title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=804
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

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

title: Five undervalued edible species inherent to autumn-winter season: nutritional composition, bioactive constituents and volatiles profile
link: https://peerj.com/articles/12488
last-modified: 2021-11-23
description: BackgroundWild edible herbs have historically been used as local nutritional and medicinal sources. These plants grow spontaneously, depending on the season. They adapt well to different edaphoclimatic conditions, generating a diversity constituent beneficial to health. They impart compounds needed in the human diet in regard to macro and micronutrients. When consumed raw, they keep their properties intact and provide health benefits. Five undervalued edible plants: Stellaria media (L.) Vill, Tropaeolum majus L., Sonchus oleraceus L., Chenopodium album L. and Diplotaxis erucoides (L.) DC are characteristic of the autumn-winter season in the Valencian coastal region and could have new sustainable agro-ecological potential for the local commercial sector. However, little information is available from the nutritional quality and bioactive composition viewpoint for these species. Concurrently, the volatiles compounds profiles describing the characteristic flavors are unknown.MethodsNutritional characteristics, bioactive compounds, and other chemical components of the fresh leaves were analyzed. In addition, the volatiles composite profile was performed. The analyzed species come from the soil reservoir; their wild growth is adjusted to the autumn season. The proximate analysis was carried out by Association of Official Analytical Chemists methods. Total antioxidants were measured as 2.2-diphenyl-1-picrylhydrzyl hydrate (DPPH) and total polyphenols content via the Folin-Ciocalteu procedure. Volatiles profile was determined by gas chromatography-mass spectrometry. The vegetative part analyzed was the tender leaves with edible potential.ResultsA high variability has been obtained in the composition of the species studied. The proximate analysis found a considerable content of fiber (1.22–5.4 g·100 g−1), potassium (157.7–1,250.6 mg·100 g−1), iron (0.6–2.0 mg·100 g−1), and a low caloric value (16.1–43.02 kcal·mg·100 g−1). In bioactive compounds analysis, a high level of antioxidants was highlighted (1,604.3–4,874.6 μmol·100 g−1), followed by chlorophylls. Volatiles profile revealed that the species were rich in benzenoids (33.8–89.9%) as the majority family. The pyrazines class was characteristic only in D. erucoides L.DiscussionFresh edible leaves of the undervalued plants show considerable nutritional potential and a high bioactive components level, which highlight the antioxidant capacity. Leaves of C. album L. stand out due to their higher concentration of nutritional compounds, while D. erucoides L. is noted for its higher antioxidant capacity. Aromatic descriptor of pyrazines detected in the leaves of D. erucoides L. is associated with the slightly spicy flavors that characterize this species. Results suggest that studied species could be of great relevance in introducing these five edible herbs as a source of new grown material, postulating them as healthy food ingredients with attractive flavors for the gourmet cuisine industry.
creator: Tamara Fukalova Fukalova
creator: María Dolores García Martínez
creator: María Dolores Raigón
uri: https://doi.org/10.7717/peerj.12488
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2021 Fukalova Fukalova et al.

title: Morphometry of cellular behavior of coelomocytes from starfish Asterias amurensis
link: https://peerj.com/articles/12514
last-modified: 2021-11-23
description: A comprehensive statistical analysis using a wide range of linear and non-linear morphological parameters enabled identification of the main stages in the in vitro dynamics of cell behavior of immune cells of the marine invertebrate Asterias amurensis (Echinodermata, Asteroidea). Three stages may be distinguished in the cell behavior, which are characterized by the differences in complexity of the cell boundary microsculpture as well as by the size and asymmetry of the cell and convex hull of the cell. The first stage (5 min after placing cells onto a substrate) is characterized by more complex cell morphology and an increase in the process number and spreading area. The second stage (15 min) is characterized by simplification of cell morphology, retraction of some processes, and rounding of cells upon continued cell spreading. At the third stage (60 min), new large processes with rounded contours emerge due to partial retraction of the flattened cell surface. Each stage is characterized by statistically significant differences in several linear and nonlinear parameters of the external morphology for all cell types.
creator: Yuriy A. Karetin
uri: https://doi.org/10.7717/peerj.12514
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Karetin

title: Long-term follow-up of applying autologous bone grafts for reconstructing tympanomastoid defects in functional cholesteatoma surgery
link: https://peerj.com/articles/12522
last-modified: 2021-11-23
description: ObjectivesThis study investigated the long-term surgical outcomes of functional cholesteatoma surgery with canal wall reconstruction using autologous bone grafts as the primary material in patients with acquired cholesteatoma.Subjects and MethodsMedical charts were retrospectively reviewed for all patients admitted to one institution for surgical intervention between 2010 and 2018. We analyzed 66 patients (66 ears) who underwent functional tympanomastoidectomy involving the use of autologous bone grafts for canal wall defect reconstruction. Surgical outcomes were evaluated by comparing preoperative audiometric results with follow-up data (at least 36 months after surgery). Logistic regression analyses were performed to determine prognostic factors related to long-term hearing success. These factors included classification and stage of cholesteatoma, stapes condition, ossicular chain damage, active infection of the middle ear, state of the contralateral ear, preoperative hearing thresholds, gender, and age.ResultsThe mean follow-up period was 49.2 months. The recidivism rate was 6% (four of 66 ears). The pure-tone average significantly improved from 50.78 ± 19.98 to 40.81 ± 21.22 dB hearing level (HL; p < 0.001). Air–bone gaps significantly improved from 26.26 ± 10.53 to 17.58 ± 8.21 dB HL (p < 0.001). In multivariate logistic regression analysis, early-stage disease (p = 0.021) and pars flaccida cholesteatoma (p = 0.036) exhibited statistically significant correlations with successful hearing preservation.ConclusionFunctional cholesteatoma surgery with autologous bone grafts reconstruction is an effective approach to significantly improve hearing with low recidivism rates. Localized disease and pars flaccida cholesteatoma were two independent predictors of successful hearing preservation.
creator: Wei-Che Lan
creator: Ching-Yuan Wang
creator: Ming-Hsui Tsai
creator: Chia-Der Lin
uri: https://doi.org/10.7717/peerj.12522
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Lan et al.

title: Acceptance of anomalous research findings: explaining treatment implausibility reduces belief in far-fetched results
link: https://peerj.com/articles/12532
last-modified: 2021-11-23
description: Research findings are best understood by considering contextual factors such as treatment plausibility: how likely it is that a studied treatment or manipulation is effective, based on theory and data. If a treatment is implausible, then more evidence should be required before believing it has an effect. The current study assessed the extent to which the interpretation of a research finding is affected by treatment plausibility. Participant age varied from 18 to 82 (M = 27.4, SD = 9.4), and about half of the participants (53%) were college students. A total of 600 participants read a brief news article about an experiment with a new type of psychotherapy for weight loss. The current study used a 2 (treatment plausibility) × 3 (results type) between-subjects factorial design. Treatment plausibility had two levels: (1) a plausible cognitive behavioral therapy and (2) an implausible ”psychic reinforcement therapy” that was described as employing psychic messages to promote weight loss. The three levels of the results type factor varied how the study results were presented in the article: (1) standard results with no mention of treatment plausibility, (2) standard results followed by interpretive statements focused on treatment plausibility, and (3) no results—the study was described as still in progress. Participants rated their belief in the effectiveness of the therapy on a scale of 0 to 100% in 10% increments. When treatment plausibility was not discussed in the article, average ratings for the implausible therapy were relatively high (M = 63.1%, SD = 25.0, 95% CI% [58.2–68.1]) and similar to those for the plausible therapy (M = 69.2%, SD = 21.5, 95% CI% [65.0–73.5]). Ratings for the implausible treatment were moderately lower when the article explained why the results supporting it were questionable (M = 48.5%, SD = 26.6, 95% CI% [43.2–53.8]). The findings of the current study suggest that students and other members of the public may draw incorrect inferences from research partly because they do not appreciate the importance of treatment plausibility. This could be remedied, though not completely, by explicitly discussing the plausibility of the treatment based on theory and prior data.
creator: W. Burt Thompson
creator: Milen L. Radell
uri: https://doi.org/10.7717/peerj.12532
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2021 Thompson and Radell