title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=801
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Chemical profiling of root bark extract from Oplopanax elatus and its in vitro biotransformation by human intestinal microbiota
link: https://peerj.com/articles/12513
last-modified: 2021-11-24
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.
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
uri: https://doi.org/10.7717/peerj.12513
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Wan et al.

title: Translation and psychometric validation of the Persian version of the Questionnaire on Smoking Urges for assessment of craving to smoke among university students
link: https://peerj.com/articles/12531
last-modified: 2021-11-24
description: BackgroundEven 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.MethodThe 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.ResultsThe 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 ICC = .95, CI = 95%, F(391, 4301) = 20.54, p < .001), concurrent validity (r = .71, p < .01), and discriminant validity (r = −.04, p > .05). Finally, subgroups based on gender, marital status, (un)employment, and educational level did not differed in their responses to the QSU 12-item.ConclusionThe Persian version of the QSU 12-item has satisfactory psychometric properties and, with a slight modification, it can be considered as a reliable and valid method to estimate smoking urges in the Iranian population. Moreover, the QSU 12-item seems appropriate to measure urge for smoking among groups of individuals with different sociodemographic backgrounds. Importantly, the QSU 12-item differentiates individuals’ desire and intention to smoke from their anticipated relief of negative affect or withdrawal symptoms, which can be important for personalizing interventions targeting individuals who want to quit smoking.
creator: Maryam Kazemitabar
creator: Danilo Garcia
uri: https://doi.org/10.7717/peerj.12531
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Kazemitabar et al.

title: Comparison of an exercise program with and without manual therapy for patients with chronic neck pain and upper cervical rotation restriction. Randomized controlled trial
link: https://peerj.com/articles/12546
last-modified: 2021-11-24
description: BackgroundCervical 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.PurposeTo 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.MethodsSingle-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.ResultsThe 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).ConclusionFour 20-min sessions of manual therapy and exercise, along with a home-exercise program, was found to be more effective than an exercise protocol and a home-exercise program in improving the neck disability index, flexion-rotation test, pain intensity, and pressure pain threshold, in the short, medium, and medium-long term in patients with chronic neck pain and upper rotation restriction. Cervical range of motion improved with the addition of manual therapy in the medium and medium-long term. The high dropout rate may have compromised the external validity of the study.
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
uri: https://doi.org/10.7717/peerj.12546
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Rodríguez-Sanz et al.

title: Thresholds of acidification impacts on macroinvertebrates adapted to seasonally acidified tropical streams: potential responses to extreme drought-driven pH declines
link: https://peerj.com/articles/11955
last-modified: 2021-11-23
description: BackgroundDrought-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.MethodsWe 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/DiscussionMayfly 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 documented or are probable in the future.
creator: Carissa Ganong
creator: Minor Hidalgo Oconitrillo
creator: Catherine Pringle
uri: https://doi.org/10.7717/peerj.11955
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Ganong et al.

title: Establishment and validation of an individualized macrophage-related gene signature to predict overall survival in patients with triple negative breast cancer
link: https://peerj.com/articles/12383
last-modified: 2021-11-23
description: BackgroundRecently, 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.MethodThe 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.ResultsFive 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 and N staging as prognostic factors. The results of ROC and decision curve analyses showed that this model had high prediction accuracy and patients could benefit therefrom. Finally, GDSC database analysis proved that patients in Cluster A were more sensitive to Vinorelbine. Separate analysis of the sensitivity of patients in Cluster A to Gemcitabine and Vinorelbine showed that the patients in Cluster A exhibited higher sensitivity to Vinorelbine. We hypothesized that these five genes were related to gemcitabine resistance and they could serve as biomarkers for clinical drug decision-making after anthracene resistance and taxane resistance in patients with advanced TNBC.ConclusionThis study found five hub prognostic genes associated with macrophages, and a prognostic model was established to predict the survival of TNBC patients. Finally, these five genes were related to gemcitabine resistance in TNBC patients.
creator: Peng Su
creator: Ziqi Peng
creator: Boyang Xu
creator: Bowen Yang
creator: Feng Jin
uri: https://doi.org/10.7717/peerj.12383
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Su et al.

title: Survival rates of adult and juvenile gyrfalcons in Iceland: estimates and drivers
link: https://peerj.com/articles/12404
last-modified: 2021-11-23
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.
creator: Frédéric Barraquand
creator: Ólafur K. Nielsen
uri: https://doi.org/10.7717/peerj.12404
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Barraquand and Nielsen

title: Effect of mesoporous bioactive glass on odontogenic differentiation of human dental pulp stem cells
link: https://peerj.com/articles/12421
last-modified: 2021-11-23
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.
creator: Lin Zhu
creator: Jingyi Li
creator: Yanmei Dong
uri: https://doi.org/10.7717/peerj.12421
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Zhu et al.

title: Response of diatom assemblages to the disruption of the running water continuum in urban areas, and its consequences on bioassessment
link: https://peerj.com/articles/12457
last-modified: 2021-11-23
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 ecological status of the stream as poor along its entire course, with the exception of this unique pond. For hydromorphologically transformed streams and rivers with disturbed channel continuity, the correct result of an incorrect diatom-based bioassessment may be retrieved after excluding species unusual for the type of ecosystem from the studied assemblages, i.e., the species which are unable to reproduce in that area and are only carried into it by the water flow. Assessment of the ecological status of aquatic ecosystems based on biotic factors is an essential tool of aquatic ecosystems monitoring in many countries. This type of assessment requires a multifaceted approach, in particular, to identify factors that may disrupt this assessment. Standardization of biomonitoring methods is an important step in correct assessment; thus, the findings of this paper will be useful in routine biomonitoring around the world.
creator: Ewelina Szczepocka
creator: Paulina Nowicka-Krawczyk
creator: Rafał M. Olszyński
creator: Joanna Żelazna-Wieczorek
uri: https://doi.org/10.7717/peerj.12457
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Szczepocka et al.

title: Workplace violence against frontline clinicians in emergency departments during the COVID-19 pandemic
link: https://peerj.com/articles/12459
last-modified: 2021-11-23
description: BackgroundFrontline 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.MethodsA cross-sectional, online study was conducted. The nine-item Workplace Violence Scale measured WPV.ResultsA 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).ConclusionsPrevalence 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.
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
uri: https://doi.org/10.7717/peerj.12459
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Liu et al.

title: A decrease in reports on road-killed animals based on citizen science during COVID-19 lockdown
link: https://peerj.com/articles/12464
last-modified: 2021-11-23
description: BackgroundTo avoid the uncontrolled spread of COVID-19 in early 2020, many countries have implemented strict lockdown measures for several weeks. In Austria, the lockdown in early spring has led to a significant drop in human outdoor activities, especially in road traffic. In Project Roadkill, a citizen science project which aims to collect data on road-killed animals, we observed a significant decrease in reported roadkills.MethodsBy asking the citizen scientists through a survey how their travelling routines were affected, we investigated if the observed decrease in roadkills was grounded in less animals being killed by traffic, or in citizen scientists staying at home and thus reporting less road-killed animals.ResultsA majority of the respondents stated that they felt to have reported less roadkills during the lockdown, regardless if they changed their travelling routine or not. This observation in combination with the overall decrease in road traffic indicates that fewer animals were killed during the lockdown. We conclude that when analyzing citizen science data, the effects of lockdown measures on reporting behaviour should be considered, because they can significantly affect data and interpretation of these data.
creator: Daniel Dörler
creator: Florian Heigl
uri: https://doi.org/10.7717/peerj.12464
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Dörler and Heigl