PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions
items: FastANI, Mash and Dashing equally differentiate between Klebsiella species
items: Cross-sectional associations between effort-reward imbalance at work and oral diseases in Japan
items: Effects of growing Coptis chinensis Franch in the natural understory vs. under a manmade scaffold on its growth, alkaloid contents, and rhizosphere soil microenvironment
items: Evaluating the readability, quality and reliability of online patient education materials on post-covid pain
items: Baleen whale inhalation variability revealed using animal-borne video tags
items: Experiencing the impossible and creativity: a targeted literature review
items: Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships
items: Knowledge, attitude and practice towards bio-medical waste management among healthcare workers: a northern Saudi study
items: Engineering a tunable bicistronic TetR autoregulation expression system in Gluconobacter oxydans

Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions
type: item
type: AcademicArticle
description: Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae Chlorella vulgaris and Chlamydomonas reinhardtii across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations. Culture growth rates and biomass achieved were compared using different methods of biomass estimation. Both species grew faster and produced the most biomass when supplied with moderate acetate concentrations (1–4 g L−1), but light was required to optimize growth rates, biomass yield, cell size and cell chlorophyll content. Higher acetate concentration (10 g L−1) inhibited algal production. The choice of growth parameter and method to estimate biomass (optical density (OD), chlorophyll a fluorescence, flow cytometry, cell counts) affected apparent responses to organic carbon, but use of OD at 600, 680 or 750 nm was consistent. There were apparent trade-offs among exponential growth rate, maximum biomass, and culture time spent in exponential phase. Different cell responses over 1–10 g L−1 acetate highlight profound physiological acclimation across a gradient of mixotrophy. In both species, cell size vs cell chlorophyll relationships were more constrained in photoautotrophic and heterotrophic cultures, but under mixotrophy, and outside exponential growth phase, these relationships were more variable. This study provides insights into algal physiological responses to mixotrophy but also has practical implications for choosing parameters for monitoring commercial algal cultivation.
format: application/pdf
format: text/html
creator: Erica B. Young
creator: Lindsay Reed
creator: John A. Berges
subject: Aquaculture, Fisheries and Fish Science
subject: Plant Science
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.13776
publisher: PeerJ Inc.
rights: © 2022 Young et al.
abstract: Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae Chlorella vulgaris and Chlamydomonas reinhardtii across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations. Culture growth rates and biomass achieved were compared using different methods of biomass estimation. Both species grew faster and produced the most biomass when supplied with moderate acetate concentrations (1–4 g L−1), but light was required to optimize growth rates, biomass yield, cell size and cell chlorophyll content. Higher acetate concentration (10 g L−1) inhibited algal production. The choice of growth parameter and method to estimate biomass (optical density (OD), chlorophyll a fluorescence, flow cytometry, cell counts) affected apparent responses to organic carbon, but use of OD at 600, 680 or 750 nm was consistent. There were apparent trade-offs among exponential growth rate, maximum biomass, and culture time spent in exponential phase. Different cell responses over 1–10 g L−1 acetate highlight profound physiological acclimation across a gradient of mixotrophy. In both species, cell size vs cell chlorophyll relationships were more constrained in photoautotrophic and heterotrophic cultures, but under mixotrophy, and outside exponential growth phase, these relationships were more variable. This study provides insights into algal physiological responses to mixotrophy but also has practical implications for choosing parameters for monitoring commercial algal cultivation.
bibliographic citation: Young et al. (2022) Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions. PeerJ 10:e13776 https://doi.org/10.7717/peerj.13776
date submitted: 2022-04-10
date accepted: 2022-07-01
issued: 2022-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Erica B.
author list: Agent
  family name: Reed
  given name: Lindsay
author list: Agent
  family name: Berges
  given name: John A.
doi: 10.7717/peerj.13776
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-21
copyright: © 2022 Young et al.
attribution name: Young et al.

FastANI, Mash and Dashing equally differentiate between Klebsiella species
type: item
type: AcademicArticle
description: Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.
format: application/pdf
format: text/html
creator: Julie E. Hernández-Salmerón
creator: Gabriel Moreno-Hagelsieb
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.13784
publisher: PeerJ Inc.
rights: © 2022 Hernández-Salmerón and Moreno-Hagelsieb
abstract: Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.
bibliographic citation: Hernández-Salmerón et al. (2022) FastANI, Mash and Dashing equally differentiate between Klebsiella species. PeerJ 10:e13784 https://doi.org/10.7717/peerj.13784
date submitted: 2021-11-26
date accepted: 2022-07-05
issued: 2022-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Salmerón
  given name: Julie E.
author list: Agent
  family name: Moreno-Hagelsieb
  given name: Gabriel
doi: 10.7717/peerj.13784
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-21
copyright: © 2022 Hernández-Salmerón and Moreno-Hagelsieb
attribution name: Hernández-Salmerón and Moreno-Hagelsieb

Cross-sectional associations between effort-reward imbalance at work and oral diseases in Japan
type: item
type: AcademicArticle
description: Background Psychological stress is a potential risk factor for oral diseases. However, evidence for the association between work stress and oral diseases is scarce. We aimed to examine the associations of work stress, according to the effort-reward imbalance model, with dental caries, periodontal status, and tooth loss. Methods This cross-sectional study included 184 regular employees at a medical university and 435 registrants of a web research company. Work stress was assessed using the effort-reward imbalance (ERI) ratio. Dental caries and tooth loss were assessed according to the number of decayed, filled, and missing teeth (DMFT) among the set of 28 teeth. Periodontal status was assessed using a self-administered questionnaire. For the DMFT, a linear regression model was used to estimate the unstandardised coefficients. A Poisson regression model was used to estimate the prevalence ratios (PRs) of poor periodontal status. Results Among medical university employees and employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was associated with −2.81 (95% CI [−4.70 to −0.92]; p-value = 0.004) and −0.84 (95% CI [−1.80 to 0.12]; p-value = 0.085) changes in the DMFT from adjusted linear regression models, respectively. In employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was also associated with 1.55 (95% CI [1.04–2.32]; p-value = 0.032) of the PR for poor periodontal status based on Poisson regression models. Conclusion ERI at work was associated with an increased risk of poor periodontal status.
format: application/pdf
format: text/html
creator: Yukihiro Sato
creator: Eiji Yoshioka
creator: Masanori Takekawa
creator: Yasuaki Saijo
subject: Dentistry
subject: Epidemiology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.13792
publisher: PeerJ Inc.
rights: © 2022 Sato et al.
abstract: Background Psychological stress is a potential risk factor for oral diseases. However, evidence for the association between work stress and oral diseases is scarce. We aimed to examine the associations of work stress, according to the effort-reward imbalance model, with dental caries, periodontal status, and tooth loss. Methods This cross-sectional study included 184 regular employees at a medical university and 435 registrants of a web research company. Work stress was assessed using the effort-reward imbalance (ERI) ratio. Dental caries and tooth loss were assessed according to the number of decayed, filled, and missing teeth (DMFT) among the set of 28 teeth. Periodontal status was assessed using a self-administered questionnaire. For the DMFT, a linear regression model was used to estimate the unstandardised coefficients. A Poisson regression model was used to estimate the prevalence ratios (PRs) of poor periodontal status. Results Among medical university employees and employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was associated with −2.81 (95% CI [−4.70 to −0.92]; p-value = 0.004) and −0.84 (95% CI [−1.80 to 0.12]; p-value = 0.085) changes in the DMFT from adjusted linear regression models, respectively. In employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was also associated with 1.55 (95% CI [1.04–2.32]; p-value = 0.032) of the PR for poor periodontal status based on Poisson regression models. Conclusion ERI at work was associated with an increased risk of poor periodontal status.
bibliographic citation: Sato et al. (2022) Cross-sectional associations between effort-reward imbalance at work and oral diseases in Japan. PeerJ 10:e13792 https://doi.org/10.7717/peerj.13792
date submitted: 2022-04-22
date accepted: 2022-07-05
issued: 2022-07-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sato
  given name: Yukihiro
author list: Agent
  family name: Yoshioka
  given name: Eiji
author list: Agent
  family name: Takekawa
  given name: Masanori
author list: Agent
  family name: Saijo
  given name: Yasuaki
doi: 10.7717/peerj.13792
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-21
copyright: © 2022 Sato et al.
attribution name: Sato et al.

Effects of growing Coptis chinensis Franch in the natural understory vs. under a manmade scaffold on its growth, alkaloid contents, and rhizosphere soil microenvironment
type: item
type: AcademicArticle
description: Background The main planting modes currently used for the production of Coptis chinensis Franch are under the shade of a manmade scaffold or a natural understory. In this study, we analysed changes in the growth, development, and alkaloids of C. chinensis when grown in a natural understory compared with under a manmade scaffold. We also clarified the differences in the rhizosphere soil microenvironment, represented by soil physicochemical factors, enzyme activity, and microbial community structure of 1- to 5-year-old C. chinensis between the different planting modes. These results will provide theoretical guidance and scientific evidence for the development, application, and extension of ecological planting technologies for C. chinensis. Results The results of this study showed that rhizome length, rhizome diameter, and rhizome weight all increased over time in both planting modes. The greatest rhizome length was reached in 4-year-old C. chinensis, while the greatest rhizome diameter and rhizome weight were obtained in 5-year-old C. chinensis. There was no significant difference in rhizome biomass between the two planting modes. The alkaloid content of the four common alkaloids in the rhizome of 5-year-old C. chinensis at the harvest stage met the standards found in the Pharmacopoeia of the People’s Republic of China; the berberine content and total alkaloids in the rhizomes were significantly higher with natural understory planting compared to planting under a manmade scaffold. A redundancy analysis revealed that the physicochemical factors and enzyme activity of rhizosphere soil were significantly correlated with variation in microbial community structure. Soil pH, available potassium, bulk density, available nitrogen, catalase, and peroxidase were all significantly correlated with bacterial and fungal community structures. Among these, soil pH was the most important factor influencing the structures of the fungal and bacterial community. In the two planting modes…
format: application/pdf
format: text/html
creator: Yu Wang
creator: Yu R. Mo
creator: Jun Tan
creator: Li X. Wu
creator: Yuan Pan
creator: Xia D. Chen
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13676
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background The main planting modes currently used for the production of Coptis chinensis Franch are under the shade of a manmade scaffold or a natural understory. In this study, we analysed changes in the growth, development, and alkaloids of C. chinensis when grown in a natural understory compared with under a manmade scaffold. We also clarified the differences in the rhizosphere soil microenvironment, represented by soil physicochemical factors, enzyme activity, and microbial community structure of 1- to 5-year-old C. chinensis between the different planting modes. These results will provide theoretical guidance and scientific evidence for the development, application, and extension of ecological planting technologies for C. chinensis. Results The results of this study showed that rhizome length, rhizome diameter, and rhizome weight all increased over time in both planting modes. The greatest rhizome length was reached in 4-year-old C. chinensis, while the greatest rhizome diameter and rhizome weight were obtained in 5-year-old C. chinensis. There was no significant difference in rhizome biomass between the two planting modes. The alkaloid content of the four common alkaloids in the rhizome of 5-year-old C. chinensis at the harvest stage met the standards found in the Pharmacopoeia of the People’s Republic of China; the berberine content and total alkaloids in the rhizomes were significantly higher with natural understory planting compared to planting under a manmade scaffold. A redundancy analysis revealed that the physicochemical factors and enzyme activity of rhizosphere soil were significantly correlated with variation in microbial community structure. Soil pH, available potassium, bulk density, available nitrogen, catalase, and peroxidase were all significantly correlated with bacterial and fungal community structures. Among these, soil pH was the most important factor influencing the structures of the fungal and bacterial community. In the two planting modes…
bibliographic citation: Wang et al. (2022) Effects of growing Coptis chinensis Franch in the natural understory vs. under a manmade scaffold on its growth, alkaloid contents, and rhizosphere soil microenvironment. PeerJ 10:e13676 https://doi.org/10.7717/peerj.13676
date submitted: 2021-11-15
date accepted: 2022-06-13
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Mo
  given name: Yu R.
author list: Agent
  family name: Tan
  given name: Jun
author list: Agent
  family name: Wu
  given name: Li X.
author list: Agent
  family name: Pan
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Xia D.
doi: 10.7717/peerj.13676
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Evaluating the readability, quality and reliability of online patient education materials on post-covid pain
type: item
type: AcademicArticle
description: Background The use of the Internet to access healthcare-related information is increasing day by day. However, there are concerns regarding the reliability and comprehensibility of this information. This study aimed to investigate the readability, reliability, and quality of Internet-based patient educational materials (PEM) related to “post-COVID-19 pain.” Methods One-hundred websites that fit the purposes of the study were identified by searching for the terms “post-COVID-19 pain” and “pain after COVID-19” using the Google search engine on February 24, 2022. The website readability was assessed using the Flesch Reading Ease Score (FRES), Flesch–Kincaid Grade Level (FKGL), Simple Measure of Gobbledygook (SMOG), and Gunning FOG (GFOG). The reliability, quality, and popularity of the websites were assessed using the JAMA score, DISCERN score/Health on the Net Foundation code of conduct, and Alexa, respectively. Results Upon investigation of the textual contents, the mean FRES was 51.40 ± 10.65 (difficult), the mean FKGL and SMOG were 10.93 ± 2.17 and 9.83 ± 1.66 years, respectively, and the mean GFOG was 13.14 ± 2.16 (very difficult). Furthermore, 24.5% of the websites were highly reliable according to JAMA scores, 8% were of high quality according to GQS values, and 10% were HONcode-compliant. There was a statistically significant difference between the website types and reliability (p = 0.003) and quality scores (p = 0.002). Conclusion The readability level of PEM on post-COVID-19 pain was considerably higher than grade 6 educational level, as recommended by the National Institutes of Health, and had low reliability and poor quality. We suggest that Internet-based PEM should have a certain degree of readability that is in accordance with the educational level of the general public and feature reliable content.
format: application/pdf
format: text/html
creator: Erkan Ozduran
creator: Sibel Büyükçoban
subject: Anesthesiology and Pain Management
subject: Global Health
subject: COVID-19
subject: Rehabilitation
description: doi:10.7717/peerj.13686
publisher: PeerJ Inc.
rights: © 2022 Ozduran and Büyükçoban
abstract: Background The use of the Internet to access healthcare-related information is increasing day by day. However, there are concerns regarding the reliability and comprehensibility of this information. This study aimed to investigate the readability, reliability, and quality of Internet-based patient educational materials (PEM) related to “post-COVID-19 pain.” Methods One-hundred websites that fit the purposes of the study were identified by searching for the terms “post-COVID-19 pain” and “pain after COVID-19” using the Google search engine on February 24, 2022. The website readability was assessed using the Flesch Reading Ease Score (FRES), Flesch–Kincaid Grade Level (FKGL), Simple Measure of Gobbledygook (SMOG), and Gunning FOG (GFOG). The reliability, quality, and popularity of the websites were assessed using the JAMA score, DISCERN score/Health on the Net Foundation code of conduct, and Alexa, respectively. Results Upon investigation of the textual contents, the mean FRES was 51.40 ± 10.65 (difficult), the mean FKGL and SMOG were 10.93 ± 2.17 and 9.83 ± 1.66 years, respectively, and the mean GFOG was 13.14 ± 2.16 (very difficult). Furthermore, 24.5% of the websites were highly reliable according to JAMA scores, 8% were of high quality according to GQS values, and 10% were HONcode-compliant. There was a statistically significant difference between the website types and reliability (p = 0.003) and quality scores (p = 0.002). Conclusion The readability level of PEM on post-COVID-19 pain was considerably higher than grade 6 educational level, as recommended by the National Institutes of Health, and had low reliability and poor quality. We suggest that Internet-based PEM should have a certain degree of readability that is in accordance with the educational level of the general public and feature reliable content.
bibliographic citation: Ozduran et al. (2022) Evaluating the readability, quality and reliability of online patient education materials on post-covid pain. PeerJ 10:e13686 https://doi.org/10.7717/peerj.13686
date submitted: 2022-03-21
date accepted: 2022-06-15
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ozduran
  given name: Erkan
author list: Agent
  family name: Büyükçoban
  given name: Sibel
doi: 10.7717/peerj.13686
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: ©2022 Ozduran and Büyükçoban
attribution name: Ozduran and Büyükçoban

Baleen whale inhalation variability revealed using animal-borne video tags
type: item
type: AcademicArticle
description: Empirical metabolic rate and oxygen consumption estimates for free-ranging whales have been limited to counting respiratory events at the surface. Because these observations were limited and generally viewed from afar, variability in respiratory properties was unknown and oxygen consumption estimates assumed constant breath-to-breath tidal volume and oxygen uptake. However, evidence suggests that cetaceans in human care vary tidal volume and breathing frequency to meet aerobic demand, which would significantly impact energetic estimates if the findings held in free-ranging species. In this study, we used suction cup-attached video tags positioned posterior to the nares of two humpback whales (Megaptera novaeangliae) and four Antarctic minke whales (Balaenoptera bonaerensis) to measure inhalation duration, relative nares expansion, and maximum nares expansion. Inhalation duration and nares expansion varied between and within initial, middle, and terminal breaths of surface sequences between dives. The initial and middle breaths exhibited the least variability and had the shortest durations and smallest nares expansions. In contrast, terminal breaths were highly variable, with the longest inhalation durations and the largest nares expansions. Our results demonstrate breath-to-breath variability in duration and nares expansion, suggesting differential oxygen exchange in each breath during the surface interval. With future validation, inhalation duration or nares area could be used alongside respiratory frequency to improve oxygen consumption estimates by accounting for breath-to-breath variation in wild whales.
format: application/pdf
format: text/html
creator: Emily C. Nazario
creator: David E. Cade
creator: K.C. Bierlich
creator: Max F. Czapanskiy
creator: Jeremy A. Goldbogen
creator: Shirel R. Kahane-Rapport
creator: Julie M. van der Hoop
creator: Merceline T. San Luis
creator: Ari S. Friedlaender
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
subject: Metabolic Sciences
description: doi:10.7717/peerj.13724
publisher: PeerJ Inc.
rights: © 2022 Nazario et al.
abstract: Empirical metabolic rate and oxygen consumption estimates for free-ranging whales have been limited to counting respiratory events at the surface. Because these observations were limited and generally viewed from afar, variability in respiratory properties was unknown and oxygen consumption estimates assumed constant breath-to-breath tidal volume and oxygen uptake. However, evidence suggests that cetaceans in human care vary tidal volume and breathing frequency to meet aerobic demand, which would significantly impact energetic estimates if the findings held in free-ranging species. In this study, we used suction cup-attached video tags positioned posterior to the nares of two humpback whales (Megaptera novaeangliae) and four Antarctic minke whales (Balaenoptera bonaerensis) to measure inhalation duration, relative nares expansion, and maximum nares expansion. Inhalation duration and nares expansion varied between and within initial, middle, and terminal breaths of surface sequences between dives. The initial and middle breaths exhibited the least variability and had the shortest durations and smallest nares expansions. In contrast, terminal breaths were highly variable, with the longest inhalation durations and the largest nares expansions. Our results demonstrate breath-to-breath variability in duration and nares expansion, suggesting differential oxygen exchange in each breath during the surface interval. With future validation, inhalation duration or nares area could be used alongside respiratory frequency to improve oxygen consumption estimates by accounting for breath-to-breath variation in wild whales.
bibliographic citation: Nazario et al. (2022) Baleen whale inhalation variability revealed using animal-borne video tags. PeerJ 10:e13724 https://doi.org/10.7717/peerj.13724
date submitted: 2022-05-05
date accepted: 2022-06-22
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nazario
  given name: Emily C.
author list: Agent
  family name: Cade
  given name: David E.
author list: Agent
  family name: Bierlich
  given name: K.C.
author list: Agent
  family name: Czapanskiy
  given name: Max F.
author list: Agent
  family name: Goldbogen
  given name: Jeremy A.
author list: Agent
  family name: Kahane-Rapport
  given name: Shirel R.
author list: Agent
  family name: van der Hoop
  given name: Julie M.
author list: Agent
  family name: San Luis
  given name: Merceline T.
author list: Agent
  family name: Friedlaender
  given name: Ari S.
doi: 10.7717/peerj.13724
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: ©2022 Nazario et al.
attribution name: Nazario et al.

Experiencing the impossible and creativity: a targeted literature review
type: item
type: AcademicArticle
description: Previous work suggests that unexpected and surprising experiences (e.g., living in another culture or looking at surreal images) promotes creative thinking. This targeted literature review examines whether the inherent cognitive disruption associated with experiencing the seemingly impossible has a similar effect. Correlational and experimental research across six domains (entertainment magic, fantasy play, virtual reality and computer gaming, dreaming, science fiction/fantasy, and anomalous experiences) provided consistent support for the hypothesis. In addition, anecdotal evidence illustrated the possible impact that the creative output associated with each of these areas may have had on technology, science, and the arts. It is argued that impossible experiences are an important driver of creative thinking, thus accounting for reports of such experiences across the lifespan and throughout history. The theoretical and practical implications of this work are discussed, along with recommendations for future research.
format: application/pdf
format: text/html
creator: Richard Wiseman
creator: Caroline Watt
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13755
publisher: PeerJ Inc.
rights: © 2022 Wiseman and Watt
abstract: Previous work suggests that unexpected and surprising experiences (e.g., living in another culture or looking at surreal images) promotes creative thinking. This targeted literature review examines whether the inherent cognitive disruption associated with experiencing the seemingly impossible has a similar effect. Correlational and experimental research across six domains (entertainment magic, fantasy play, virtual reality and computer gaming, dreaming, science fiction/fantasy, and anomalous experiences) provided consistent support for the hypothesis. In addition, anecdotal evidence illustrated the possible impact that the creative output associated with each of these areas may have had on technology, science, and the arts. It is argued that impossible experiences are an important driver of creative thinking, thus accounting for reports of such experiences across the lifespan and throughout history. The theoretical and practical implications of this work are discussed, along with recommendations for future research.
bibliographic citation: Wiseman et al. (2022) Experiencing the impossible and creativity: a targeted literature review. PeerJ 10:e13755 https://doi.org/10.7717/peerj.13755
date submitted: 2022-05-25
date accepted: 2022-06-28
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiseman
  given name: Richard
author list: Agent
  family name: Watt
  given name: Caroline
doi: 10.7717/peerj.13755
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: © 2022 Wiseman and Watt
attribution name: Wiseman and Watt

Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships
type: item
type: AcademicArticle
description: Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
format: application/pdf
format: text/html
creator: Isabel Duarte-Velázquez
creator: Javier de la Mora
creator: Jorge Humberto Ramírez-Prado
creator: Alondra Aguillón-Bárcenas
creator: Fátima Tornero-Gutiérrez
creator: Eugenia Cordero-Loreto
creator: Fernando Anaya-Velázquez
creator: Itzel Páramo-Pérez
creator: Ángeles Rangel-Serrano
creator: Sergio Rodrigo Muñoz-Carranza
creator: Oscar Eduardo Romero-González
creator: Luis Rafael Cardoso-Reyes
creator: Ricardo Alberto Rodríguez-Ojeda
creator: Héctor Manuel Mora-Montes
creator: Naurú Idalia Vargas-Maya
creator: Felipe Padilla-Vaca
creator: Bernardo Franco
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.13772
publisher: PeerJ Inc.
rights: © 2022 Duarte-Velázquez et al.
abstract: Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
bibliographic citation: Duarte-Velázquez et al. (2022) Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 10:e13772 https://doi.org/10.7717/peerj.13772
date submitted: 2022-03-29
date accepted: 2022-07-01
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duarte-Velázquez
  given name: Isabel
author list: Agent
  family name: de la Mora
  given name: Javier
author list: Agent
  family name: Ramírez-Prado
  given name: Jorge Humberto
author list: Agent
  family name: Aguillón-Bárcenas
  given name: Alondra
author list: Agent
  family name: Tornero-Gutiérrez
  given name: Fátima
author list: Agent
  family name: Cordero-Loreto
  given name: Eugenia
author list: Agent
  family name: Anaya-Velázquez
  given name: Fernando
author list: Agent
  family name: Páramo-Pérez
  given name: Itzel
author list: Agent
  family name: Rangel-Serrano
  given name: Ángeles
author list: Agent
  family name: Muñoz-Carranza
  given name: Sergio Rodrigo
author list: Agent
  family name: Romero-González
  given name: Oscar Eduardo
author list: Agent
  family name: Cardoso-Reyes
  given name: Luis Rafael
author list: Agent
  family name: Rodríguez-Ojeda
  given name: Ricardo Alberto
author list: Agent
  family name: Mora-Montes
  given name: Héctor Manuel
author list: Agent
  family name: Vargas-Maya
  given name: Naurú Idalia
author list: Agent
  family name: Padilla-Vaca
  given name: Felipe
author list: Agent
  family name: Franco
  given name: Bernardo
doi: 10.7717/peerj.13772
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: © 2022 Duarte-Velázquez et al.
attribution name: Duarte-Velázquez et al.

Knowledge, attitude and practice towards bio-medical waste management among healthcare workers: a northern Saudi study
type: item
type: AcademicArticle
description: Background Health care workers (HCWs) involved in day-to-day care and other healthcare activities play a significant role in biomedical waste (BMW) management. The World Health Organization stated some of the causes for the failure of BMW management, namely, lack of awareness of the health hazards related to BMW and inadequate trained HCWs in BMW management. The present study assessed knowledge, attitude, and practice (KAP) towards BMW management among the HCWs in northern Saudi Arabia. Methodology The present study assessed KAP through a self-administered and validated questionnaire. Using a multistage probability sampling method, 384 HCWs from different healthcare facilities participated in this survey. We performed binomial logistic regression analysis to find association between KAP subscales and sociodemographic characteristics. Spearman’s correlation test was performed to find the strength and direction of correlation (rho) between KAP scores. Results Of the population studied, high knowledge, attitude, and practice scores were found in 47.1%, 65.1%, and 49.5% of the HCWs, respectively. The present study found that knowledge score was significantly higher among the age group from 30 to 39 years (ref: age less than 30 years: AOR = 2.25, 95% CI [1.05–4.85], p = 0.04) and non- Saudi nationals (ref: Saudi: AOR = 2.84, 95% CI [1.63–4.94], p < 0.001) The attitude score towards BMW management was significantly lower among the HCWs working in tertiary care settings (ref: PHC: AOR = 0.38, 95% CI [0.12–0.69], p = 0.01). Regarding the practice score, the male categories had a significantly higher score (ref: female: AOR = 1.82, 95% CI [1.19 –2.99], p = 0.02), while pharmacist (ref: physicians: AOR = 0.39, 95% CI [0.18–0.58], p = 0.02) and lab technicians (ref: physicians: AOR = 0.31, 95% CI [0.11–0.53], p = 0.02) had a significant lower practice score. The test results revealed a weak positive correlation of knowledge with the attitude scores (rho = 0.249, p = 0.001), an…
format: application/pdf
format: text/html
creator: Ashokkumar Thirunavukkarasu
creator: Ahmad Homoud Al-Hazmi
creator: Umar Farooq Dar
creator: Ahmed Mohammed Alruwaili
creator: Saleh Dhifallah Alsharari
creator: Fahad Adel Alazmi
creator: Saif Farhan Alruwaili
creator: Abdullah Mohammed Alarjan
subject: Nursing
subject: Public Health
subject: Science and Medical Education
subject: COVID-19
subject: Healthcare Services
description: doi:10.7717/peerj.13773
publisher: PeerJ Inc.
rights: © 2022 Thirunavukkarasu et al.
abstract: Background Health care workers (HCWs) involved in day-to-day care and other healthcare activities play a significant role in biomedical waste (BMW) management. The World Health Organization stated some of the causes for the failure of BMW management, namely, lack of awareness of the health hazards related to BMW and inadequate trained HCWs in BMW management. The present study assessed knowledge, attitude, and practice (KAP) towards BMW management among the HCWs in northern Saudi Arabia. Methodology The present study assessed KAP through a self-administered and validated questionnaire. Using a multistage probability sampling method, 384 HCWs from different healthcare facilities participated in this survey. We performed binomial logistic regression analysis to find association between KAP subscales and sociodemographic characteristics. Spearman’s correlation test was performed to find the strength and direction of correlation (rho) between KAP scores. Results Of the population studied, high knowledge, attitude, and practice scores were found in 47.1%, 65.1%, and 49.5% of the HCWs, respectively. The present study found that knowledge score was significantly higher among the age group from 30 to 39 years (ref: age less than 30 years: AOR = 2.25, 95% CI [1.05–4.85], p = 0.04) and non- Saudi nationals (ref: Saudi: AOR = 2.84, 95% CI [1.63–4.94], p < 0.001) The attitude score towards BMW management was significantly lower among the HCWs working in tertiary care settings (ref: PHC: AOR = 0.38, 95% CI [0.12–0.69], p = 0.01). Regarding the practice score, the male categories had a significantly higher score (ref: female: AOR = 1.82, 95% CI [1.19 –2.99], p = 0.02), while pharmacist (ref: physicians: AOR = 0.39, 95% CI [0.18–0.58], p = 0.02) and lab technicians (ref: physicians: AOR = 0.31, 95% CI [0.11–0.53], p = 0.02) had a significant lower practice score. The test results revealed a weak positive correlation of knowledge with the attitude scores (rho = 0.249, p = 0.001), an…
bibliographic citation: Thirunavukkarasu et al. (2022) Knowledge, attitude and practice towards bio-medical waste management among healthcare workers: a northern Saudi study. PeerJ 10:e13773 https://doi.org/10.7717/peerj.13773
date submitted: 2022-03-03
date accepted: 2022-07-01
issued: 2022-07-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thirunavukkarasu
  given name: Ashokkumar
author list: Agent
  family name: Al-Hazmi
  given name: Ahmad Homoud
author list: Agent
  family name: Dar
  given name: Umar Farooq
author list: Agent
  family name: Alruwaili
  given name: Ahmed Mohammed
author list: Agent
  family name: Alsharari
  given name: Saleh Dhifallah
author list: Agent
  family name: Alazmi
  given name: Fahad Adel
author list: Agent
  family name: Alruwaili
  given name: Saif Farhan
author list: Agent
  family name: Alarjan
  given name: Abdullah Mohammed
doi: 10.7717/peerj.13773
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-20
copyright: ©2022 Thirunavukkarasu et al.
attribution name: Thirunavukkarasu et al.

Engineering a tunable bicistronic TetR autoregulation expression system in Gluconobacter oxydans
type: item
type: AcademicArticle
description: Acetic acid bacteria are well-known for their ability to incompletely oxidize their carbon sources. Many of the products of these oxidations find industrial uses. Metabolic engineering of acetic acid bacteria would improve production efficiency and yield by allowing controllable gene expression. However, the molecular tools necessary for regulating gene expression have only recently started being explored. To this end the ability of the activation-dependent Plux system and two constitutive repression Ptet systems were examined for their ability to modulate gene expression in Gluconobacter oxydans. The activation-dependent Plux system increased gene expression approximately 5-fold regardless of the strength of the constitutive promoter used to express the luxR transcriptional activator. The Ptet system was tunable and had a nearly 20-fold induction when the tetR gene was expressed from the strong constitutive promoters P0169 and P264, but only had a 4-fold induction when a weak constitutive promoter (P452) was used for tetR expression. However, the Ptet system was somewhat leaky when uninduced. To mitigate this background activity, a bicistronic TetR expression system was constructed. Based on molecular modeling, this system is predicted to have low background activity when not induced with anhydrotetracycline. The bicistronic system was inducible up to >3,000-fold and was highly tunable with almost no background expression when uninduced, making this bicistronic system potentially useful for engineering G. oxydans and possibly other acetic acid bacteria. These expression systems add to the newly growing repertoire of suitable regulatable promoter systems in acetic acid bacteria.
format: application/pdf
format: text/html
creator: Monica Bertucci
creator: Ky Ariano
creator: Meg Zumsteg
creator: Paul Schweiger
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.13639
publisher: PeerJ Inc.
rights: © 2022 Bertucci et al.
abstract: Acetic acid bacteria are well-known for their ability to incompletely oxidize their carbon sources. Many of the products of these oxidations find industrial uses. Metabolic engineering of acetic acid bacteria would improve production efficiency and yield by allowing controllable gene expression. However, the molecular tools necessary for regulating gene expression have only recently started being explored. To this end the ability of the activation-dependent Plux system and two constitutive repression Ptet systems were examined for their ability to modulate gene expression in Gluconobacter oxydans. The activation-dependent Plux system increased gene expression approximately 5-fold regardless of the strength of the constitutive promoter used to express the luxR transcriptional activator. The Ptet system was tunable and had a nearly 20-fold induction when the tetR gene was expressed from the strong constitutive promoters P0169 and P264, but only had a 4-fold induction when a weak constitutive promoter (P452) was used for tetR expression. However, the Ptet system was somewhat leaky when uninduced. To mitigate this background activity, a bicistronic TetR expression system was constructed. Based on molecular modeling, this system is predicted to have low background activity when not induced with anhydrotetracycline. The bicistronic system was inducible up to >3,000-fold and was highly tunable with almost no background expression when uninduced, making this bicistronic system potentially useful for engineering G. oxydans and possibly other acetic acid bacteria. These expression systems add to the newly growing repertoire of suitable regulatable promoter systems in acetic acid bacteria.
bibliographic citation: Bertucci et al. (2022) Engineering a tunable bicistronic TetR autoregulation expression system in Gluconobacter oxydans. PeerJ 10:e13639 https://doi.org/10.7717/peerj.13639
date submitted: 2021-12-23
date accepted: 2022-06-06
issued: 2022-07-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bertucci
  given name: Monica
author list: Agent
  family name: Ariano
  given name: Ky
author list: Agent
  family name: Zumsteg
  given name: Meg
author list: Agent
  family name: Schweiger
  given name: Paul
doi: 10.7717/peerj.13639
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-19
copyright: © 2022 Bertucci et al.
attribution name: Bertucci et al.

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