PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Proteomic analysis reveals some common proteins in the kidney stone matrix
items: HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures
items: Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology
items: Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
items: Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels
items: Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage
items: A bright idea—metabarcoding arthropods from light fixtures
items: Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis
items: ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
items: How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China

Proteomic analysis reveals some common proteins in the kidney stone matrix
type: item
type: AcademicArticle
description: Background Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research. Methods We conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue. Results We included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no sig…
format: application/pdf
format: text/html
creator: Yuanyuan Yang
creator: Senyuan Hong
creator: Cong Li
creator: Jiaqiao Zhang
creator: Henglong Hu
creator: Xiaolong Chen
creator: Kehua Jiang
creator: Fa Sun
creator: Qing Wang
creator: Shaogang Wang
subject: Bioinformatics
subject: Nephrology
subject: Pathology
subject: Urology
subject: Histology
description: doi:10.7717/peerj.11872
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Proteins are the most abundant component of kidney stone matrices and their presence may reflect the process of the stone’s formation. Many studies have explored the proteomics of urinary stones and crystals. We sought to comprehensively identify the proteins found in kidney stones and to identify new, reliable biomolecules for use in nephrolithiasis research. Methods We conducted bioinformatics research in November 2020 on the proteomics of urinary stones and crystals. We used the ClusterProfiler R package to transform proteins into their corresponding genes and Ensembl IDs. In each study we located where proteomic results intersected to determine the 20 most frequently identified stone matrix proteins. We used the Human Protein Atlas to obtain the biological information of the 20 proteins and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis to explore their biological functions. We also performed immunohistochemistry to detect the expression of the top five stone matrix proteins in renal tissue. Results We included 19 relevant studies for analysis. We then identified 1,409 proteins in the stone matrix after the duplicates were removed. The 20 most-commonly identified stone matrix proteins were: S100A8, S100A9, uromodulin, albumin, osteopontin, lactotransferrin, vitamin K-dependent protein Z, prothrombin, hemoglobin subunit beta, myeloperoxidase, mannan-binding lectin serine protease 2, lysozyme C, complement C3, serum amyloid P-component, cathepsin G, vitronectin, apolipoprotein A-1, eosinophil cationic protein, fibrinogen alpha chain, and apolipoprotein D. GO and KEGG analysis revealed that these proteins were typically engaged in inflammation and immune response.Immunohistochemistry of the top five stone matrix proteins in renal tissue showed that the expression of S100A8, S100A9, and osteopontin increased, while uromodulin decreased in kidney stone patients. Albumin was rarely expressed in the kidney with no sig…
bibliographic citation: Yang et al. (2021) Proteomic analysis reveals some common proteins in the kidney stone matrix. PeerJ 9:e11872 https://doi.org/10.7717/peerj.11872
date submitted: 2021-02-17
date accepted: 2021-07-06
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yuanyuan
author list: Agent
  family name: Hong
  given name: Senyuan
author list: Agent
  family name: Li
  given name: Cong
author list: Agent
  family name: Zhang
  given name: Jiaqiao
author list: Agent
  family name: Hu
  given name: Henglong
author list: Agent
  family name: Chen
  given name: Xiaolong
author list: Agent
  family name: Jiang
  given name: Kehua
author list: Agent
  family name: Sun
  given name: Fa
author list: Agent
  family name: Wang
  given name: Qing
author list: Agent
  family name: Wang
  given name: Shaogang
doi: 10.7717/peerj.11872
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Yang et al.
attribution name: Yang et al.

HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures
type: item
type: AcademicArticle
description: Background In risk assessment, genotoxicity is a key factor to determine the safety for the consumer. Most in vitro genotoxicity assays were developed for the assessment of pure substances. However, in recent years more attention has been given to complex mixtures, where usually low amounts of a substance are present. For high-throughput screening, a toxicologically sensitive assay should be used, covering a broad range of genotoxic substances and detecting them at low concentrations. HepG2 cells have been recommended as one of the prime candidates for genotoxicity testing, as they are p53 competent, less prone towards cytotoxic effects and tend to have some metabolic activity. Methods A HepG2 liver cell line was characterized for its suitability for genotoxicity assessment. For this, a luciferase based reporter gene assay revolving around the p53 pathway was validated for the analysis of pure substances and of complex mixtures. Further, the cell’s capability to detect genotoxins correctly with and without an exogenous metabolizing system, namely rat liver S9, was assessed. Results The assay proved to have a high toxicological sensitivity (87.5%) and specificity (94%). Further, the endogenous metabolizing system of the HepG2 cells was able to detect some genotoxins, which are known to depend on an enzymatic system. When complex mixtures were added this did not lead to any adverse effects concerning the assays performance and cytotoxicity was not an issue. Discussion The HepGentox proved to have a high toxicological sensitivity and specificity for the tested substances, with similar or even lower lowest effective concentration (LEC) values, compared to other regulatory mammalian assays. This combines some important aspects in one test system, while also being less time and material consuming and covering several genotoxicity endpoints. As the assay performs well with and without an exogenous metabolizing system, no animal liver fractions have to be used, which applic…
format: application/pdf
format: text/html
creator: Elisabeth Pinter
creator: Christina Friedl
creator: Alexandra Irnesberger
creator: Thomas Czerny
creator: Tina Piwonka
creator: Alfonso Peñarroya
creator: Manfred Tacker
creator: Elisabeth Riegel
subject: Cell Biology
subject: Food Science and Technology
subject: Toxicology
description: doi:10.7717/peerj.11883
publisher: PeerJ Inc.
rights: © 2021 Pinter et al.
abstract: Background In risk assessment, genotoxicity is a key factor to determine the safety for the consumer. Most in vitro genotoxicity assays were developed for the assessment of pure substances. However, in recent years more attention has been given to complex mixtures, where usually low amounts of a substance are present. For high-throughput screening, a toxicologically sensitive assay should be used, covering a broad range of genotoxic substances and detecting them at low concentrations. HepG2 cells have been recommended as one of the prime candidates for genotoxicity testing, as they are p53 competent, less prone towards cytotoxic effects and tend to have some metabolic activity. Methods A HepG2 liver cell line was characterized for its suitability for genotoxicity assessment. For this, a luciferase based reporter gene assay revolving around the p53 pathway was validated for the analysis of pure substances and of complex mixtures. Further, the cell’s capability to detect genotoxins correctly with and without an exogenous metabolizing system, namely rat liver S9, was assessed. Results The assay proved to have a high toxicological sensitivity (87.5%) and specificity (94%). Further, the endogenous metabolizing system of the HepG2 cells was able to detect some genotoxins, which are known to depend on an enzymatic system. When complex mixtures were added this did not lead to any adverse effects concerning the assays performance and cytotoxicity was not an issue. Discussion The HepGentox proved to have a high toxicological sensitivity and specificity for the tested substances, with similar or even lower lowest effective concentration (LEC) values, compared to other regulatory mammalian assays. This combines some important aspects in one test system, while also being less time and material consuming and covering several genotoxicity endpoints. As the assay performs well with and without an exogenous metabolizing system, no animal liver fractions have to be used, which applic…
bibliographic citation: Pinter et al. (2021) HepGentox: a novel promising HepG2 reportergene-assay for the detection of genotoxic substances in complex mixtures. PeerJ 9:e11883 https://doi.org/10.7717/peerj.11883
date submitted: 2021-01-07
date accepted: 2021-07-09
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pinter
  given name: Elisabeth
author list: Agent
  family name: Friedl
  given name: Christina
author list: Agent
  family name: Irnesberger
  given name: Alexandra
author list: Agent
  family name: Czerny
  given name: Thomas
author list: Agent
  family name: Piwonka
  given name: Tina
author list: Agent
  family name: Peñarroya
  given name: Alfonso
author list: Agent
  family name: Tacker
  given name: Manfred
author list: Agent
  family name: Riegel
  given name: Elisabeth
doi: 10.7717/peerj.11883
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Pinter et al.
attribution name: Pinter et al.

Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology
type: item
type: AcademicArticle
description: Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats.
format: application/pdf
format: text/html
creator: Raoul Manenti
creator: Beatrice Piazza
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11711
publisher: PeerJ Inc.
rights: © 2021 Manenti and Piazza
abstract: Springs are interfaces between groundwater and surface habitats and may play an important role in the study of subterranean animals. In this systematic evidence review and meta-analysis, we explore whether observations of stygobionts in springs are relevant and more common than observations of epigean animals in groundwater. We searched the Web of Science database for papers on groundwater fauna and spring fauna. For each paper we found, we recorded whether the paper reported the occurrence of typical stygobionts in springs, of surface animals in groundwater, or of the same taxa in both habitats. If so, we recorded how many such species were reported. We also recorded the scientific discipline of each study and the year of publication. Our search yielded 342 papers. A considerable number of these papers reported stygobionts in springs: 20% of papers dealing with groundwater fauna and 16% of papers dealing with spring fauna reported the occurrence of stygobionts in spring habitats. Both the number of papers that mentioned stygobionts in springs, and the number of stygobiont species that were documented in springs, were higher than equivalent measures for the occurrence of surface fauna underground. We also detected a positive relationship between year of publication and the number of reports of stygofauna in springs. To broaden the insights from biological research on underground environments, we suggest that springs should be considered not only as simple sampling points of stygobionts but also as core stygobiont habitats.
bibliographic citation: Manenti et al. (2021) Between darkness and light: spring habitats provide new perspectives for modern researchers on groundwater biology. PeerJ 9:e11711 https://doi.org/10.7717/peerj.11711
date submitted: 2021-04-13
date accepted: 2021-06-10
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manenti
  given name: Raoul
author list: Agent
  family name: Piazza
  given name: Beatrice
doi: 10.7717/peerj.11711
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Manenti and Piazza
attribution name: Manenti and Piazza

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping
type: item
type: AcademicArticle
description: Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.
format: application/pdf
format: text/html
creator: Zeeshan Ahmed
creator: Eduard Gibert Renart
creator: Saman Zeeshan
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Medical Genetics
subject: Data Science
description: doi:10.7717/peerj.11724
publisher: PeerJ Inc.
rights: © 2021 Ahmed et al.
abstract: Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.
bibliographic citation: Ahmed et al. (2021) Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PeerJ 9:e11724 https://doi.org/10.7717/peerj.11724
date submitted: 2021-03-29
date accepted: 2021-06-14
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmed
  given name: Zeeshan
author list: Agent
  family name: Renart
  given name: Eduard Gibert
author list: Agent
  family name: Zeeshan
  given name: Saman
doi: 10.7717/peerj.11724
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Ahmed et al.
attribution name: Ahmed et al.

Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels
type: item
type: AcademicArticle
description: Backgroud This study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger. Methods We recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups. Results Although the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM). Conclusion We concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive t…
format: application/pdf
format: text/html
creator: Yingfen Ying
creator: Xiaosheng Lu
creator: Huina Zhang
creator: Samuel Kofi Arhin
creator: Xiaohong Hou
creator: Zefan Wang
creator: Han Wu
creator: Jieqiang Lu
creator: Yunbing Tang
subject: Evidence Based Medicine
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.11785
publisher: PeerJ Inc.
rights: © 2021 Ying et al.
abstract: Backgroud This study’s objectives were to compare the clinical, perinatal, and obstetrical outcomes of patients with different estradiol (E2) levels in fresh single-blastocyst-transfer (SBT) cycles under an early follicular phase prolonged regimen on the day of trigger. Methods We recruited patients in fresh SBT cycles (n = 771) undergoing early follicular phase prolonged protocols with β-hCG values above 10 IU/L between June 2016 and December 2018. Patients who met the inclusion and exclusion criteria were divided into four groups according to their serum E2 level percentages on the day of trigger: <25th, 25th–50th, 51st–75th, and >75th percentile groups. Results Although the rates of clinical pregnancy (85.57% (166/194)), embryo implantation 86.60% (168/194), ongoing pregnancy (71.13% (138/194)), and live birth (71.13% (138/194)) were lowest in the >75th percentile group, we did not observe any significant differences (all P > 0.05). We used this information to predict the rate of severe ovarian hyperstimulation syndrome (OHSS) area under the curve (AUC) = 72.39%, P = 0.029, cut off value of E2 = 2,893 pg/ml with the 75% sensitivity and 70% specificity. The 51st–75th percentile group had the highest rates of low birth weight infants (11.73% (19/162), P = 0.0408), premature delivery (11.43% (20/175), P = 0.0269), admission to the neonatal intensive care unit (NICU) (10.49% (17/162), P = 0.0029), twin pregnancies (8.57% (15/175), P = 0.0047), and monochorionic diamniotic pregnancies (8.57% (15/175); P = 0.001). We did not observe statistical differences in obstetrics complications, including gestational diabetes mellitus (GDM), gestational hypertension, placenta previa, premature rupture of membranes (PROM), and preterm premature rupture of membranes (PPROM). Conclusion We concluded that serum E2 levels on the day of trigger were not good predictors of live birth rate or perinatal and obstetrical outcomes. However, we found that high E2 levels may not be conducive t…
bibliographic citation: Ying et al. (2021) Clinical and perinatal outcomes of fresh single-blastocyst-transfer cycles under an early follicular phase prolonged protocol according to day of trigger estradiol levels. PeerJ 9:e11785 https://doi.org/10.7717/peerj.11785
date submitted: 2020-09-25
date accepted: 2021-06-24
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ying
  given name: Yingfen
author list: Agent
  family name: Lu
  given name: Xiaosheng
author list: Agent
  family name: Zhang
  given name: Huina
author list: Agent
  family name: Arhin
  given name: Samuel Kofi
author list: Agent
  family name: Hou
  given name: Xiaohong
author list: Agent
  family name: Wang
  given name: Zefan
author list: Agent
  family name: Wu
  given name: Han
author list: Agent
  family name: Lu
  given name: Jieqiang
author list: Agent
  family name: Tang
  given name: Yunbing
doi: 10.7717/peerj.11785
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Ying et al.
attribution name: Ying et al.

Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage
type: item
type: AcademicArticle
description: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize.
format: application/pdf
format: text/html
creator: Baizhao Ren
creator: Juan Hu
creator: Peng Liu
creator: Bin Zhao
creator: Jiwang Zhang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.11834
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Waterlogging was one of the main abiotic stresses affecting maize yield and growth in the North China Plain, while ridge tillage effectually improved soil environment, enhanced crop stress resistance to waterlogging, and increased grain yield of waterlogged maize. In order to explore the responses of nitrogen (N) efficiency and antioxidant system of summer maize to waterlogging stress under different tillage, a field experiment was conducted to explore N use efficiency, leaf activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), and malondialdehyde (MDA) content of waterlogged maize Denghai 605 (DH605) and Zhengdan 958 (ZD958) under different tillage system (ridge planting and flat planting). Our results showed that ridge tillage was beneficial to ameliorate waterlogging damages on antioxidant system by increasing SOD, POD, and CAT activities, and decreasing MDA content. Moreover, ridge tillage significantly increased N efficiency of waterlogged maize. N translocation amount (NTA), N translocation efficiency (NTE), N contribution proportion (NCP), N harvest index (NHI), and N use efficiency (NUE) of waterlogging treatment under ridge planting system (W-V3+R) for DH605 was increased by 108%, 69%, 60%, 8% and 16%, while ZD958 increased by 248%, 132%, 146%, 13% and 16%, respectively, compared to those of waterlogging treatment under flat planting system (W-V3). Ultimately, ridge tillage led to a significant yield improvement by 39% and 50% for DH605 and ZD958, respectively, compared to that of W-V3. In conclusion, ridge tillage was conducive to retard leaf aging, and enhance nitrogen efficiency, thereby resulting in a yield improvement of waterlogged summer maize.
bibliographic citation: Ren et al. (2021) Responses of nitrogen efficiency and antioxidant system of summer maize to waterlogging stress under different tillage. PeerJ 9:e11834 https://doi.org/10.7717/peerj.11834
date submitted: 2021-03-30
date accepted: 2021-06-30
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Baizhao
author list: Agent
  family name: Hu
  given name: Juan
author list: Agent
  family name: Liu
  given name: Peng
author list: Agent
  family name: Zhao
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Jiwang
doi: 10.7717/peerj.11834
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Ren et al.
attribution name: Ren et al.

A bright idea—metabarcoding arthropods from light fixtures
type: item
type: AcademicArticle
description: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
format: application/pdf
format: text/html
creator: Vasco Elbrecht
creator: Angie Lindner
creator: Laura Manerus
creator: Dirk Steinke
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11841
publisher: PeerJ Inc.
rights: © 2021 Elbrecht et al.
abstract: Arthropod communities in buildings have not been extensively studied, although humans have always shared their homes with them. In this study we explored if arthropod DNA can be retrieved and metabarcoded from indoor environments through the collection of dead specimens in light fixtures to better understand what shapes arthropod diversity in our homes. Insects were collected from 45 light fixtures at the Centre for Biodiversity Genomics (CBG, Guelph, Canada), and by community scientists at 12 different residential homes in Southern Ontario. The CBG ground floor of the CBG showed the greatest arthropod diversity, especially in light fixtures that were continuously illuminated. The community scientist samples varied strongly by light fixture type, lightbulb used, time passed since lamp was last cleaned, and specimen size. In all cases, the majority of OTUs was not shared between samples even within the same building. This study demonstrates that light fixtures might be a useful resource to determine arthropod diversity in our homes, but individual samples are likely not representative of the full diversity.
bibliographic citation: Elbrecht et al. (2021) A bright idea—metabarcoding arthropods from light fixtures. PeerJ 9:e11841 https://doi.org/10.7717/peerj.11841
date submitted: 2021-05-25
date accepted: 2021-07-01
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elbrecht
  given name: Vasco
author list: Agent
  family name: Lindner
  given name: Angie
author list: Agent
  family name: Manerus
  given name: Laura
author list: Agent
  family name: Steinke
  given name: Dirk
doi: 10.7717/peerj.11841
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: © 2021 Elbrecht et al.
attribution name: Elbrecht et al.

Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis
type: item
type: AcademicArticle
description: Background Nurses’ knowledge regarding palliative and end-of-life (EOL) care has been documented, but the competence of nurses in Taiwan has not been deeply analyzed and may affect the use of EOL care. Purpose We aimed to (1) assess the palliative care knowledge, competence and attitude of nurses in a general hospital and (2) examine the paths connecting nurses’ demographic characteristics, previous experiences, knowledge, competence, and attitude. Method A correlational, cross-sectional survey design was implemented to recruit 682 eligible nurses. The questionnaires included demographic information and palliative and EOL care knowledge, attitude, and competence scales. Path analysis was employed for statistical analysis using structural equation modeling. Results Overall, 76% of the questions assessing palliative and hospice knowledge were answered correctly. Nurses’ palliative attitudes were divided into “positive perception” and “negative perception”. “Positive perception” was highly correlated with competence (r = 0.48, p < 0.001), but “negative perception” was not significantly correlated with competence (r = −0.07, p = 0.25). “Positive perception” (β = −0.01, p = 0.84) and competence (β = 0.02, p = 0.80) were not related to palliative knowledge. “Negative perception”, however, was negatively associated with palliative knowledge (β = −0.20, p < 0.01). Conclusions This study suggests continuing education to decrease nurses’ “negative perception” attitude regarding the provision of information to patients and families to provide better palliative and EOL care. Implications for Practice Nurses’ attitudes and competences with respect to palliative care and EOL care are critical. Areas for further research and advanced palliative and EOL care-related education and training are suggested and may be applied in future clinical interventions.
format: application/pdf
format: text/html
creator: Hung-Yu Lin
creator: Chun-I Chen
creator: Chu-Yun Lu
creator: Shu-Chuan Lin
creator: Chiung-Yu Huang
subject: Geriatrics
subject: Nursing
subject: Science and Medical Education
subject: Palliative Care
description: doi:10.7717/peerj.11864
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Nurses’ knowledge regarding palliative and end-of-life (EOL) care has been documented, but the competence of nurses in Taiwan has not been deeply analyzed and may affect the use of EOL care. Purpose We aimed to (1) assess the palliative care knowledge, competence and attitude of nurses in a general hospital and (2) examine the paths connecting nurses’ demographic characteristics, previous experiences, knowledge, competence, and attitude. Method A correlational, cross-sectional survey design was implemented to recruit 682 eligible nurses. The questionnaires included demographic information and palliative and EOL care knowledge, attitude, and competence scales. Path analysis was employed for statistical analysis using structural equation modeling. Results Overall, 76% of the questions assessing palliative and hospice knowledge were answered correctly. Nurses’ palliative attitudes were divided into “positive perception” and “negative perception”. “Positive perception” was highly correlated with competence (r = 0.48, p < 0.001), but “negative perception” was not significantly correlated with competence (r = −0.07, p = 0.25). “Positive perception” (β = −0.01, p = 0.84) and competence (β = 0.02, p = 0.80) were not related to palliative knowledge. “Negative perception”, however, was negatively associated with palliative knowledge (β = −0.20, p < 0.01). Conclusions This study suggests continuing education to decrease nurses’ “negative perception” attitude regarding the provision of information to patients and families to provide better palliative and EOL care. Implications for Practice Nurses’ attitudes and competences with respect to palliative care and EOL care are critical. Areas for further research and advanced palliative and EOL care-related education and training are suggested and may be applied in future clinical interventions.
bibliographic citation: Lin et al. (2021) Nurses’ knowledge, attitude, and competence regarding palliative and end-of-life care: a path analysis. PeerJ 9:e11864 https://doi.org/10.7717/peerj.11864
date submitted: 2020-12-03
date accepted: 2021-07-05
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Hung-Yu
author list: Agent
  family name: Chen
  given name: Chun-I
author list: Agent
  family name: Lu
  given name: Chu-Yun
author list: Agent
  family name: Lin
  given name: Shu-Chuan
author list: Agent
  family name: Huang
  given name: Chiung-Yu
doi: 10.7717/peerj.11864
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Lin et al.
attribution name: Lin et al.

ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences
type: item
type: AcademicArticle
description: Background High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs. Methods The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments. Results The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimi…
format: application/pdf
format: text/html
creator: Dylan Catlett
creator: Kevin Son
creator: Connie Liang
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.11865
publisher: PeerJ Inc.
rights: © 2021 Catlett et al.
abstract: Background High-throughput sequencing of phylogenetically informative marker genes is a widely used method to assess the diversity and composition of microbial communities. Taxonomic assignment of sampled marker gene sequences (referred to as amplicon sequence variants, or ASVs) imparts ecological significance to these genetic data. To assign taxonomy to an ASV, a taxonomic assignment algorithm compares the ASV to a collection of reference sequences (a reference database) with known taxonomic affiliations. However, many taxonomic assignment algorithms and reference databases are available, and the optimal algorithm and database for a particular scientific question is often unclear. Here, we present the ensembleTax R package, which provides an efficient framework for integrating taxonomic assignments predicted with any number of taxonomic assignment algorithms and reference databases to determine ensemble taxonomic assignments for ASVs. Methods The ensembleTax R package relies on two core algorithms: taxmapper and assign.ensembleTax. The taxmapper algorithm maps taxonomic assignments derived from one reference database onto the taxonomic nomenclature (a set of taxonomic naming and ranking conventions) of another reference database. The assign.ensembleTax algorithm computes ensemble taxonomic assignments for each ASV in a data set based on any number of taxonomic assignments determined with independent methods. Various parameters allow analysts to prioritize obtaining either more ASVs with more predicted clade names or more robust clade name predictions supported by multiple independent methods in ensemble taxonomic assignments. Results The ensembleTax R package is used to compute two sets of ensemble taxonomic assignments for a collection of protistan ASVs sampled from the coastal ocean. Comparisons of taxonomic assignments predicted by individual methods with those predicted by ensemble methods show that conservative implementations of the ensembleTax package minimi…
bibliographic citation: Catlett et al. (2021) ensembleTax: an R package for determinations of ensemble taxonomic assignments of phylogenetically-informative marker gene sequences. PeerJ 9:e11865 https://doi.org/10.7717/peerj.11865
date submitted: 2021-03-31
date accepted: 2021-07-05
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catlett
  given name: Dylan
author list: Agent
  family name: Son
  given name: Kevin
author list: Agent
  family name: Liang
  given name: Connie
doi: 10.7717/peerj.11865
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Catlett et al.
attribution name: Catlett et al.

How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China
type: item
type: AcademicArticle
description: Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.
format: application/pdf
format: text/html
creator: Lijiao Wang
creator: Xin Jing
creator: Jincheng Han
creator: Lei Yu
creator: Yutao Wang
creator: Ping Liu
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.11873
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Carbon distribution in plants and ecological stoichiometry in soils are important indicators of element cycling and ecosystem stability. In this study, five forest ages, young forest (YF), middle-aged forest (MAF), near-mature forest (NMF), mature forest (MF), and over-mature forest (OMF) in a Pinus tabuliformis plantation were chosen to illustrate interactions among the C: N: P stoichiometry in soils and carbon distribution in plants, in the mountainous area of eastern Liaoning, China. Carbon content was highest in the leaves of MAF (505.90 g⋅kg−1) and NMF (509.00 g⋅kg−1) and the trunks of YF (503.72 g⋅kg−1), MF (509.73 g⋅kg−1), and OMF (504.90 g⋅kg−1), and was lowest in the branches over the entire life cycle of the aboveground components (335.00 g⋅kg−1). The carbon content of the fine roots decreased with soil layer depth. In YF, MAF, and NMF carbon content of fine roots at 0.5 m was always higher than that of fine roots at 1 m; however, it was the opposite in MF and OMF. The carbon content of the leaves changed with forest age; however, carbon content of branches, trunks and fine roots did not change significantly. Soil total carbon (TC), total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) content was highest in the OMF. Soil TC, TN and AP content, and TC: TN, TC: TP and TN: TP ratio decreased with increasing soil depth. Soil TC, TN, and TP content had a significant effect on the carbon content of fine roots (p < 0.05). The leaf carbon content and soil element content changed obviously with forest age, and the soil TN, TP and AP increased, which might reduce the carbon content allocation of fine roots.
bibliographic citation: Wang et al. (2021) How C: N: P stoichiometry in soils and carbon distribution in plants respond to forest age in a Pinus tabuliformis plantation in the mountainous area of eastern Liaoning Province, China. PeerJ 9:e11873 https://doi.org/10.7717/peerj.11873
date submitted: 2021-02-08
date accepted: 2021-07-06
issued: 2021-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lijiao
author list: Agent
  family name: Jing
  given name: Xin
author list: Agent
  family name: Han
  given name: Jincheng
author list: Agent
  family name: Yu
  given name: Lei
author list: Agent
  family name: Wang
  given name: Yutao
author list: Agent
  family name: Liu
  given name: Ping
doi: 10.7717/peerj.11873
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-26
copyright: ©2021 Wang et al.
attribution name: Wang et al.

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