PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A flexible and accurate method for electroencephalography rhythms extraction based on circulant singular spectrum analysis
items: Growth and survival among Hawaiian corals outplanted from tanks to an ocean nursery are driven by individual genotype and species differences rather than preconditioning to thermal stress
items: Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF)
items: Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia
items: RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability
items: ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells
items: Novel decorating behaviour of silk retreats in a challenging habitat
items: Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds
items: Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability
items: E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces

A flexible and accurate method for electroencephalography rhythms extraction based on circulant singular spectrum analysis
type: item
type: AcademicArticle
description: Rhythms extraction from electroencephalography (EEG) signals can be used to monitor the physiological and pathological states of the brain and has attracted much attention in recent studies. A flexible and accurate method for EEG rhythms extraction was proposed by incorporating a novel circulant singular spectrum analysis (CiSSA). The EEG signals are decomposed into the sum of a set of orthogonal reconstructed components (RCs) at known frequencies. The frequency bandwidth of each RC is limited to a particular brain rhythm band, with no frequency mixing between different RCs. The RCs are then grouped flexibly to extract the desired EEG rhythms based on the known frequencies. The extracted brain rhythms are accurate and no mixed components of other rhythms or artifacts are included. Simulated EEG data based on the Markov Process Amplitude EEG model and experimental EEG data in the eyes-open and eyes-closed states were used to verify the CiSSA-based method. The results showed that the CiSSA-based method is flexible in alpha rhythms extraction and has a higher accuracy in distinguishing between the eyes-open and eyes-closed states, compared with the basic SSA method, the wavelet decomposition method, and the finite impulse response filtering method.
format: application/pdf
format: text/html
creator: Hai Hu
creator: Zihang Pu
creator: Peng Wang
subject: Bioengineering
subject: Bioinformatics
subject: Computational Biology
subject: Neuroscience
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.13096
publisher: PeerJ Inc.
rights: © 2022 Hu et al.
abstract: Rhythms extraction from electroencephalography (EEG) signals can be used to monitor the physiological and pathological states of the brain and has attracted much attention in recent studies. A flexible and accurate method for EEG rhythms extraction was proposed by incorporating a novel circulant singular spectrum analysis (CiSSA). The EEG signals are decomposed into the sum of a set of orthogonal reconstructed components (RCs) at known frequencies. The frequency bandwidth of each RC is limited to a particular brain rhythm band, with no frequency mixing between different RCs. The RCs are then grouped flexibly to extract the desired EEG rhythms based on the known frequencies. The extracted brain rhythms are accurate and no mixed components of other rhythms or artifacts are included. Simulated EEG data based on the Markov Process Amplitude EEG model and experimental EEG data in the eyes-open and eyes-closed states were used to verify the CiSSA-based method. The results showed that the CiSSA-based method is flexible in alpha rhythms extraction and has a higher accuracy in distinguishing between the eyes-open and eyes-closed states, compared with the basic SSA method, the wavelet decomposition method, and the finite impulse response filtering method.
bibliographic citation: Hu et al. (2022) A flexible and accurate method for electroencephalography rhythms extraction based on circulant singular spectrum analysis. PeerJ 10:e13096 https://doi.org/10.7717/peerj.13096
date submitted: 2021-05-12
date accepted: 2022-02-20
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Hai
author list: Agent
  family name: Pu
  given name: Zihang
author list: Agent
  family name: Wang
  given name: Peng
doi: 10.7717/peerj.13096
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: © 2022 Hu et al.
attribution name: Hu et al.

Growth and survival among Hawaiian corals outplanted from tanks to an ocean nursery are driven by individual genotype and species differences rather than preconditioning to thermal stress
type: item
type: AcademicArticle
description: The drastic decline in coral coverage has stimulated an interest in reef restoration, and various iterations of coral nurseries have been used to augment restoration strategies. Here we examine the growth of two species of Hawaiian Montipora that were maintained in mesocosms under either ambient or warmed annual bleaching conditions for two consecutive years prior to outplanting to determine whether preconditioning aided coral restoration efforts. Using coral trees to create a nearby ocean nursery, we examined whether: (1) previous ex situ mesocosm growth would mirror in situ coral tree nursery growth; and (2) thermal ex situ stress-hardening would predict future success during natural warming events in situ for corals moved from tanks to trees. For Montipora capitata, we found that variation in growth was explained primarily by genotype; growth rates in the mesocosms were similar to those in situ, irrespective of preconditioning. Variation in M. flabellata growth, however, was explained by both genotype and culture method such that an individual M. flabellata colony that grew well in the tanks did not necessarily perform as well on the coral trees. For both species, previous exposure to elevated temperatures in the mesocosms provided no benefit to either growth or survival during a warming event in the coral tree nursery compared to those grown in ambient temperatures. Overall, M. capitata performed better in the tree nursery with higher net growth, lower mortality, and was subject to less predation than M. flabellata. Our results show little benefit of the additional cost and time of stress-hardening these corals prior to outplanting because it is unlikely to aid resilience to future warming events. These results also suggest that selecting corals for restoration based on long-term genotype growth performance may be more effective for optimal outcomes but should be weighed against other factors, such as coral morphology, in situ nursery method, location, and other…
format: application/pdf
format: text/html
creator: E. Michael Henley
creator: Jessica Bouwmeester
creator: Christopher P. Jury
creator: Robert J. Toonen
creator: Mariko Quinn
creator: Claire V.A. Lager
creator: Mary Hagedorn
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.13112
publisher: PeerJ Inc.
rights: © 2022 Henley et al.
abstract: The drastic decline in coral coverage has stimulated an interest in reef restoration, and various iterations of coral nurseries have been used to augment restoration strategies. Here we examine the growth of two species of Hawaiian Montipora that were maintained in mesocosms under either ambient or warmed annual bleaching conditions for two consecutive years prior to outplanting to determine whether preconditioning aided coral restoration efforts. Using coral trees to create a nearby ocean nursery, we examined whether: (1) previous ex situ mesocosm growth would mirror in situ coral tree nursery growth; and (2) thermal ex situ stress-hardening would predict future success during natural warming events in situ for corals moved from tanks to trees. For Montipora capitata, we found that variation in growth was explained primarily by genotype; growth rates in the mesocosms were similar to those in situ, irrespective of preconditioning. Variation in M. flabellata growth, however, was explained by both genotype and culture method such that an individual M. flabellata colony that grew well in the tanks did not necessarily perform as well on the coral trees. For both species, previous exposure to elevated temperatures in the mesocosms provided no benefit to either growth or survival during a warming event in the coral tree nursery compared to those grown in ambient temperatures. Overall, M. capitata performed better in the tree nursery with higher net growth, lower mortality, and was subject to less predation than M. flabellata. Our results show little benefit of the additional cost and time of stress-hardening these corals prior to outplanting because it is unlikely to aid resilience to future warming events. These results also suggest that selecting corals for restoration based on long-term genotype growth performance may be more effective for optimal outcomes but should be weighed against other factors, such as coral morphology, in situ nursery method, location, and other…
bibliographic citation: Henley et al. (2022) Growth and survival among Hawaiian corals outplanted from tanks to an ocean nursery are driven by individual genotype and species differences rather than preconditioning to thermal stress. PeerJ 10:e13112 https://doi.org/10.7717/peerj.13112
date submitted: 2021-07-22
date accepted: 2022-02-22
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henley
  given name: E. Michael
author list: Agent
  family name: Bouwmeester
  given name: Jessica
author list: Agent
  family name: Jury
  given name: Christopher P.
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Quinn
  given name: Mariko
author list: Agent
  family name: Lager
  given name: Claire V.A.
author list: Agent
  family name: Hagedorn
  given name: Mary
doi: 10.7717/peerj.13112
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: © 2022 Henley et al.
attribution name: Henley et al.

Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF)
type: item
type: AcademicArticle
description: Background Pain is the leading cause of animal suffering, hence the importance of validated tools to ensure its appropriate evaluation and treatment. We aimed to test the psychometric properties of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF) in eight languages. Methods The original scale was condensed from ten to four items. The content validation was performed by five specialists in veterinary anesthesia and analgesia. The English version of the scale was translated and back-translated into Chinese, French, German, Italian, Japanese, Portuguese and Spanish by fluent English and native speaker translators. Videos of the perioperative period of 30 cats submitted to ovariohysterectomy (preoperative, after surgery, after rescue analgesia and 24 h after surgery) were randomly evaluated twice (one-month interval) by one evaluator for each language unaware of the pain condition. After watching each video, the evaluators scored the unidimensional, UFEPS-SF and Glasgow composite multidimensional feline pain scales. Statistical analyses were carried out using R software for intra and interobserver reliability, principal component analysis, criteria concurrent and predictive validities, construct validity, item-total correlation, internal consistency, specificity, sensitivity, the definition of the intervention score for rescue analgesia and diagnostic uncertainty zone, according to the receiver operating characteristic (ROC) curve. Results UFEPS-SF intra- and inter-observer reliability were ≥0.92 and 0.84, respectively, for all observers. According to the principal component analysis, UFEPS-SF is a unidimensional scale. Concurrent criterion validity was confirmed by the high correlation between UFEPS-SF and all other scales (≥0.9). The total score and all items of UFEPS-SF increased after surgery (pain), decreased to baseline after analgesia and were intermediate at 24 h after surgery (moderate pain), confirming responsiveness and construct validity. It…
format: application/pdf
format: text/html
creator: Stelio P.L. Luna
creator: Pedro H.E. Trindade
creator: Beatriz P. Monteiro
creator: Nadia Crosignani
creator: Giorgia della Rocca
creator: Helene L.M. Ruel
creator: Kazuto Yamashita
creator: Peter Kronen
creator: Chia Te Tseng
creator: Lívia Teixeira
creator: Paulo V. Steagall
subject: Animal Behavior
subject: Veterinary Medicine
subject: Anesthesiology and Pain Management
description: doi:10.7717/peerj.13134
publisher: PeerJ Inc.
rights: © 2022 Luna et al.
abstract: Background Pain is the leading cause of animal suffering, hence the importance of validated tools to ensure its appropriate evaluation and treatment. We aimed to test the psychometric properties of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF) in eight languages. Methods The original scale was condensed from ten to four items. The content validation was performed by five specialists in veterinary anesthesia and analgesia. The English version of the scale was translated and back-translated into Chinese, French, German, Italian, Japanese, Portuguese and Spanish by fluent English and native speaker translators. Videos of the perioperative period of 30 cats submitted to ovariohysterectomy (preoperative, after surgery, after rescue analgesia and 24 h after surgery) were randomly evaluated twice (one-month interval) by one evaluator for each language unaware of the pain condition. After watching each video, the evaluators scored the unidimensional, UFEPS-SF and Glasgow composite multidimensional feline pain scales. Statistical analyses were carried out using R software for intra and interobserver reliability, principal component analysis, criteria concurrent and predictive validities, construct validity, item-total correlation, internal consistency, specificity, sensitivity, the definition of the intervention score for rescue analgesia and diagnostic uncertainty zone, according to the receiver operating characteristic (ROC) curve. Results UFEPS-SF intra- and inter-observer reliability were ≥0.92 and 0.84, respectively, for all observers. According to the principal component analysis, UFEPS-SF is a unidimensional scale. Concurrent criterion validity was confirmed by the high correlation between UFEPS-SF and all other scales (≥0.9). The total score and all items of UFEPS-SF increased after surgery (pain), decreased to baseline after analgesia and were intermediate at 24 h after surgery (moderate pain), confirming responsiveness and construct validity. It…
bibliographic citation: Luna et al. (2022) Multilingual validation of the short form of the Unesp-Botucatu Feline Pain Scale (UFEPS-SF). PeerJ 10:e13134 https://doi.org/10.7717/peerj.13134
date submitted: 2021-12-14
date accepted: 2022-02-26
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luna
  given name: Stelio P.L.
author list: Agent
  family name: Trindade
  given name: Pedro H.E.
author list: Agent
  family name: Monteiro
  given name: Beatriz P.
author list: Agent
  family name: Crosignani
  given name: Nadia
author list: Agent
  family name: della Rocca
  given name: Giorgia
author list: Agent
  family name: Ruel
  given name: Helene L.M.
author list: Agent
  family name: Yamashita
  given name: Kazuto
author list: Agent
  family name: Kronen
  given name: Peter
author list: Agent
  family name: Tseng
  given name: Chia Te
author list: Agent
  family name: Teixeira
  given name: Lívia
author list: Agent
  family name: Steagall
  given name: Paulo V.
doi: 10.7717/peerj.13134
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: ©2022 Luna et al.
attribution name: Luna et al.

Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia
type: item
type: AcademicArticle
description: Background Human papillomavirus (HPV) is a well-known cause of cervical cancer. The prevalence of HPV, insufficient preventive services, inadequate treatment access, socioeconomic conditions, certain cultural causes and values and opinions regarding cervical cancer have been established as factors contributing to the occurrence of cervical cancer in various parts of the world. Objective To determine university students’ knowledge, attitudes and perceptions regarding HPV and its vaccine. Material and Methods The present cross-sectional study included students enrolled at the University of Hail, Saudi Arabia. Data were collected from January to May 2020 using a previously validated 26-item questionnaire. Results A total of 386 participants responded to the survey; the response rate was 80%. The majority of the respondents (63%) were male and 332 (86%) respondents were single among the overall study population. Most respondents were aged 21–25 years (75.6%), followed by 26–30 years (12.7%). In total, 130 (33.7%) respondents reported that they had heard of HPV before, while 174 (45.1%) reported that HPV infections are rare in Saudi Arabia. Furthermore, 102 (26.4%) respondents thought that HPV causes genital warts, while almost 29.5% believed that HPV infection is a sexually transmitted disease. Nearly 76.2% of the respondents did not believe that HPV infection can occur without symptoms. Moreover, 53.4% of the respondents stated that they did not know the health problems associated with HPV infection, while 148 (38.8%) stated that cervical cancer is a health problem associated with HPV infection. When asked about their understanding of the HPV vaccine, nearly 267 (62.2%) respondents believed that there is no vaccine for HPV, while 239 (61.9%) believed that the vaccine does not minimise the risk of cervical cancer. In addition, the respondents reported that they would be far more likely to get an HPV vaccine if recommended by their doctors [relative importance index (RII…
format: application/pdf
format: text/html
creator: Farhan Alshammari
creator: Kashif Ullah Khan
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.13140
publisher: PeerJ Inc.
rights: © 2022 Alshammari and Khan
abstract: Background Human papillomavirus (HPV) is a well-known cause of cervical cancer. The prevalence of HPV, insufficient preventive services, inadequate treatment access, socioeconomic conditions, certain cultural causes and values and opinions regarding cervical cancer have been established as factors contributing to the occurrence of cervical cancer in various parts of the world. Objective To determine university students’ knowledge, attitudes and perceptions regarding HPV and its vaccine. Material and Methods The present cross-sectional study included students enrolled at the University of Hail, Saudi Arabia. Data were collected from January to May 2020 using a previously validated 26-item questionnaire. Results A total of 386 participants responded to the survey; the response rate was 80%. The majority of the respondents (63%) were male and 332 (86%) respondents were single among the overall study population. Most respondents were aged 21–25 years (75.6%), followed by 26–30 years (12.7%). In total, 130 (33.7%) respondents reported that they had heard of HPV before, while 174 (45.1%) reported that HPV infections are rare in Saudi Arabia. Furthermore, 102 (26.4%) respondents thought that HPV causes genital warts, while almost 29.5% believed that HPV infection is a sexually transmitted disease. Nearly 76.2% of the respondents did not believe that HPV infection can occur without symptoms. Moreover, 53.4% of the respondents stated that they did not know the health problems associated with HPV infection, while 148 (38.8%) stated that cervical cancer is a health problem associated with HPV infection. When asked about their understanding of the HPV vaccine, nearly 267 (62.2%) respondents believed that there is no vaccine for HPV, while 239 (61.9%) believed that the vaccine does not minimise the risk of cervical cancer. In addition, the respondents reported that they would be far more likely to get an HPV vaccine if recommended by their doctors [relative importance index (RII…
bibliographic citation: Alshammari et al. (2022) Knowledge, attitudes and perceptions regarding human papillomavirus among university students in Hail, Saudi Arabia. PeerJ 10:e13140 https://doi.org/10.7717/peerj.13140
date submitted: 2021-11-15
date accepted: 2022-02-28
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alshammari
  given name: Farhan
author list: Agent
  family name: Khan
  given name: Kashif Ullah
doi: 10.7717/peerj.13140
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: © 2022 Alshammari and Khan
attribution name: Alshammari and Khan

RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability
type: item
type: AcademicArticle
description: Heart rate and heart rate variability have enabled insight into a myriad of psychophysiological phenomena. There is now an influx of research attempting using these metrics within both laboratory settings (typically derived through electrocardiography or pulse oximetry) and ecologically-rich contexts (via wearable photoplethysmography, i.e., smartwatches). However, these signals can be prone to artifacts and a low signal to noise ratio, which traditionally are detected and removed through visual inspection. Here, we developed an open-source Python package, RapidHRV, dedicated to the preprocessing, analysis, and visualization of heart rate and heart rate variability. Each of these modules can be executed with one line of code and includes automated cleaning. In simulated data, RapidHRV demonstrated excellent recovery of heart rate across most levels of noise (>=10 dB) and moderate-to-excellent recovery of heart rate variability even at relatively low signal to noise ratios (>=20 dB) and sampling rates (>=20 Hz). Validation in real datasets shows good-to-excellent recovery of heart rate and heart rate variability in electrocardiography and finger photoplethysmography recordings. Validation in wrist photoplethysmography demonstrated RapidHRV estimations were sensitive to heart rate and its variability under low motion conditions, but estimates were less stable under higher movement settings.
format: application/pdf
format: text/html
creator: Peter A. Kirk
creator: Alexander Davidson Bryan
creator: Sarah N. Garfinkel
creator: Oliver J. Robinson
subject: Bioinformatics
subject: Neuroscience
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.13147
publisher: PeerJ Inc.
rights: © 2022 Kirk et al.
abstract: Heart rate and heart rate variability have enabled insight into a myriad of psychophysiological phenomena. There is now an influx of research attempting using these metrics within both laboratory settings (typically derived through electrocardiography or pulse oximetry) and ecologically-rich contexts (via wearable photoplethysmography, i.e., smartwatches). However, these signals can be prone to artifacts and a low signal to noise ratio, which traditionally are detected and removed through visual inspection. Here, we developed an open-source Python package, RapidHRV, dedicated to the preprocessing, analysis, and visualization of heart rate and heart rate variability. Each of these modules can be executed with one line of code and includes automated cleaning. In simulated data, RapidHRV demonstrated excellent recovery of heart rate across most levels of noise (>=10 dB) and moderate-to-excellent recovery of heart rate variability even at relatively low signal to noise ratios (>=20 dB) and sampling rates (>=20 Hz). Validation in real datasets shows good-to-excellent recovery of heart rate and heart rate variability in electrocardiography and finger photoplethysmography recordings. Validation in wrist photoplethysmography demonstrated RapidHRV estimations were sensitive to heart rate and its variability under low motion conditions, but estimates were less stable under higher movement settings.
bibliographic citation: Kirk et al. (2022) RapidHRV: an open-source toolbox for extracting heart rate and heart rate variability. PeerJ 10:e13147 https://doi.org/10.7717/peerj.13147
date submitted: 2021-05-11
date accepted: 2022-03-01
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kirk
  given name: Peter A.
author list: Agent
  family name: Davidson Bryan
  given name: Alexander
author list: Agent
  family name: Garfinkel
  given name: Sarah N.
author list: Agent
  family name: Robinson
  given name: Oliver J.
doi: 10.7717/peerj.13147
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: © 2022 Kirk et al.
attribution name: Kirk et al.

ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells
type: item
type: AcademicArticle
description: Purpose The Numb protein plays a vital role in tumor development. The main aim of this study was to identify ATP11A, which is associated with the biological behavior of pancreatic cancer, and elucidate its relationship with Numb and the underlying mechanism behind this relationship. Methods First, data retrieved from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEX) databases was used to investigate the expression of ATP11A mRNA and its relationship with Numb mRNA in pancreatic cancer. Western blot assays on 31 pairs of pancreatic cancer tissues and paracancerous tissues, and immunohistochemical assays on 81 pancreatic cancer specimens were performed in order to verify the expression of ATP11A in pancreatic cancer at the protein level. Next, ATP11A was overexpressed or knocked down to observe its effects on the invasion and migration ability of pancreatic cancer cells and the changes of downstream proteins. Rescue assays were conducted to determine the mechanism through which ATP11A affects Numb, ZEB1, Snail2 and other proteins. Furthermore, immunoprecipitation assays were performed to explore the interaction between ATP11A and Numb. Finally, pancreatic cancer cells were stimulated with TGFB1 and ATP11A expression was examined to explore whether the effect of ATP11A on EMT was TGFB dependent. Results At the mRNA level, the expression of ATP11A in pancreatic cancer tissues was significantly higher than in normal pancreatic tissues (P < 0.001). ATP11A expression was also highly correlated with Numb expression (R = 0.676). At the protein level, ATP11A expression in pancreatic cancer tissues was significantly higher than that in paracancerous tissues (P = 0.0009), and high ATP11A expression was also correlated with a worse prognosis. Moreover, our results showed that ATP11A can promote the invasion and migration of pancreatic cancer cells. Additionally, ATP11A could positively regulate the expression of Numb PRRL, Snail2 and ZEB1 proteins. The rescue …
format: application/pdf
format: text/html
creator: Lin Chen
creator: Jingtong Tang
creator: Weiwei Sheng
creator: Jian Sun
creator: Yuteng Ma
creator: Ming Dong
subject: Cell Biology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.13172
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Purpose The Numb protein plays a vital role in tumor development. The main aim of this study was to identify ATP11A, which is associated with the biological behavior of pancreatic cancer, and elucidate its relationship with Numb and the underlying mechanism behind this relationship. Methods First, data retrieved from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEX) databases was used to investigate the expression of ATP11A mRNA and its relationship with Numb mRNA in pancreatic cancer. Western blot assays on 31 pairs of pancreatic cancer tissues and paracancerous tissues, and immunohistochemical assays on 81 pancreatic cancer specimens were performed in order to verify the expression of ATP11A in pancreatic cancer at the protein level. Next, ATP11A was overexpressed or knocked down to observe its effects on the invasion and migration ability of pancreatic cancer cells and the changes of downstream proteins. Rescue assays were conducted to determine the mechanism through which ATP11A affects Numb, ZEB1, Snail2 and other proteins. Furthermore, immunoprecipitation assays were performed to explore the interaction between ATP11A and Numb. Finally, pancreatic cancer cells were stimulated with TGFB1 and ATP11A expression was examined to explore whether the effect of ATP11A on EMT was TGFB dependent. Results At the mRNA level, the expression of ATP11A in pancreatic cancer tissues was significantly higher than in normal pancreatic tissues (P < 0.001). ATP11A expression was also highly correlated with Numb expression (R = 0.676). At the protein level, ATP11A expression in pancreatic cancer tissues was significantly higher than that in paracancerous tissues (P = 0.0009), and high ATP11A expression was also correlated with a worse prognosis. Moreover, our results showed that ATP11A can promote the invasion and migration of pancreatic cancer cells. Additionally, ATP11A could positively regulate the expression of Numb PRRL, Snail2 and ZEB1 proteins. The rescue …
bibliographic citation: Chen et al. (2022) ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells. PeerJ 10:e13172 https://doi.org/10.7717/peerj.13172
date submitted: 2021-10-04
date accepted: 2022-03-06
issued: 2022-03-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Lin
author list: Agent
  family name: Tang
  given name: Jingtong
author list: Agent
  family name: Sheng
  given name: Weiwei
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Ma
  given name: Yuteng
author list: Agent
  family name: Dong
  given name: Ming
doi: 10.7717/peerj.13172
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-23
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Novel decorating behaviour of silk retreats in a challenging habitat
type: item
type: AcademicArticle
description: Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat.
format: application/pdf
format: text/html
creator: Alfonso Aceves-Aparicio
creator: Donald James McLean
creator: Zoe Wild
creator: Jutta M. Schneider
creator: Marie E. Herberstein
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.12839
publisher: PeerJ Inc.
rights: © 2022 Aceves-Aparicio et al.
abstract: Many ecological interactions of spiders with their potential prey and predators are affected by the visibility of their bodies and silk, especially in habitats with lower structural complexity that expose spiders. For instance, the surface of tree trunks harbours relatively limited structures to hide in and may expose residents to visual detection by prey and predators. Here we provide the first detailed description of the novel retreat building strategy of the tree trunk jumping spider Arasia mullion. Using fields surveys, we monitored and measured over 115 spiders and 554 silk retreats. These spiders build silk retreats on the exposed surface of tree trunks, where they remain as sedentary permanent residents. Furthermore, the spiders decorate the silk retreats with bark debris that they collect from the immediate surrounding. We discuss the role of silk decoration in the unusual sedentary behaviour of these spiders and the potential mechanisms that allow A. mullion to engineer their niche in a challenging habitat.
bibliographic citation: Aceves-Aparicio et al. (2022) Novel decorating behaviour of silk retreats in a challenging habitat. PeerJ 10:e12839 https://doi.org/10.7717/peerj.12839
date submitted: 2021-05-18
date accepted: 2022-01-05
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aceves-Aparicio
  given name: Alfonso
author list: Agent
  family name: McLean
  given name: Donald James
author list: Agent
  family name: Wild
  given name: Zoe
author list: Agent
  family name: Schneider
  given name: Jutta M.
author list: Agent
  family name: Herberstein
  given name: Marie E.
doi: 10.7717/peerj.12839
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Aceves-Aparicio et al.
attribution name: Aceves-Aparicio et al.

Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds
type: item
type: AcademicArticle
description: Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian–early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural mod…
format: application/pdf
format: text/html
creator: Ludwig Luthardt
creator: Mathias Merbitz
creator: Evgeny Fridland
creator: Ronny Rößler
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.13051
publisher: PeerJ Inc.
rights: © 2022 Luthardt et al.
abstract: Our understanding of fossil floras through geological time is mainly based on various differently preserved plant parts, often found isolated under restricted taphonomic circumstances. Preservation of whole plants is exceptionally rare in the geological record but provides the most reliable proof of ancient plants, especially those lacking a nearest living relative like the late Paleozoic pteridosperms. Among them, the medullosan seed ferns represent the largest and most essential systematic group. Medullosaleans are well known from the large Euramerican tropical swamp forests of Carboniferous age, but also from seasonally dry, clastic-soil habitats of Late Pennsylvanian–early Permian intramontane basins in central Europe. An exceptional taphonomic window that offered three-dimensional preservation of early Permian plants is located in Chemnitz, eastern Germany. Here, a forest ecosystem had been buried by pyroclastic deposits in a geological instant, 291 ± 2 Ma ago. Medullosaleans are both abundant and diverse in this striking autochthonous assemblage. The upper part of a Medullosa stellata var. typica individual broke at its top resulting from the overload of volcanic ash and was buried upside-down in the basal pyroclastics. The tree crown consists of the anatomically preserved apical stem, ten attached Alethopteris schneideri foliated fronds with Myeloxylon-type petioles and rachises. Though already discovered during the scientific excavation in 2010, the remarkable find required several years of preparation work, documentation, and reconstruction. The fronds were up to 3.5 m long, bifurcating, and bore numerous bipinnately compound pinnae preserved pulvinated in life position. The apical stem vascular system consists of a cylindrical peripheral vascular segment and up to 87 central accessory strands, each surrounded by manoxylic wood and secondary phloem. The reconstructed tree is supposed to have been self-supporting and of slender stature. Its architectural mod…
bibliographic citation: Luthardt et al. (2022) Upside-down in volcanic ash: crown reconstruction of the early Permian seed fern Medullosa stellata with attached foliated fronds. PeerJ 10:e13051 https://doi.org/10.7717/peerj.13051
date submitted: 2021-12-07
date accepted: 2022-02-12
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luthardt
  given name: Ludwig
author list: Agent
  family name: Merbitz
  given name: Mathias
author list: Agent
  family name: Fridland
  given name: Evgeny
author list: Agent
  family name: Rößler
  given name: Ronny
doi: 10.7717/peerj.13051
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Luthardt et al.
attribution name: Luthardt et al.

Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability
type: item
type: AcademicArticle
description: Background Phosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils. Methods In this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities. Results Compared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90–32, xj120–12, xj120–31, and xj180–22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120–12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains. Conclusions The results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains.
format: application/pdf
format: text/html
creator: Qiuju Peng
creator: Yang Xiao
creator: Su Zhang
creator: Changwei Zhou
creator: Ailin Xie
creator: Zhu Li
creator: Aijuan Tan
creator: Lihong Zhou
creator: Yudan Xie
creator: Jinyi Zhao
creator: Chenglin Wu
creator: Lei Luo
creator: Jie Huang
creator: Tengxia He
creator: Ran Sun
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.13076
publisher: PeerJ Inc.
rights: © 2022 Peng et al.
abstract: Background Phosphorus (P) is abundant in soils, including organic and inorganic forms. Nevertheless, most of P compounds cannot be absorbed and used by plants. Aspergillus niger v. Tiegh is a strain that can efficiently degrade P compounds in soils. Methods In this study, A. niger xj strain was mutated using Atmospheric Room Temperature Plasma (ARTP) technology and the strains were screened by Mo-Sb Colorimetry with strong P-solubilizing abilities. Results Compared with the A. niger xj strain, setting the treatment time of mutagenesis to 120 s, four positive mutant strains marked as xj 90–32, xj120–12, xj120–31, and xj180–22 had higher P-solubilizing rates by 50.3%, 57.5%, 55.9%, and 61.4%, respectively. Among them, the xj120–12 is a highly efficient P solubilizing and growth-promoting strain with good application prospects. The growth characteristics such as plant height, root length, and dry and fresh biomass of peanut (Arachis hypogaea L.) increased by 33.5%, 43.8%, 43.4%, and 33.6%, respectively. Besides available P, the chlorophyll and soluble protein contents also vary degrees of increase in the P-solubilizing mutant strains. Conclusions The results showed that the ARTP mutagenesis technology can improve the P solubilization abilities of the A. niger mutant strains and make the biomass of peanut plants was enhanced of mutant strains.
bibliographic citation: Peng et al. (2022) Mutation breeding of Aspergillus niger by atmospheric room temperature plasma to enhance phosphorus solubilization ability. PeerJ 10:e13076 https://doi.org/10.7717/peerj.13076
date submitted: 2021-12-10
date accepted: 2022-02-16
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Qiuju
author list: Agent
  family name: Xiao
  given name: Yang
author list: Agent
  family name: Zhang
  given name: Su
author list: Agent
  family name: Zhou
  given name: Changwei
author list: Agent
  family name: Xie
  given name: Ailin
author list: Agent
  family name: Li
  given name: Zhu
author list: Agent
  family name: Tan
  given name: Aijuan
author list: Agent
  family name: Zhou
  given name: Lihong
author list: Agent
  family name: Xie
  given name: Yudan
author list: Agent
  family name: Zhao
  given name: Jinyi
author list: Agent
  family name: Wu
  given name: Chenglin
author list: Agent
  family name: Luo
  given name: Lei
author list: Agent
  family name: Huang
  given name: Jie
author list: Agent
  family name: He
  given name: Tengxia
author list: Agent
  family name: Sun
  given name: Ran
doi: 10.7717/peerj.13076
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Peng et al.
attribution name: Peng et al.

E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces
type: item
type: AcademicArticle
description: Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the …
format: application/pdf
format: text/html
creator: Vitor Pimentel Dos Santos
creator: André Rodrigues
creator: Gabriel Dutra
creator: Luana Bastos
creator: Diego Mariano
creator: José Gutembergue Mendonça
creator: Yan Jerônimo Gomes Lobo
creator: Eduardo Mendes
creator: Giovana Maia
creator: Karina dos Santos Machado
creator: Adriano Velasque Werhli
creator: Gerd Rocha
creator: Leonardo Henrique França de Lima
creator: Raquel de Melo-Minardi
subject: Bioinformatics
subject: Computational Biology
subject: COVID-19
description: doi:10.7717/peerj.13099
publisher: PeerJ Inc.
rights: © 2022 Dos Santos et al.
abstract: Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1′/β1′, as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the …
bibliographic citation: Dos Santos et al. (2022) E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. PeerJ 10:e13099 https://doi.org/10.7717/peerj.13099
date submitted: 2021-09-24
date accepted: 2022-02-21
issued: 2022-03-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dos Santos
  given name: Vitor Pimentel
author list: Agent
  family name: Rodrigues
  given name: André
author list: Agent
  family name: Dutra
  given name: Gabriel
author list: Agent
  family name: Bastos
  given name: Luana
author list: Agent
  family name: Mariano
  given name: Diego
author list: Agent
  family name: Mendonça
  given name: José Gutembergue
author list: Agent
  family name: Lobo
  given name: Yan Jerônimo Gomes
author list: Agent
  family name: Mendes
  given name: Eduardo
author list: Agent
  family name: Maia
  given name: Giovana
author list: Agent
  family name: Machado
  given name: Karina dos Santos
author list: Agent
  family name: Werhli
  given name: Adriano Velasque
author list: Agent
  family name: Rocha
  given name: Gerd
author list: Agent
  family name: de Lima
  given name: Leonardo Henrique França
author list: Agent
  family name: de Melo-Minardi
  given name: Raquel
doi: 10.7717/peerj.13099
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-22
copyright: © 2022 Dos Santos et al.
attribution name: Dos Santos et al.

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