3 inflammasome and Sirtuin-1 (Sirt-1) expression. An intracerebroventricular injection of Sirt-1 siRNA was administered to assess the activation of the NLRP3 inflammasome. Results Tet significantly reduced the neurological deficits, infarction volume, and cerebral water content in MCAO mice. Moreover, it inhibited I/R-induced over expression of NLRP3, cleaved caspase-1, interleukin (IL)-1β, IL-18, and Sirt-1. Sirt-1 knockdown with siRNA greatly blocked the Tet-induced reduction of neurological severity score and infarct volume, and reversed the inhibition of NLRP3 inflammasome activation. Conclusion Our results demonstrate that Tet has benefits for cerebral I/R injury, which are partially related to the suppression of NLRP3 inflammasome activation via upregulating Sirt-1.
format: application/pdf
format: text/html
creator: Jun Wang
creator: Ming Guo
creator: Ruojia Ma
creator: Maolin Wu
creator: Yamei Zhang
subject: Cognitive Disorders
subject: Pharmacology
description: doi:10.7717/peerj.9042
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background & Aims Tetrandrine (Tet) has been reported to have anti-inflammatory effects and protect from the ischemic strokes. The NLRP3 inflammasome plays a key role in cerebral ischemia/reperfusion (I/R)-induced inflammatory lesions. However, the molecular mechanisms of Tet related to the progression of cerebral ischemia are still unclear. Therefore, the aim of this study was to investigate the possible effects of Tet on cerebral ischemia and the related mechanisms involved in NLRP3 inflammasome. Methods C57BL/6J mice used as a cerebral I/R injury model underwent middle cerebral artery occlusion (MCAO) for 2 h following reperfusion for 24 h. Tet (30 mg/kg/day, i.p.) was administered for seven days and 30 min before and after MCAO. Their brain tissues were evaluated for NLRP3 inflammasome and Sirtuin-1 (Sirt-1) expression. An intracerebroventricular injection of Sirt-1 siRNA was administered to assess the activation of the NLRP3 inflammasome. Results Tet significantly reduced the neurological deficits, infarction volume, and cerebral water content in MCAO mice. Moreover, it inhibited I/R-induced over expression of NLRP3, cleaved caspase-1, interleukin (IL)-1β, IL-18, and Sirt-1. Sirt-1 knockdown with siRNA greatly blocked the Tet-induced reduction of neurological severity score and infarct volume, and reversed the inhibition of NLRP3 inflammasome activation. Conclusion Our results demonstrate that Tet has benefits for cerebral I/R injury, which are partially related to the suppression of NLRP3 inflammasome activation via upregulating Sirt-1.
bibliographic citation: Wang et al. (2020) Tetrandrine alleviates cerebral ischemia/reperfusion injury by suppressing NLRP3 inflammasome activation via Sirt-1. PeerJ 8:e9042 https://doi.org/10.7717/peerj.9042
date submitted: 2020-01-06
date accepted: 2020-04-01
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jun
author list: Agent
  family name: Guo
  given name: Ming
author list: Agent
  family name: Ma
  given name: Ruojia
author list: Agent
  family name: Wu
  given name: Maolin
author list: Agent
  family name: Zhang
  given name: Yamei
doi: 10.7717/peerj.9042
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Public perspectives and media reporting of wolf reintroduction in Colorado
type: item
type: AcademicArticle
description: In the state of Colorado, a citizen ballot initiative to reintroduce gray wolves (Canis lupus) is eliciting polarization and conflict among multiple stakeholder and interest groups. Given this complex social landscape, we examined the social context surrounding wolf reintroduction in Colorado as of 2019. We used an online survey of 734 Coloradans representative in terms of age and gender, and we sampled from different regions across the state, to examine public beliefs and attitudes related to wolf reintroduction and various wolf management options. We also conducted a content analysis of media coverage on potential wolf reintroduction in 10 major daily Colorado newspapers from January 2019, when the signature-gathering effort for the wolf reintroduction initiative began, through the end of January 2020, when the initiative was officially added to the ballot. Our findings suggest a high degree of social tolerance or desire for wolf reintroduction in Colorado across geographies, stakeholder groups, and demographics. However, we also find that a portion of the public believes that wolves would negatively impact their livelihoods, primarily because of concerns over the safety of people and pets, loss of hunting opportunities, and potential wolf predation on livestock. These concerns—particularly those related to livestock losses—are strongly reflected in the media. We find that media coverage has focused only on a few of the many perceived positive and negative impacts of wolf reintroduction identified among the public. Our findings highlight the need to account for this diversity of perspectives in future decisions and to conduct public outreach regarding likely impacts of wolf reintroduction.
format: application/pdf
format: text/html
creator: Rebecca Niemiec
creator: Richard E.W. Berl
creator: Mireille Gonzalez
creator: Tara Teel
creator: Cassiopeia Camara
creator: Matthew Collins
creator: Jonathan Salerno
creator: Kevin Crooks
creator: Courtney Schultz
creator: Stewart Breck
creator: Dana Hoag
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.9074
publisher: PeerJ Inc.
rights: © 2020
abstract: In the state of Colorado, a citizen ballot initiative to reintroduce gray wolves (Canis lupus) is eliciting polarization and conflict among multiple stakeholder and interest groups. Given this complex social landscape, we examined the social context surrounding wolf reintroduction in Colorado as of 2019. We used an online survey of 734 Coloradans representative in terms of age and gender, and we sampled from different regions across the state, to examine public beliefs and attitudes related to wolf reintroduction and various wolf management options. We also conducted a content analysis of media coverage on potential wolf reintroduction in 10 major daily Colorado newspapers from January 2019, when the signature-gathering effort for the wolf reintroduction initiative began, through the end of January 2020, when the initiative was officially added to the ballot. Our findings suggest a high degree of social tolerance or desire for wolf reintroduction in Colorado across geographies, stakeholder groups, and demographics. However, we also find that a portion of the public believes that wolves would negatively impact their livelihoods, primarily because of concerns over the safety of people and pets, loss of hunting opportunities, and potential wolf predation on livestock. These concerns—particularly those related to livestock losses—are strongly reflected in the media. We find that media coverage has focused only on a few of the many perceived positive and negative impacts of wolf reintroduction identified among the public. Our findings highlight the need to account for this diversity of perspectives in future decisions and to conduct public outreach regarding likely impacts of wolf reintroduction.
bibliographic citation: Niemiec et al. (2020) Public perspectives and media reporting of wolf reintroduction in Colorado. PeerJ 8:e9074 https://doi.org/10.7717/peerj.9074
date submitted: 2020-01-14
date accepted: 2020-04-07
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Niemiec
  given name: Rebecca
author list: Agent
  family name: Berl
  given name: Richard E.W.
author list: Agent
  family name: Gonzalez
  given name: Mireille
author list: Agent
  family name: Teel
  given name: Tara
author list: Agent
  family name: Camara
  given name: Cassiopeia
author list: Agent
  family name: Collins
  given name: Matthew
author list: Agent
  family name: Salerno
  given name: Jonathan
author list: Agent
  family name: Crooks
  given name: Kevin
author list: Agent
  family name: Schultz
  given name: Courtney
author list: Agent
  family name: Breck
  given name: Stewart
author list: Agent
  family name: Hoag
  given name: Dana
doi: 10.7717/peerj.9074
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07

Resampling-based methods for biologists
type: item
type: AcademicArticle
description: Ecological data often violate common assumptions of traditional parametric statistics (e.g., that residuals are Normally distributed, have constant variance, and cases are independent). Modern statistical methods are well equipped to handle these complications, but they can be challenging for non-statisticians to understand and implement. Rather than default to increasingly complex statistical methods, resampling-based methods can sometimes provide an alternative method for performing statistical inference, while also facilitating a deeper understanding of foundational concepts in frequentist statistics (e.g., sampling distributions, confidence intervals, p-values). Using simple examples and case studies, we demonstrate how resampling-based methods can help elucidate core statistical concepts and provide alternative methods for tackling challenging problems across a broad range of ecological applications.
format: application/pdf
format: text/html
creator: John R. Fieberg
creator: Kelsey Vitense
creator: Douglas H. Johnson
subject: Computational Biology
subject: Ecology
subject: Statistics
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.9089
publisher: PeerJ Inc.
rights: © 2020 Fieberg et al.
abstract: Ecological data often violate common assumptions of traditional parametric statistics (e.g., that residuals are Normally distributed, have constant variance, and cases are independent). Modern statistical methods are well equipped to handle these complications, but they can be challenging for non-statisticians to understand and implement. Rather than default to increasingly complex statistical methods, resampling-based methods can sometimes provide an alternative method for performing statistical inference, while also facilitating a deeper understanding of foundational concepts in frequentist statistics (e.g., sampling distributions, confidence intervals, p-values). Using simple examples and case studies, we demonstrate how resampling-based methods can help elucidate core statistical concepts and provide alternative methods for tackling challenging problems across a broad range of ecological applications.
bibliographic citation: Fieberg et al. (2020) Resampling-based methods for biologists. PeerJ 8:e9089 https://doi.org/10.7717/peerj.9089
date submitted: 2019-10-23
date accepted: 2020-04-08
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fieberg
  given name: John R.
author list: Agent
  family name: Vitense
  given name: Kelsey
author list: Agent
  family name: Johnson
  given name: Douglas H.
doi: 10.7717/peerj.9089
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: © 2020 Fieberg et al.
attribution name: Fieberg et al.

Evaluation of a novel syndromic surveillance system for the detection of the 2007 melamine-related nephrotoxicosis foodborne outbreak in dogs and cats in the United States
type: item
type: AcademicArticle
description: The 2007 nephrotoxicosis outbreak associated with melamine and cyanuric acid adulteration of pet foods in the United States sparked an urgent need for a nationwide companion animal surveillance program. In 2016, we introduced a syndromic surveillance system based on a novel epidemiological algorithm, the proportionate diagnostic outcome ratio (PDOR). The PDOR procedure was validated using simulated outbreaks of foodborne illness (i.e., aflatoxicosis and gastrointestinal illness) in dogs and cats. In this study, we further evaluated the PDOR procedure using the 2007 melamine-related outbreak of nephrotoxicosis. The performance of the PDOR procedure was assessed by the time to alert and positive predictive value (PPV). Electronic medical records of dogs and cats seen at networked primary care veterinary hospitals across the United States were retrieved from a centralized database. The data of four relevant syndromic components: elevated serum creatinine concentration, vomiting, anorexia, and lethargy from July 28, 2006 to May 31, 2007 were prospectively analyzed using the PDOR algorithm. The results showed that the alerts generated from the analysis of elevated serum creatinine concentration could have led to an early detection of this nephrotoxicosis foodborne outbreak and were well matched to the reported timeline of the outbreak. Additionally, we also observed variations in the performance of the PDOR procedure across age of animals and syndromic components, with the PPVs ranged from 0.61 to 1.0. Combined with the findings from previous evaluations using simulated outbreak scenarios, this study provided additional evidence that the PDOR procedure can be applied in syndromic surveillance to effectively and accurately detect various types of foodborne illness outbreaks in companion animals. However, the interpretations of and responses to alerts require an understanding of clinical veterinary medicine and relevant syndromic knowledge, and should not be based solely o…
format: application/pdf
format: text/html
creator: Hsin-Yi Weng
creator: Mark A.L. Gaona
creator: Philip H. Kass
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.9093
publisher: PeerJ Inc.
rights: © 2020 Weng et al.
abstract: The 2007 nephrotoxicosis outbreak associated with melamine and cyanuric acid adulteration of pet foods in the United States sparked an urgent need for a nationwide companion animal surveillance program. In 2016, we introduced a syndromic surveillance system based on a novel epidemiological algorithm, the proportionate diagnostic outcome ratio (PDOR). The PDOR procedure was validated using simulated outbreaks of foodborne illness (i.e., aflatoxicosis and gastrointestinal illness) in dogs and cats. In this study, we further evaluated the PDOR procedure using the 2007 melamine-related outbreak of nephrotoxicosis. The performance of the PDOR procedure was assessed by the time to alert and positive predictive value (PPV). Electronic medical records of dogs and cats seen at networked primary care veterinary hospitals across the United States were retrieved from a centralized database. The data of four relevant syndromic components: elevated serum creatinine concentration, vomiting, anorexia, and lethargy from July 28, 2006 to May 31, 2007 were prospectively analyzed using the PDOR algorithm. The results showed that the alerts generated from the analysis of elevated serum creatinine concentration could have led to an early detection of this nephrotoxicosis foodborne outbreak and were well matched to the reported timeline of the outbreak. Additionally, we also observed variations in the performance of the PDOR procedure across age of animals and syndromic components, with the PPVs ranged from 0.61 to 1.0. Combined with the findings from previous evaluations using simulated outbreak scenarios, this study provided additional evidence that the PDOR procedure can be applied in syndromic surveillance to effectively and accurately detect various types of foodborne illness outbreaks in companion animals. However, the interpretations of and responses to alerts require an understanding of clinical veterinary medicine and relevant syndromic knowledge, and should not be based solely o…
bibliographic citation: Weng et al. (2020) Evaluation of a novel syndromic surveillance system for the detection of the 2007 melamine-related nephrotoxicosis foodborne outbreak in dogs and cats in the United States. PeerJ 8:e9093 https://doi.org/10.7717/peerj.9093
date submitted: 2020-01-08
date accepted: 2020-04-09
issued: 2020-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weng
  given name: Hsin-Yi
author list: Agent
  family name: Gaona
  given name: Mark A.L.
author list: Agent
  family name: Kass
  given name: Philip H.
doi: 10.7717/peerj.9093
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-07
copyright: © 2020 Weng et al.
attribution name: Weng et al.

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