PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Biomechanics of the medial meniscus in the osteoarthritic knee joint
items: Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota
items: Translation and psychometric validation of the Persian version of the Questionnaire on Smoking Urges for assessment of craving to smoke among university students
items: Comparison of an exercise program with and without manual therapy for patients with chronic neck pain and upper cervical rotation restriction. Randomized controlled trial
items: Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines
items: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
items: Survival rates of adult and juvenile gyrfalcons in Iceland: estimates and drivers
items: Effect of mesoporous bioactive glass on odontogenic differentiation of human dental pulp stem cells
items: Response of diatom assemblages to the disruption of the running water continuum in urban areas, and its consequences on bioassessment
items: Workplace violence against frontline clinicians in emergency departments during the COVID-19 pandemic

Biomechanics of the medial meniscus in the osteoarthritic knee joint
type: item
type: AcademicArticle
description: Background Increased mechanical loading and pathological response of joint tissue to the abnormal mechanical stress can cause degradation of cartilage characteristic of knee osteoarthritis (OA). Despite osteoarthritis is risk factor for the development of meniscal lesions the mechanism of degenerative meniscal lesions is still unclear. Therefore, the aim of the study is to investigate the influence of medial compartment knee OA on the stress state and deformation of the medial meniscus. Methods The finite element method was used to simulate the stance phase of the gait cycle. An intact knee model was prepared based on magnetic resonance scans of the left knee joint of a healthy volunteer. Degenerative changes in the medial knee OA model were simulated by nonuniform reduction in articular cartilage thickness in specific areas and by a decrease in the material parameters of cartilage and menisci. Two additional models were created to separately evaluate the effect of alterations in articular cartilage geometry and material parameters of the soft tissues on the results. A nonlinear dynamic analysis was performed for standardized knee loads applied to the tibia bone. Results The maximum von Mises stress of 26.8 MPa was observed in the posterior part of the medial meniscus body in the OA model. The maximal hoop stress for the first peak of total force was 83% greater in the posterior horn and only 11% greater in the anterior horn of the medial meniscus in the OA model than in the intact model. The reduction in cartilage thickness caused an increase of 57% in medial translation of the medial meniscus body. A decrease in the compressive modulus of menisci resulted in a 2.5-fold greater reduction in the meniscal body width compared to the intact model. Conclusions Higher hoop stress levels on the inner edge of the posterior part of the medial meniscus in the OA model than in the intact model are associated with a greater medial translation of the meniscus body and a greater…
format: application/pdf
format: text/html
creator: Karol Daszkiewicz
creator: Piotr Łuczkiewicz
subject: Bioengineering
subject: Anatomy and Physiology
subject: Orthopedics
subject: Computational Science
subject: Biomechanics
description: doi:10.7717/peerj.12509
publisher: PeerJ Inc.
rights: © 2021 Daszkiewicz and Łuczkiewicz
abstract: Background Increased mechanical loading and pathological response of joint tissue to the abnormal mechanical stress can cause degradation of cartilage characteristic of knee osteoarthritis (OA). Despite osteoarthritis is risk factor for the development of meniscal lesions the mechanism of degenerative meniscal lesions is still unclear. Therefore, the aim of the study is to investigate the influence of medial compartment knee OA on the stress state and deformation of the medial meniscus. Methods The finite element method was used to simulate the stance phase of the gait cycle. An intact knee model was prepared based on magnetic resonance scans of the left knee joint of a healthy volunteer. Degenerative changes in the medial knee OA model were simulated by nonuniform reduction in articular cartilage thickness in specific areas and by a decrease in the material parameters of cartilage and menisci. Two additional models were created to separately evaluate the effect of alterations in articular cartilage geometry and material parameters of the soft tissues on the results. A nonlinear dynamic analysis was performed for standardized knee loads applied to the tibia bone. Results The maximum von Mises stress of 26.8 MPa was observed in the posterior part of the medial meniscus body in the OA model. The maximal hoop stress for the first peak of total force was 83% greater in the posterior horn and only 11% greater in the anterior horn of the medial meniscus in the OA model than in the intact model. The reduction in cartilage thickness caused an increase of 57% in medial translation of the medial meniscus body. A decrease in the compressive modulus of menisci resulted in a 2.5-fold greater reduction in the meniscal body width compared to the intact model. Conclusions Higher hoop stress levels on the inner edge of the posterior part of the medial meniscus in the OA model than in the intact model are associated with a greater medial translation of the meniscus body and a greater…
bibliographic citation: Daszkiewicz et al. (2021) Biomechanics of the medial meniscus in the osteoarthritic knee joint. PeerJ 9:e12509 https://doi.org/10.7717/peerj.12509
date submitted: 2021-05-27
date accepted: 2021-10-27
issued: 2021-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Daszkiewicz
  given name: Karol
author list: Agent
  family name: Łuczkiewicz
  given name: Piotr
doi: 10.7717/peerj.12509
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-24
copyright: ©2021 Daszkiewicz and Łuczkiewicz
attribution name: Daszkiewicz and Łuczkiewicz

Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota
type: item
type: AcademicArticle
description: Oplopanax elatus (Nakai) Nakai, in the Araliaceae family, has been used in traditional Chinese medicine (TCM) to treat diseases as an adaptogen for thousands of years. This study established an ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF/MS) method to identify chemical components and biotransformation metabolites of root bark extract from O. elatus. A total of 18 compounds were characterized in O. elatus extract, and 62 metabolites by human intestinal microbiota were detected. Two polyynes, falcarindiol and oplopandiol were recognized as the main components of O. elatus, whose metabolites are further illustrated. Several metabolic pathways were proposed to generate the detected metabolites, including methylation, hydrogenation, demethylation, dehydroxylation, and hydroxylation. These findings indicated that intestinal microbiota might play an essential role in mediating the bioactivity of O. elatus.
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creator: Jin-Yi Wan
creator: Jing-Xuan Wan
creator: Shilei Wang
creator: Xiaolu Wang
creator: Wenqian Guo
creator: Han Ma
creator: Yuqi Wu
creator: Chong-Zhi Wang
creator: Lian-Wen Qi
creator: Ping Li
creator: Haiqiang Yao
creator: Chun-Su Yuan
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.12513
publisher: PeerJ Inc.
rights: © 2021 Wan et al.
abstract: Oplopanax elatus (Nakai) Nakai, in the Araliaceae family, has been used in traditional Chinese medicine (TCM) to treat diseases as an adaptogen for thousands of years. This study established an ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF/MS) method to identify chemical components and biotransformation metabolites of root bark extract from O. elatus. A total of 18 compounds were characterized in O. elatus extract, and 62 metabolites by human intestinal microbiota were detected. Two polyynes, falcarindiol and oplopandiol were recognized as the main components of O. elatus, whose metabolites are further illustrated. Several metabolic pathways were proposed to generate the detected metabolites, including methylation, hydrogenation, demethylation, dehydroxylation, and hydroxylation. These findings indicated that intestinal microbiota might play an essential role in mediating the bioactivity of O. elatus.
bibliographic citation: Wan et al. (2021) Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota. PeerJ 9:e12513 https://doi.org/10.7717/peerj.12513
date submitted: 2021-08-23
date accepted: 2021-10-27
issued: 2021-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Jin-Yi
author list: Agent
  family name: Wan
  given name: Jing-Xuan
author list: Agent
  family name: Wang
  given name: Shilei
author list: Agent
  family name: Wang
  given name: Xiaolu
author list: Agent
  family name: Guo
  given name: Wenqian
author list: Agent
  family name: Ma
  given name: Han
author list: Agent
  family name: Wu
  given name: Yuqi
author list: Agent
  family name: Wang
  given name: Chong-Zhi
author list: Agent
  family name: Qi
  given name: Lian-Wen
author list: Agent
  family name: Li
  given name: Ping
author list: Agent
  family name: Yao
  given name: Haiqiang
author list: Agent
  family name: Yuan
  given name: Chun-Su
doi: 10.7717/peerj.12513
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-24
copyright: © 2021 Wan et al.
attribution name: Wan et al.

Translation and psychometric validation of the Persian version of the Questionnaire on Smoking Urges for assessment of craving to smoke among university students
type: item
type: AcademicArticle
description: Background Even though tobacco is one of the most preventable causes of death worldwide, it endangers more than 8 million people yearly. In this context, meta-analyses suggest that a significant part of the general Iranian population over 15 years of age smoke and that there is a need for good screening tools for smoking cravings and urges in Iran. The present study reported the translation and investigated the psychometric properties (i.e., factor structure, validity, and reliability) of the Persian version of the Questionnaire on Smoking Urges (QSU) with 12 items in the Iranian context. Method The translation process and content validity of the items were examined entirely in an expert panel using the Content Validity Index. The total sample of participants in which the translated version was tested consisted of 392 (172 female, 220 male, Mage = 22.31 years, SD = 2.90) university students who answered the QSU 12-item at the start of their participation in smoking cessation interventions. The QSU 12-item was firstly translated, then piloted using a subsample of 150 university students and finally validity and reliability of the instrument were investigated using a subsample of 242 participants. We tested the proposed models in the literature, that is, a 1-factor solution and a 2-factor solution with six items on each factor (Factor 1: desire/intention to smoke; Factor 2: relief of negative affect or withdrawal symptoms and anticipation of positive outcome). At last, we tested differences across differences in QSU-scores across different subgroups of individuals based on their demographics. Results The results suggested that, in contrast to past studies, a modified 2-factor model, using five items for Factor 1 and 7 items for Factor 2, was the best fitting model (CFI = .95, RMSEA = .09, CI = 90%). Additionally, the QSU 12-item Persian version showed good convergent and divergent validity, internal consistency (Factor 1 = .94, Factor 2 = .97), ICC (average measure IC…
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format: text/html
creator: Maryam Kazemitabar
creator: Danilo Garcia
subject: Drugs and Devices
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.12531
publisher: PeerJ Inc.
rights: © 2021 Kazemitabar et al.
abstract: Background Even though tobacco is one of the most preventable causes of death worldwide, it endangers more than 8 million people yearly. In this context, meta-analyses suggest that a significant part of the general Iranian population over 15 years of age smoke and that there is a need for good screening tools for smoking cravings and urges in Iran. The present study reported the translation and investigated the psychometric properties (i.e., factor structure, validity, and reliability) of the Persian version of the Questionnaire on Smoking Urges (QSU) with 12 items in the Iranian context. Method The translation process and content validity of the items were examined entirely in an expert panel using the Content Validity Index. The total sample of participants in which the translated version was tested consisted of 392 (172 female, 220 male, Mage = 22.31 years, SD = 2.90) university students who answered the QSU 12-item at the start of their participation in smoking cessation interventions. The QSU 12-item was firstly translated, then piloted using a subsample of 150 university students and finally validity and reliability of the instrument were investigated using a subsample of 242 participants. We tested the proposed models in the literature, that is, a 1-factor solution and a 2-factor solution with six items on each factor (Factor 1: desire/intention to smoke; Factor 2: relief of negative affect or withdrawal symptoms and anticipation of positive outcome). At last, we tested differences across differences in QSU-scores across different subgroups of individuals based on their demographics. Results The results suggested that, in contrast to past studies, a modified 2-factor model, using five items for Factor 1 and 7 items for Factor 2, was the best fitting model (CFI = .95, RMSEA = .09, CI = 90%). Additionally, the QSU 12-item Persian version showed good convergent and divergent validity, internal consistency (Factor 1 = .94, Factor 2 = .97), ICC (average measure IC…
bibliographic citation: Kazemitabar et al. (2021) Translation and psychometric validation of the Persian version of the Questionnaire on Smoking Urges for assessment of craving to smoke among university students. PeerJ 9:e12531 https://doi.org/10.7717/peerj.12531
date submitted: 2021-03-29
date accepted: 2021-11-02
issued: 2021-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kazemitabar
  given name: Maryam
author list: Agent
  family name: Garcia
  given name: Danilo
doi: 10.7717/peerj.12531
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-24
copyright: ©2021 Kazemitabar et al.
attribution name: Kazemitabar et al.

Comparison of an exercise program with and without manual therapy for patients with chronic neck pain and upper cervical rotation restriction. Randomized controlled trial
type: item
type: AcademicArticle
description: Background Cervical exercise has been shown to be an effective treatment for neck pain, but there is still a need for more clinical trials evaluating the effectiveness of adding manual therapy to the exercise approach. There is a lack of evidence on the effect of these techniques in patients with neck pain and upper cervical rotation restriction. Purpose To compare the effectiveness of adding manual therapy to a cervical exercise protocol for the treatment of patients with chronic neck pain and upper cervical rotation restriction. Methods Single-blind randomized clinical trial. Fifty-eight subjects: 29 for the Manual Therapy+Exercise (MT+Exercise) Group and 29 for the Exercise group. Neck disability index, pain intensity (0–10), pressure pain threshold (kPa), flexion-rotation test (°), and cervical range of motion (°) were measured at the beginning and at the end of the intervention, and at 3-and 6-month follow-ups. The MT+Exercise Group received one 20-min session of manual therapy and exercise once a week for 4 weeks and home exercise. The Exercise Group received one 20-min session of exercise once a week for 4 weeks and home exercise. Results The MT+Exercise Group showed significant better values post-intervention in all variables: neck disability index: 0% patient with moderate, severe, or complete disability compared to 31% in the Exercise Group (p = 0.000) at 6-months; flexion-rotation test (p = 0.000) and pain intensity (p = 0.000) from the first follow-up to the end of the study; cervical flexion (p = 0.002), extension (p = 0.002), right lateral-flexion (p = 0.000), left lateral-flexion (p = 0.001), right rotation (p = 0.000) and left rotation (p = 0.005) at 6-months of the study, except for flexion, with significative changes from 3-months of follow up; pressure pain threshold from the first follow-up to the end of the study (p values range: 0.003–0.000). Conclusion Four 20-min sessions of manual therapy and exercise, along with a home-exercise program, was…
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creator: Jacobo Rodríguez-Sanz
creator: Miguel Malo-Urriés
creator: María Orosia Lucha-López
creator: Carlos López-de-Celis
creator: Albert Pérez-Bellmunt
creator: Jaime Corral-de-Toro
creator: César Hidalgo-García
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Kinesiology
subject: Orthopedics
subject: Public Health
description: doi:10.7717/peerj.12546
publisher: PeerJ Inc.
rights: © 2021 Rodríguez-Sanz et al.
abstract: Background Cervical exercise has been shown to be an effective treatment for neck pain, but there is still a need for more clinical trials evaluating the effectiveness of adding manual therapy to the exercise approach. There is a lack of evidence on the effect of these techniques in patients with neck pain and upper cervical rotation restriction. Purpose To compare the effectiveness of adding manual therapy to a cervical exercise protocol for the treatment of patients with chronic neck pain and upper cervical rotation restriction. Methods Single-blind randomized clinical trial. Fifty-eight subjects: 29 for the Manual Therapy+Exercise (MT+Exercise) Group and 29 for the Exercise group. Neck disability index, pain intensity (0–10), pressure pain threshold (kPa), flexion-rotation test (°), and cervical range of motion (°) were measured at the beginning and at the end of the intervention, and at 3-and 6-month follow-ups. The MT+Exercise Group received one 20-min session of manual therapy and exercise once a week for 4 weeks and home exercise. The Exercise Group received one 20-min session of exercise once a week for 4 weeks and home exercise. Results The MT+Exercise Group showed significant better values post-intervention in all variables: neck disability index: 0% patient with moderate, severe, or complete disability compared to 31% in the Exercise Group (p = 0.000) at 6-months; flexion-rotation test (p = 0.000) and pain intensity (p = 0.000) from the first follow-up to the end of the study; cervical flexion (p = 0.002), extension (p = 0.002), right lateral-flexion (p = 0.000), left lateral-flexion (p = 0.001), right rotation (p = 0.000) and left rotation (p = 0.005) at 6-months of the study, except for flexion, with significative changes from 3-months of follow up; pressure pain threshold from the first follow-up to the end of the study (p values range: 0.003–0.000). Conclusion Four 20-min sessions of manual therapy and exercise, along with a home-exercise program, was…
bibliographic citation: Rodríguez-Sanz et al. (2021) Comparison of an exercise program with and without manual therapy for patients with chronic neck pain and upper cervical rotation restriction. Randomized controlled trial. PeerJ 9:e12546 https://doi.org/10.7717/peerj.12546
date submitted: 2021-04-29
date accepted: 2021-11-04
issued: 2021-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Sanz
  given name: Jacobo
author list: Agent
  family name: Malo-Urriés
  given name: Miguel
author list: Agent
  family name: Lucha-López
  given name: María Orosia
author list: Agent
  family name: López-de-Celis
  given name: Carlos
author list: Agent
  family name: Pérez-Bellmunt
  given name: Albert
author list: Agent
  family name: Corral-de-Toro
  given name: Jaime
author list: Agent
  family name: Hidalgo-García
  given name: César
doi: 10.7717/peerj.12546
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-24
copyright: © 2021 Rodríguez-Sanz et al.
attribution name: Rodríguez-Sanz et al.

Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines
type: item
type: AcademicArticle
description: Background Drought-driven acidification events of increasing frequency and severity are expected as a consequence of climate change, and these events may expose macroinvertebrate taxa to increased acidification beyond their tolerance levels. Recent work in lowland Costa Rica has shown that poorly-buffered tropical streams exhibit natural seasonal variation in pH, with extremely low levels (<4.5) after extreme dry seasons). Our goal was to determine the threshold of pH effects on survival of three tropical stream macroinvertebrate taxa. Methods We conducted laboratory mesocosm experiments to determine acidification effects (using diluted HCl) on three focal macroinvertebrate taxa collected from a poorly-buffered stream at La Selva Biological Station: (1) mayfly naiads (Ephemeroptera: Leptophlebiidae: Traverella holzenthali), (2) adult shrimp (Decapoda: Palaemonidae: Macrobrachium olfersii), and (3) larval midges (Diptera: Chironomidae). We also compared the effect of pH on survival and growth rates of larval midges from a poorly-buffered (pH 4.3–6.9) vs. a naturally well-buffered (pH 5.1–6.9) stream. Results/Discussion Mayfly and shrimp survival decreased between pH 4.0 and 3.5, overlapping with the range of lowest pH levels (3.6–4.0) recorded during a previous extreme El Niño Southern Oscillation event in 1998 and suggesting that increasingly extreme acidification events induced by climate change may negatively affect their survival. In contrast, survival of larval midges was unaffected by pH regimes at/above 3.5, indicating tolerance to pH levels experienced in poorly-buffered stream during seasonal acidification, which has presumably occurred over millennia. These findings highlight the potential importance of historical pH regimes in structuring macroinvertebrate communities. These results are relevant not only to lowland Neotropical streams, but also signal the need for further research in lotic ecosystems worldwide where drought-driven pH declines have been doc…
format: application/pdf
format: text/html
creator: Carissa Ganong
creator: Minor Hidalgo Oconitrillo
creator: Catherine Pringle
subject: Ecology
subject: Zoology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11955
publisher: PeerJ Inc.
rights: © 2021 Ganong et al.
abstract: Background Drought-driven acidification events of increasing frequency and severity are expected as a consequence of climate change, and these events may expose macroinvertebrate taxa to increased acidification beyond their tolerance levels. Recent work in lowland Costa Rica has shown that poorly-buffered tropical streams exhibit natural seasonal variation in pH, with extremely low levels (<4.5) after extreme dry seasons). Our goal was to determine the threshold of pH effects on survival of three tropical stream macroinvertebrate taxa. Methods We conducted laboratory mesocosm experiments to determine acidification effects (using diluted HCl) on three focal macroinvertebrate taxa collected from a poorly-buffered stream at La Selva Biological Station: (1) mayfly naiads (Ephemeroptera: Leptophlebiidae: Traverella holzenthali), (2) adult shrimp (Decapoda: Palaemonidae: Macrobrachium olfersii), and (3) larval midges (Diptera: Chironomidae). We also compared the effect of pH on survival and growth rates of larval midges from a poorly-buffered (pH 4.3–6.9) vs. a naturally well-buffered (pH 5.1–6.9) stream. Results/Discussion Mayfly and shrimp survival decreased between pH 4.0 and 3.5, overlapping with the range of lowest pH levels (3.6–4.0) recorded during a previous extreme El Niño Southern Oscillation event in 1998 and suggesting that increasingly extreme acidification events induced by climate change may negatively affect their survival. In contrast, survival of larval midges was unaffected by pH regimes at/above 3.5, indicating tolerance to pH levels experienced in poorly-buffered stream during seasonal acidification, which has presumably occurred over millennia. These findings highlight the potential importance of historical pH regimes in structuring macroinvertebrate communities. These results are relevant not only to lowland Neotropical streams, but also signal the need for further research in lotic ecosystems worldwide where drought-driven pH declines have been doc…
bibliographic citation: Ganong et al. (2021) Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines. PeerJ 9:e11955 https://doi.org/10.7717/peerj.11955
date submitted: 2020-12-21
date accepted: 2021-07-21
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ganong
  given name: Carissa
author list: Agent
  family name: Hidalgo Oconitrillo
  given name: Minor
author list: Agent
  family name: Pringle
  given name: Catherine
doi: 10.7717/peerj.11955
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: ©2021 Ganong et al.
attribution name: Ganong et al.

Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
type: item
type: AcademicArticle
description: Background Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration. Method The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs. Results Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes …
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format: text/html
creator: Peng Su
creator: Ziqi Peng
creator: Boyang Xu
creator: Bowen Yang
creator: Feng Jin
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.12383
publisher: PeerJ Inc.
rights: © 2021 Su et al.
abstract: Background Recently, researchers have classified highly heterogeneous triple negative breast cancer (TNBC) into different subtypes from different perspectives and investigated the characteristics of different subtypes to pursue individualized treatment. With the increase of immunotherapy and its preliminary application in TNBC treatment, the value of immune-related strategies in the treatment of TNBC has been initially reflected. Based thereon, this study plans to classify and further explore TNBC from the perspective of immune cell infiltration. Method The fractions of immune cells of TNBC patients were assessed by six immune component analysis methods in The Cancer Genome Atlas (TCGA) database. Hub genes significantly related to poor prognosis were verified by weighted gene co-expression network analysis (WGCNA) analysis, Lasso analysis, and univariate KM analysis. Two cohorts of TNBC patients with complete prognosis information were collected for validation analysis. Finally, the Genomics of Drug Sensitivity in Cancer (GDSC) database was adopted to ascertain the sensitivity differences of different populations based on hub-gene grouping to different chemotherapy drugs. Results Five hub genes (CD79A, CXCL13, IGLL5, LHFPL2, and PLEKHF1) of the key co-expression gene module could divide TNBC patients into two groups (Cluster A and Cluster B) based on consistency cluster analysis. The patients with Cluster A were responsible for significantly worse prognosis than the patients with Cluster B (P = 0.023). In addition, another classification method, PCoA, and two other datasets (GSE103091 and GSE76124), were used to obtain consistent results with previous findings, which verified the stability of the classification method and dataset in this study. The grouping criteria based on the previous results were developed and the accuracy of the cut-off values was validated. A prognosis model of TNBC patients was then constructed based on the grouping results of five hub genes …
bibliographic citation: Su et al. (2021) Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer. PeerJ 9:e12383 https://doi.org/10.7717/peerj.12383
date submitted: 2021-05-13
date accepted: 2021-10-04
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Peng
author list: Agent
  family name: Peng
  given name: Ziqi
author list: Agent
  family name: Xu
  given name: Boyang
author list: Agent
  family name: Yang
  given name: Bowen
author list: Agent
  family name: Jin
  given name: Feng
doi: 10.7717/peerj.12383
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: ©2021 Su et al.
attribution name: Su et al.

Survival rates of adult and juvenile gyrfalcons in Iceland: estimates and drivers
type: item
type: AcademicArticle
description: Knowledge of survival rates and their potential covariation with environmental drivers, for both adults and juveniles, is paramount to forecast the population dynamics of long-lived animals. Long-lived bird and mammal populations are indeed very sensitive to change in survival rates, especially that of adults. Here we report the first survival estimates for the Icelandic gyrfalcon (Falco rusticolus) obtained by capture-mark-recapture methods. We use a mark-recapture-recovery model combining live and dead encounters into a unified analysis, in a Bayesian framework. Annual survival was estimated at 0.83 for adults and 0.40 for juveniles. Positive effects of main prey density on juvenile survival (5% increase in survival from min to max density) were possible though not likely. Weather effects on juvenile survival were even less likely. The variability in observed lifespan suggests that adult birds could suffer from human-induced alteration of survival rates.
format: application/pdf
format: text/html
creator: Frédéric Barraquand
creator: Ólafur K. Nielsen
subject: Ecology
subject: Zoology
subject: Statistics
subject: Population Biology
description: doi:10.7717/peerj.12404
publisher: PeerJ Inc.
rights: © 2021 Barraquand and Nielsen
abstract: Knowledge of survival rates and their potential covariation with environmental drivers, for both adults and juveniles, is paramount to forecast the population dynamics of long-lived animals. Long-lived bird and mammal populations are indeed very sensitive to change in survival rates, especially that of adults. Here we report the first survival estimates for the Icelandic gyrfalcon (Falco rusticolus) obtained by capture-mark-recapture methods. We use a mark-recapture-recovery model combining live and dead encounters into a unified analysis, in a Bayesian framework. Annual survival was estimated at 0.83 for adults and 0.40 for juveniles. Positive effects of main prey density on juvenile survival (5% increase in survival from min to max density) were possible though not likely. Weather effects on juvenile survival were even less likely. The variability in observed lifespan suggests that adult birds could suffer from human-induced alteration of survival rates.
bibliographic citation: Barraquand et al. (2021) Survival rates of adult and juvenile gyrfalcons in Iceland: estimates and drivers. PeerJ 9:e12404 https://doi.org/10.7717/peerj.12404
date submitted: 2020-11-24
date accepted: 2021-10-07
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barraquand
  given name: Frédéric
author list: Agent
  family name: Nielsen
  given name: Ólafur K.
doi: 10.7717/peerj.12404
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: © 2021 Barraquand and Nielsen
attribution name: Barraquand and Nielsen

Effect of mesoporous bioactive glass on odontogenic differentiation of human dental pulp stem cells
type: item
type: AcademicArticle
description: Healthy pulp tissue plays an important role in normal function and long-term retention of teeth. Mesoporous bioactive glass (MBG) as a kind of regenerative biomaterials shows the potential in preserving the vital pulp. In this study, MBG prepared by organic template method combined with sol-gel method were used in human dental pulp cell culture and ectopic mineralization experiment. Real-Time PCR was used to explore its ability to induce odontogenic differentiation of dental pulp cells. MBG and rat crowns were implanted under the skin of nude mice for 4 weeks to observe the formation of pulp dentin complex. We found that MBG can release Si and Ca ions and has a strong mineralization activity in vitro. The co-culture of MBG with human dental pulp cells promoted the expression of DMP-1 (dentin matrix protein-1) and ALP (alkalinephosphatase) without affecting cell proliferation. After 4 weeks of subcutaneous implantation in nude mice, the formation of hard tissue with regular structure under the material could be seen, and the structure was similar to dentin tubules. These results indicate that MBG can induce the differentiation of dental pulp cells and the formation of dental pulp-dentin complex and has the potential to promote the repair and regeneration of dental pulp injuries.
format: application/pdf
format: text/html
creator: Lin Zhu
creator: Jingyi Li
creator: Yanmei Dong
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
subject: Histology
description: doi:10.7717/peerj.12421
publisher: PeerJ Inc.
rights: © 2021 Zhu et al.
abstract: Healthy pulp tissue plays an important role in normal function and long-term retention of teeth. Mesoporous bioactive glass (MBG) as a kind of regenerative biomaterials shows the potential in preserving the vital pulp. In this study, MBG prepared by organic template method combined with sol-gel method were used in human dental pulp cell culture and ectopic mineralization experiment. Real-Time PCR was used to explore its ability to induce odontogenic differentiation of dental pulp cells. MBG and rat crowns were implanted under the skin of nude mice for 4 weeks to observe the formation of pulp dentin complex. We found that MBG can release Si and Ca ions and has a strong mineralization activity in vitro. The co-culture of MBG with human dental pulp cells promoted the expression of DMP-1 (dentin matrix protein-1) and ALP (alkalinephosphatase) without affecting cell proliferation. After 4 weeks of subcutaneous implantation in nude mice, the formation of hard tissue with regular structure under the material could be seen, and the structure was similar to dentin tubules. These results indicate that MBG can induce the differentiation of dental pulp cells and the formation of dental pulp-dentin complex and has the potential to promote the repair and regeneration of dental pulp injuries.
bibliographic citation: Zhu et al. (2021) Effect of mesoporous bioactive glass on odontogenic differentiation of human dental pulp stem cells. PeerJ 9:e12421 https://doi.org/10.7717/peerj.12421
date submitted: 2021-07-12
date accepted: 2021-10-11
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Lin
author list: Agent
  family name: Li
  given name: Jingyi
author list: Agent
  family name: Dong
  given name: Yanmei
doi: 10.7717/peerj.12421
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: © 2021 Zhu et al.
attribution name: Zhu et al.

Response of diatom assemblages to the disruption of the running water continuum in urban areas, and its consequences on bioassessment
type: item
type: AcademicArticle
description: Transformation of river and stream channels disrupts their natural ecological cycles and interrupts the continuum of their ecosystems. Changes in natural hydromorphological conditions transform lotic communities into those atypical of flowing waters, resulting in bioassessment procedures yielding incorrect results. This study shows how hydromorphological transformations of ecosystems affect the ecological status bioassessment results by disturbing diatom communities typical for rivers. Moreover, the article presents a new biological assessment procedure for urban transformed rivers including the verification of the community structure based on autecology and quantity of species. The ecological status of the ecosystem was assessed using benthic diatom assemblages and supported with results of hydrochemical analysis. The structure of the assemblages and their relationships between individual sampling sites were clarified by shade plot and multivariate data analyses. The analysis of dominant species vitality at sampling sites and their autecology gave the foundation for modification of taxa data matrix and recalculation the diatom indices. Biological assessment showed that one of the artificial ponds constructed at the stream channel was characterized by good ecological status, and its presence strongly affected the state of the downstream ecosystem following the development of a unique assemblage of diatoms that prefer oligosaprobic and oligotrophic waters. The presence of these species was also noted in the downstream sections, but most of the cells were dead. As the indicator values of these taxa are high, their presence artificially increased the ecological status of the stream, resulting in the hydrochemical assessment not being in line with the bioassessment. Therefore, a new procedure was adopted in which non-characteristic taxa for the downstream sections were excluded from analysis. This approach corrected the results of bioassessment characterizing the ecolog…
format: application/pdf
format: text/html
creator: Ewelina Szczepocka
creator: Paulina Nowicka-Krawczyk
creator: Rafał M. Olszyński
creator: Joanna Żelazna-Wieczorek
subject: Ecology
subject: Plant Science
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.12457
publisher: PeerJ Inc.
rights: © 2021 Szczepocka et al.
abstract: Transformation of river and stream channels disrupts their natural ecological cycles and interrupts the continuum of their ecosystems. Changes in natural hydromorphological conditions transform lotic communities into those atypical of flowing waters, resulting in bioassessment procedures yielding incorrect results. This study shows how hydromorphological transformations of ecosystems affect the ecological status bioassessment results by disturbing diatom communities typical for rivers. Moreover, the article presents a new biological assessment procedure for urban transformed rivers including the verification of the community structure based on autecology and quantity of species. The ecological status of the ecosystem was assessed using benthic diatom assemblages and supported with results of hydrochemical analysis. The structure of the assemblages and their relationships between individual sampling sites were clarified by shade plot and multivariate data analyses. The analysis of dominant species vitality at sampling sites and their autecology gave the foundation for modification of taxa data matrix and recalculation the diatom indices. Biological assessment showed that one of the artificial ponds constructed at the stream channel was characterized by good ecological status, and its presence strongly affected the state of the downstream ecosystem following the development of a unique assemblage of diatoms that prefer oligosaprobic and oligotrophic waters. The presence of these species was also noted in the downstream sections, but most of the cells were dead. As the indicator values of these taxa are high, their presence artificially increased the ecological status of the stream, resulting in the hydrochemical assessment not being in line with the bioassessment. Therefore, a new procedure was adopted in which non-characteristic taxa for the downstream sections were excluded from analysis. This approach corrected the results of bioassessment characterizing the ecolog…
bibliographic citation: Szczepocka et al. (2021) Response of diatom assemblages to the disruption of the running water continuum in urban areas, and its consequences on bioassessment. PeerJ 9:e12457 https://doi.org/10.7717/peerj.12457
date submitted: 2021-06-28
date accepted: 2021-10-18
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szczepocka
  given name: Ewelina
author list: Agent
  family name: Nowicka-Krawczyk
  given name: Paulina
author list: Agent
  family name: Olszyński
  given name: Rafał M.
author list: Agent
  family name: Żelazna-Wieczorek
  given name: Joanna
doi: 10.7717/peerj.12457
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: ©2021 Szczepocka et al.
attribution name: Szczepocka et al.

Workplace violence against frontline clinicians in emergency departments during the COVID-19 pandemic
type: item
type: AcademicArticle
description: Background Frontline clinicians working in emergency departments (ED) were at disportionate risk of workplace violence (WPV). We investigated the prevalence of WPV and its relationship with quality of life (QOL) in this group of health professionals in China during the COVID-19 pandemic. Methods A cross-sectional, online study was conducted. The nine-item Workplace Violence Scale measured WPV. Results A total of 1,103 ED clinicians participated in this study. The overall prevalence of WPV against ED clinicians was 29.2% (95% CI [26.5%-31.9%]). Having family/friends/colleagues infected with COVID-19 (Odds Ratio (OR) = 1.82, P = 0.01), current smoking (OR = 2.98, P < 0.01) and severity of anxiety symptoms (OR = 1.08, P < 0.01) were independently and positively associated with WPV, while working in emergency intensive care units (OR = 0.45, P < 0.01) was negatively associated with WPV. After controlling for covariates, clinicians experiencing WPV had a lower global QOL compared to those without (F(1, 1103) = 10.9,P < 0.01). Conclusions Prevalence of workplace violence against ED clinicians was common in China during the COVID-19 pandemic. Due to the negative impact of WPV on QOL and quality of care, timely preventive measures should be undertaken for ED clinicians.
format: application/pdf
format: text/html
creator: Rui Liu
creator: Yue Li
creator: Ying An
creator: Ling Zhang
creator: Feng-Rong An
creator: Jia Luo
creator: Aiping Wang
creator: Yan-Jie Zhao
creator: Anzhe Yuan
creator: Teris Cheung
creator: Gabor S. Ungvari
creator: Ming-Zhao Qin
creator: Yu-Tao Xiang
subject: Emergency and Critical Care
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.12459
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Frontline clinicians working in emergency departments (ED) were at disportionate risk of workplace violence (WPV). We investigated the prevalence of WPV and its relationship with quality of life (QOL) in this group of health professionals in China during the COVID-19 pandemic. Methods A cross-sectional, online study was conducted. The nine-item Workplace Violence Scale measured WPV. Results A total of 1,103 ED clinicians participated in this study. The overall prevalence of WPV against ED clinicians was 29.2% (95% CI [26.5%-31.9%]). Having family/friends/colleagues infected with COVID-19 (Odds Ratio (OR) = 1.82, P = 0.01), current smoking (OR = 2.98, P < 0.01) and severity of anxiety symptoms (OR = 1.08, P < 0.01) were independently and positively associated with WPV, while working in emergency intensive care units (OR = 0.45, P < 0.01) was negatively associated with WPV. After controlling for covariates, clinicians experiencing WPV had a lower global QOL compared to those without (F(1, 1103) = 10.9,P < 0.01). Conclusions Prevalence of workplace violence against ED clinicians was common in China during the COVID-19 pandemic. Due to the negative impact of WPV on QOL and quality of care, timely preventive measures should be undertaken for ED clinicians.
bibliographic citation: Liu et al. (2021) Workplace violence against frontline clinicians in emergency departments during the COVID-19 pandemic. PeerJ 9:e12459 https://doi.org/10.7717/peerj.12459
date submitted: 2021-04-29
date accepted: 2021-10-18
issued: 2021-11-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Li
  given name: Yue
author list: Agent
  family name: An
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Ling
author list: Agent
  family name: An
  given name: Feng-Rong
author list: Agent
  family name: Luo
  given name: Jia
author list: Agent
  family name: Wang
  given name: Aiping
author list: Agent
  family name: Zhao
  given name: Yan-Jie
author list: Agent
  family name: Yuan
  given name: Anzhe
author list: Agent
  family name: Cheung
  given name: Teris
author list: Agent
  family name: Ungvari
  given name: Gabor S.
author list: Agent
  family name: Qin
  given name: Ming-Zhao
author list: Agent
  family name: Xiang
  given name: Yu-Tao
doi: 10.7717/peerj.12459
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-23
copyright: ©2021 Liu et al.
attribution name: Liu et al.

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