PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
items: New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
items: The impact of COVID-19 and control measures on public health in Thailand, 2020
items: In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
items: A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
items: Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
items: Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
items: https://peerj.com/articles/12872
items: New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
items: 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway

Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
type: item
type: AcademicArticle
description: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
format: application/pdf
format: text/html
creator: Xiuxiu Dong
creator: Zhiyong Zhang
creator: Shaoming Wang
creator: Zihui Shen
creator: Xiaojiao Cheng
creator: Xinhua Lv
creator: Xiaozhen Pu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12928
publisher: PeerJ Inc.
rights: © 2022 Dong et al.
abstract: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
bibliographic citation: Dong et al. (2022) Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China. PeerJ 10:e12928 https://doi.org/10.7717/peerj.12928
date submitted: 2021-09-06
date accepted: 2022-01-20
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Xiuxiu
author list: Agent
  family name: Zhang
  given name: Zhiyong
author list: Agent
  family name: Wang
  given name: Shaoming
author list: Agent
  family name: Shen
  given name: Zihui
author list: Agent
  family name: Cheng
  given name: Xiaojiao
author list: Agent
  family name: Lv
  given name: Xinhua
author list: Agent
  family name: Pu
  given name: Xiaozhen
doi: 10.7717/peerj.12928
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Dong et al.
attribution name: Dong et al.

New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
type: item
type: AcademicArticle
description: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
format: application/pdf
format: text/html
creator: Julia Zograf
creator: Vladimir Mordukhovich
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12946
publisher: PeerJ Inc.
rights: © 2022 Zograf and Mordukhovich
abstract: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
bibliographic citation: Zograf et al. (2022) New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea). PeerJ 10:e12946 https://doi.org/10.7717/peerj.12946
date submitted: 2021-11-19
date accepted: 2022-01-25
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zograf
  given name: Julia
author list: Agent
  family name: Mordukhovich
  given name: Vladimir
doi: 10.7717/peerj.12946
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Zograf and Mordukhovich
attribution name: Zograf and Mordukhovich

The impact of COVID-19 and control measures on public health in Thailand, 2020
type: item
type: AcademicArticle
description: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
format: application/pdf
format: text/html
creator: Ritthideach Yorsaeng
creator: Nungruthai Suntronwong
creator: Ilada Thongpan
creator: Watchaporn Chuchaona
creator: Fajar Budi Lestari
creator: Siripat Pasittungkul
creator: Jiratchaya Puenpa
creator: Kamolthip Atsawawaranunt
creator: Chollasap Sharma
creator: Natthinee Sudhinaraset
creator: Anek Mungaomklang
creator: Rungrueng Kitphati
creator: Nasamon Wanlapakorn
creator: Yong Poovorawan
subject: Epidemiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12960
publisher: PeerJ Inc.
rights: © 2022 Yorsaeng et al.
abstract: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
bibliographic citation: Yorsaeng et al. (2022) The impact of COVID-19 and control measures on public health in Thailand, 2020. PeerJ 10:e12960 https://doi.org/10.7717/peerj.12960
date submitted: 2021-08-27
date accepted: 2022-01-27
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yorsaeng
  given name: Ritthideach
author list: Agent
  family name: Suntronwong
  given name: Nungruthai
author list: Agent
  family name: Thongpan
  given name: Ilada
author list: Agent
  family name: Chuchaona
  given name: Watchaporn
author list: Agent
  family name: Lestari
  given name: Fajar Budi
author list: Agent
  family name: Pasittungkul
  given name: Siripat
author list: Agent
  family name: Puenpa
  given name: Jiratchaya
author list: Agent
  family name: Atsawawaranunt
  given name: Kamolthip
author list: Agent
  family name: Sharma
  given name: Chollasap
author list: Agent
  family name: Sudhinaraset
  given name: Natthinee
author list: Agent
  family name: Mungaomklang
  given name: Anek
author list: Agent
  family name: Kitphati
  given name: Rungrueng
author list: Agent
  family name: Wanlapakorn
  given name: Nasamon
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.12960
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Yorsaeng et al.
attribution name: Yorsaeng et al.

In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
type: item
type: AcademicArticle
description: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
format: application/pdf
format: text/html
creator: Hany Elsawy
creator: Mohammed Almalki
creator: Omar Elmenshawy
creator: Ashraf Abdel-Moneim
subject: Biochemistry
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.12986
publisher: PeerJ Inc.
rights: © 2022 Elsawy et al.
abstract: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
bibliographic citation: Elsawy et al. (2022) In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury. PeerJ 10:e12986 https://doi.org/10.7717/peerj.12986
date submitted: 2021-11-08
date accepted: 2022-02-01
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elsawy
  given name: Hany
author list: Agent
  family name: Almalki
  given name: Mohammed
author list: Agent
  family name: Elmenshawy
  given name: Omar
author list: Agent
  family name: Abdel-Moneim
  given name: Ashraf
doi: 10.7717/peerj.12986
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Elsawy et al.
attribution name: Elsawy et al.

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
type: item
type: AcademicArticle
description: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
format: application/pdf
format: text/html
creator: Gaurav Vaidya
creator: Nico Cellinese
creator: Hilmar Lapp
subject: Bioinformatics
subject: Evolutionary Studies
subject: Taxonomy
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.12618
publisher: PeerJ Inc.
rights: © 2022 Vaidya et al.
abstract: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
bibliographic citation: Vaidya et al. (2022) A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 https://doi.org/10.7717/peerj.12618
date submitted: 2021-03-23
date accepted: 2021-11-18
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaidya
  given name: Gaurav
author list: Agent
  family name: Cellinese
  given name: Nico
author list: Agent
  family name: Lapp
  given name: Hilmar
doi: 10.7717/peerj.12618
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Vaidya et al.
attribution name: Vaidya et al.

Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
type: item
type: AcademicArticle
description: Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
format: application/pdf
format: text/html
creator: Swaha Pattanaik
creator: Mike T. John
creator: Seungwon Chung
creator: San Keller
subject: Dentistry
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12717
publisher: PeerJ Inc.
rights: © 2022 Pattanaik et al.
abstract: Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
bibliographic citation: Pattanaik et al. (2022) Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?. PeerJ 10:e12717 https://doi.org/10.7717/peerj.12717
date submitted: 2021-10-11
date accepted: 2021-12-09
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pattanaik
  given name: Swaha
author list: Agent
  family name: John
  given name: Mike T.
author list: Agent
  family name: Chung
  given name: Seungwon
author list: Agent
  family name: Keller
  given name: San
doi: 10.7717/peerj.12717
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Pattanaik et al.
attribution name: Pattanaik et al.

Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
type: item
type: AcademicArticle
description: Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
format: application/pdf
format: text/html
creator: Lindsay Isernia
creator: Clive D.L. Wynne
creator: Leanna House
creator: Erica N. Feuerbacher
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.12834
publisher: PeerJ Inc.
rights: © 2022 Isernia et al.
abstract: Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
bibliographic citation: Isernia et al. (2022) Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure. PeerJ 10:e12834 https://doi.org/10.7717/peerj.12834
date submitted: 2020-09-28
date accepted: 2022-01-04
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Isernia
  given name: Lindsay
author list: Agent
  family name: Wynne
  given name: Clive D.L.
author list: Agent
  family name: House
  given name: Leanna
author list: Agent
  family name: Feuerbacher
  given name: Erica N.
doi: 10.7717/peerj.12834
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Isernia et al.
attribution name: Isernia et al.

https://peerj.com/articles/12872
type: item
type: AcademicArticle
title: From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation
description: Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
format: application/pdf
format: text/html
creator: Qi Liu
creator: Chengqian Lv
creator: Yanan Jiang
creator: Kunpeng Luo
creator: Yang Gao
creator: Jingyang Liu
creator: Xu Zhang
creator: Jan Mohammad Omar
creator: Shizhu Jin
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.12872
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
bibliographic citation: Liu et al. (2022) From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation. PeerJ 10:e12872 https://doi.org/10.7717/peerj.12872
date submitted: 2021-11-09
date accepted: 2022-01-11
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Qi
author list: Agent
  family name: Lv
  given name: Chengqian
author list: Agent
  family name: Jiang
  given name: Yanan
author list: Agent
  family name: Luo
  given name: Kunpeng
author list: Agent
  family name: Gao
  given name: Yang
author list: Agent
  family name: Liu
  given name: Jingyang
author list: Agent
  family name: Zhang
  given name: Xu
author list: Agent
  family name: Mohammad Omar
  given name: Jan
author list: Agent
  family name: Jin
  given name: Shizhu
doi: 10.7717/peerj.12872
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Liu et al.
attribution name: Liu et al.

New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
type: item
type: AcademicArticle
description: We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
format: application/pdf
format: text/html
creator: Martin R. Langer
creator: Anna E. Weinmann
creator: Walid A. Makled
creator: Janine Könen
creator: Andrew J. Gooday
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.12884
publisher: PeerJ Inc.
rights: © 2022 Langer et al.
abstract: We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
bibliographic citation: Langer et al. (2022) New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans. PeerJ 10:e12884 https://doi.org/10.7717/peerj.12884
date submitted: 2021-11-03
date accepted: 2022-01-13
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langer
  given name: Martin R.
author list: Agent
  family name: Weinmann
  given name: Anna E.
author list: Agent
  family name: Makled
  given name: Walid A.
author list: Agent
  family name: Könen
  given name: Janine
author list: Agent
  family name: Gooday
  given name: Andrew J.
doi: 10.7717/peerj.12884
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Langer et al.
attribution name: Langer et al.

7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway
type: item
type: AcademicArticle
description: Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
format: application/pdf
format: text/html
creator: Qinxiang Zhou
creator: Hao Tang
creator: Dingqun Bai
creator: Yuhan Kong
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.12886
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
bibliographic citation: Zhou et al. (2022) 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway. PeerJ 10:e12886 https://doi.org/10.7717/peerj.12886
date submitted: 2021-09-27
date accepted: 2022-01-14
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Qinxiang
author list: Agent
  family name: Tang
  given name: Hao
author list: Agent
  family name: Bai
  given name: Dingqun
author list: Agent
  family name: Kong
  given name: Yuhan
doi: 10.7717/peerj.12886
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

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