PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Six new species of Pristimantis (Anura: Strabomantidae) from Llanganates National Park and Sangay National Park in Amazonian cloud forests of Ecuador
items: Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique
items: Mobile phone addiction and non-suicidal self-injury among adolescents in China
items: Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand
items: Habitat selection of black grouse in an isolated population in northern Germany—the importance of mixing dry and wet habitats
items: Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review
items: isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting
items: Signal peptidase 21 suppresses cell proliferation, migration, and invasion via the PTEN-PI3K/Akt signaling pathway in lung adenocarcinoma
items: Hand port-site infection after hand-assisted laparoscopic donor nephrectomy for living-donor kidney transplantation: a retrospective cohort study
items: Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms

Six new species of Pristimantis (Anura: Strabomantidae) from Llanganates National Park and Sangay National Park in Amazonian cloud forests of Ecuador
type: item
type: AcademicArticle
description: We describe six new species of rainfrogs of the genus Pristimantis (Strabomantidae) from Amazonian cloud forests in Ecuador. We also present a phylogeny showing the relationships of the new species. The phylogeny is based on mitochondrial genes 16S rRNA (16S), 12 rRNA (12S), NADH-ubiquinone oxidoreductase chain 1 (ND1) and the nuclear gene recombination-activating 1 (RAG1). We also describe the osteology of two of the new species using high-resolution x-ray computed tomography. The new species belong to two clades. The first clade is sister to the subgenus Huicundomantis and includes P. tamia sp. nov., P. miktos, and P. mallii. Pristimantis tamia sp. nov. is morphologically similar to P. miktos, P. mallii, P. martiae, and P. incomptus, but differs from them by lacking vocal slits and tympanic membrane and by having light greenish blue iris. Based in our results we expand the subgenus Huicundomantis to include the P. miktos species group. The second clade is remarkable by being highly divergent and consisting exclusively of new species: P. anaiae sp. nov., P. glendae sp. nov., P. kunam sp. nov., P. resistencia sp. nov., and P. venegasi sp. nov. The new species resemble P. roni, P. yanezi, P. llanganati, P. katoptroides, P. verecundus, and P. mutabilis but can be distinguished from them by lacking vocal slits and tympanic membrane and by having large dark round areas with thin clear borders in the sacral region. All six new species occur in the eastern slopes of the Ecuadorian Andes and are known from a single locality in Llanganates or Sangay National Park. We recommend assigning all of them to the Data Deficient (DD) Red List category. Based in our high-resolution x-ray tomographies, we report the presence of structures that appear to be intercalary elements. This would be the first report of such structures in Terrarana.
format: application/pdf
format: text/html
creator: Jhael A. Ortega
creator: Jorge Brito
creator: Santiago R. Ron
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13761
publisher: PeerJ Inc.
rights: © 2022 Ortega et al.
abstract: We describe six new species of rainfrogs of the genus Pristimantis (Strabomantidae) from Amazonian cloud forests in Ecuador. We also present a phylogeny showing the relationships of the new species. The phylogeny is based on mitochondrial genes 16S rRNA (16S), 12 rRNA (12S), NADH-ubiquinone oxidoreductase chain 1 (ND1) and the nuclear gene recombination-activating 1 (RAG1). We also describe the osteology of two of the new species using high-resolution x-ray computed tomography. The new species belong to two clades. The first clade is sister to the subgenus Huicundomantis and includes P. tamia sp. nov., P. miktos, and P. mallii. Pristimantis tamia sp. nov. is morphologically similar to P. miktos, P. mallii, P. martiae, and P. incomptus, but differs from them by lacking vocal slits and tympanic membrane and by having light greenish blue iris. Based in our results we expand the subgenus Huicundomantis to include the P. miktos species group. The second clade is remarkable by being highly divergent and consisting exclusively of new species: P. anaiae sp. nov., P. glendae sp. nov., P. kunam sp. nov., P. resistencia sp. nov., and P. venegasi sp. nov. The new species resemble P. roni, P. yanezi, P. llanganati, P. katoptroides, P. verecundus, and P. mutabilis but can be distinguished from them by lacking vocal slits and tympanic membrane and by having large dark round areas with thin clear borders in the sacral region. All six new species occur in the eastern slopes of the Ecuadorian Andes and are known from a single locality in Llanganates or Sangay National Park. We recommend assigning all of them to the Data Deficient (DD) Red List category. Based in our high-resolution x-ray tomographies, we report the presence of structures that appear to be intercalary elements. This would be the first report of such structures in Terrarana.
bibliographic citation: Ortega et al. (2022) Six new species of Pristimantis (Anura: Strabomantidae) from Llanganates National Park and Sangay National Park in Amazonian cloud forests of Ecuador. PeerJ 10:e13761 https://doi.org/10.7717/peerj.13761
date submitted: 2022-03-03
date accepted: 2022-06-29
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ortega
  given name: Jhael A.
author list: Agent
  family name: Brito
  given name: Jorge
author list: Agent
  family name: Ron
  given name: Santiago R.
doi: 10.7717/peerj.13761
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: © 2022 Ortega et al.
attribution name: Ortega et al.

Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique
type: item
type: AcademicArticle
description: Background Seagrass beds are essential habitats in coastal ecosystems, providing valuable ecosystem services, but are threatened by various climate change and human activities. Seagrass monitoring by remote sensing have been conducted over past decades using satellite and aerial images, which have low resolution to analyze changes in the composition of different seagrass species in the meadows. Recently, unmanned aerial vehicles (UAVs) have allowed us to obtain much higher resolution images, which is promising in observing fine-scale changes in seagrass species composition. Furthermore, image processing techniques based on deep learning can be applied to the discrimination of seagrass species that were difficult based only on color variation. In this study, we conducted mapping of a multispecific seagrass bed in Saroma-ko Lagoon, Hokkaido, Japan, and compared the accuracy of the three discrimination methods of seagrass bed areas and species composition, i.e., pixel-based classification, object-based classification, and the application of deep neural network. Methods We set five benthic classes, two seagrass species (Zostera marina and Z. japonica), brown and green macroalgae, and no vegetation for creating a benthic cover map. High-resolution images by UAV photography enabled us to produce a map at fine scales (<1 cm resolution). Results The application of a deep neural network successfully classified the two seagrass species. The accuracy of seagrass bed classification was the highest (82%) when the deep neural network was applied. Conclusion Our results highlighted that a combination of UAV mapping and deep learning could help monitor the spatial extent of seagrass beds and classify their species composition at very fine scales.
format: application/pdf
format: text/html
creator: Satoru Tahara
creator: Kenji Sudo
creator: Takehisa Yamakita
creator: Masahiro Nakaoka
subject: Bioengineering
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14017
publisher: PeerJ Inc.
rights: © 2022 Tahara et al.
abstract: Background Seagrass beds are essential habitats in coastal ecosystems, providing valuable ecosystem services, but are threatened by various climate change and human activities. Seagrass monitoring by remote sensing have been conducted over past decades using satellite and aerial images, which have low resolution to analyze changes in the composition of different seagrass species in the meadows. Recently, unmanned aerial vehicles (UAVs) have allowed us to obtain much higher resolution images, which is promising in observing fine-scale changes in seagrass species composition. Furthermore, image processing techniques based on deep learning can be applied to the discrimination of seagrass species that were difficult based only on color variation. In this study, we conducted mapping of a multispecific seagrass bed in Saroma-ko Lagoon, Hokkaido, Japan, and compared the accuracy of the three discrimination methods of seagrass bed areas and species composition, i.e., pixel-based classification, object-based classification, and the application of deep neural network. Methods We set five benthic classes, two seagrass species (Zostera marina and Z. japonica), brown and green macroalgae, and no vegetation for creating a benthic cover map. High-resolution images by UAV photography enabled us to produce a map at fine scales (<1 cm resolution). Results The application of a deep neural network successfully classified the two seagrass species. The accuracy of seagrass bed classification was the highest (82%) when the deep neural network was applied. Conclusion Our results highlighted that a combination of UAV mapping and deep learning could help monitor the spatial extent of seagrass beds and classify their species composition at very fine scales.
bibliographic citation: Tahara et al. (2022) Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique. PeerJ 10:e14017 https://doi.org/10.7717/peerj.14017
date submitted: 2022-02-28
date accepted: 2022-08-16
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tahara
  given name: Satoru
author list: Agent
  family name: Sudo
  given name: Kenji
author list: Agent
  family name: Yamakita
  given name: Takehisa
author list: Agent
  family name: Nakaoka
  given name: Masahiro
doi: 10.7717/peerj.14017
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: © 2022 Tahara et al.
attribution name: Tahara et al.

Mobile phone addiction and non-suicidal self-injury among adolescents in China
type: item
type: AcademicArticle
description: Background Non-suicidal self-injury (NSSI) has recently widely discussed. Independently, mobile phone addiction (MPA) has also attracted academic attention. A few research have examined the correlation between the two. However, there is inadequate knowledge to characterize this relationship altogether. This study further explores the correlation between MPA and NSSI, specifically repeated and severe NSSI. Method A population-based cross-sectional survey was conducted among 2,719 adolescents in Lincang, Yunnan. The mobile phone addiction index (MPAI) and the Modified Adolescents Self-Harm Survey (MASHS) were administered in combination. The connection between the MPAI and NSSI, as well as both repeated and severe NSSI, was studied using univariate and multivariate logistic regression models. (The copyright holders have permitted the authors to use the MPAI and the MASHS). Results The prevalence of NSSI was 47.11% (95% CI [36.2–58.0%]), and the detection rate of MPA was 11.11% (95% CI [6.7–18.0%]). The prevalence of NSSI among those with MPA was 4.280 times (95% CI [3.480–5.266]) that of respondents not exhibiting MPA. In addition, all subscales of the MPAI, except for the feeling anxious and lost subscale (FALS), were positively correlated with NSSI. Risk factors, represented by odds ratios, of repeated NSSI with the inability to control cravings subscale (ICCS), the FALS, and the withdrawal and escape subscale (WES) was 1.052 (95% CI [1.032–1.072]), 1.028 (95% CI [1.006–1.051]), and 1.048 (95% CI [1.019–1.078]) respectively. Risk factors of these same three subscales for severe NSSI, had odds ratios of 1.048 (95% CI [1.029–1.068]), 1.033 (95% CI [1.009–1.057]), and 1.045 (95% CI [1.018–1.073]). Conclusion MPA was shown to be a risk factor for NSSI in adolescents. Individuals with high scores on the ICCS, the WES, and the FALS were more prone to experience repeated and severe NSSI. As a result, early assessment using the MPAI to determine the need for intervention ca…
format: application/pdf
format: text/html
creator: Rui Wang
creator: Runxu Yang
creator: Hailiang Ran
creator: Xiufeng Xu
creator: Guangya Yang
creator: TianLan Wang
creator: Yusan Che
creator: Die Fang
creator: Jin Lu
creator: Yuanyuan Xiao
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.14057
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Non-suicidal self-injury (NSSI) has recently widely discussed. Independently, mobile phone addiction (MPA) has also attracted academic attention. A few research have examined the correlation between the two. However, there is inadequate knowledge to characterize this relationship altogether. This study further explores the correlation between MPA and NSSI, specifically repeated and severe NSSI. Method A population-based cross-sectional survey was conducted among 2,719 adolescents in Lincang, Yunnan. The mobile phone addiction index (MPAI) and the Modified Adolescents Self-Harm Survey (MASHS) were administered in combination. The connection between the MPAI and NSSI, as well as both repeated and severe NSSI, was studied using univariate and multivariate logistic regression models. (The copyright holders have permitted the authors to use the MPAI and the MASHS). Results The prevalence of NSSI was 47.11% (95% CI [36.2–58.0%]), and the detection rate of MPA was 11.11% (95% CI [6.7–18.0%]). The prevalence of NSSI among those with MPA was 4.280 times (95% CI [3.480–5.266]) that of respondents not exhibiting MPA. In addition, all subscales of the MPAI, except for the feeling anxious and lost subscale (FALS), were positively correlated with NSSI. Risk factors, represented by odds ratios, of repeated NSSI with the inability to control cravings subscale (ICCS), the FALS, and the withdrawal and escape subscale (WES) was 1.052 (95% CI [1.032–1.072]), 1.028 (95% CI [1.006–1.051]), and 1.048 (95% CI [1.019–1.078]) respectively. Risk factors of these same three subscales for severe NSSI, had odds ratios of 1.048 (95% CI [1.029–1.068]), 1.033 (95% CI [1.009–1.057]), and 1.045 (95% CI [1.018–1.073]). Conclusion MPA was shown to be a risk factor for NSSI in adolescents. Individuals with high scores on the ICCS, the WES, and the FALS were more prone to experience repeated and severe NSSI. As a result, early assessment using the MPAI to determine the need for intervention ca…
bibliographic citation: Wang et al. (2022) Mobile phone addiction and non-suicidal self-injury among adolescents in China. PeerJ 10:e14057 https://doi.org/10.7717/peerj.14057
date submitted: 2022-04-11
date accepted: 2022-08-25
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Rui
author list: Agent
  family name: Yang
  given name: Runxu
author list: Agent
  family name: Ran
  given name: Hailiang
author list: Agent
  family name: Xu
  given name: Xiufeng
author list: Agent
  family name: Yang
  given name: Guangya
author list: Agent
  family name: Wang
  given name: TianLan
author list: Agent
  family name: Che
  given name: Yusan
author list: Agent
  family name: Fang
  given name: Die
author list: Agent
  family name: Lu
  given name: Jin
author list: Agent
  family name: Xiao
  given name: Yuanyuan
doi: 10.7717/peerj.14057
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand
type: item
type: AcademicArticle
description: During an epidemic, real-time estimation of the effective reproduction number supports decision makers to introduce timely and effective public health measures. We estimate the time-varying effective reproduction number, Rt, during Aotearoa New Zealand’s August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available EpiNow2 model to New Zealand case data. While we do not explicitly model non-pharmaceutical interventions or vaccination coverage, these two factors were the leading drivers of variation in transmission in this period and we describe how changes in these factors coincided with changes in Rt. Alert Level 4, New Zealand’s most stringent restriction setting which includes stay-at-home measures, was initially effective at reducing the median Rtto 0.6 (90% CrI 0.4, 0.8) on 29 August 2021. As New Zealand eased certain restrictions and switched from an elimination strategy to a suppression strategy, Rt subsequently increased to a median 1.3 (1.2, 1.4). Increasing vaccination coverage along with regional restrictions were eventually sufficient to reduce Rtbelow 1. The outbreak peaked at an estimated 198 (172, 229) new infected cases on 10 November, after which cases declined until January 2022. We continue to update Rtestimates in real time as new case data become available to inform New Zealand’s ongoing pandemic response.
format: application/pdf
format: text/html
creator: Rachelle N. Binny
creator: Audrey Lustig
creator: Shaun C. Hendy
creator: Oliver J. Maclaren
creator: Kannan M. Ridings
creator: Giorgia Vattiato
creator: Michael J. Plank
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.14119
publisher: PeerJ Inc.
rights: © 2022 Binny et al.
abstract: During an epidemic, real-time estimation of the effective reproduction number supports decision makers to introduce timely and effective public health measures. We estimate the time-varying effective reproduction number, Rt, during Aotearoa New Zealand’s August 2021 outbreak of the Delta variant of SARS-CoV-2, by fitting the publicly available EpiNow2 model to New Zealand case data. While we do not explicitly model non-pharmaceutical interventions or vaccination coverage, these two factors were the leading drivers of variation in transmission in this period and we describe how changes in these factors coincided with changes in Rt. Alert Level 4, New Zealand’s most stringent restriction setting which includes stay-at-home measures, was initially effective at reducing the median Rtto 0.6 (90% CrI 0.4, 0.8) on 29 August 2021. As New Zealand eased certain restrictions and switched from an elimination strategy to a suppression strategy, Rt subsequently increased to a median 1.3 (1.2, 1.4). Increasing vaccination coverage along with regional restrictions were eventually sufficient to reduce Rtbelow 1. The outbreak peaked at an estimated 198 (172, 229) new infected cases on 10 November, after which cases declined until January 2022. We continue to update Rtestimates in real time as new case data become available to inform New Zealand’s ongoing pandemic response.
bibliographic citation: Binny et al. (2022) Real-time estimation of the effective reproduction number of SARS-CoV-2 in Aotearoa New Zealand. PeerJ 10:e14119 https://doi.org/10.7717/peerj.14119
date submitted: 2022-05-07
date accepted: 2022-09-04
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Binny
  given name: Rachelle N.
author list: Agent
  family name: Lustig
  given name: Audrey
author list: Agent
  family name: Hendy
  given name: Shaun C.
author list: Agent
  family name: Maclaren
  given name: Oliver J.
author list: Agent
  family name: Ridings
  given name: Kannan M.
author list: Agent
  family name: Vattiato
  given name: Giorgia
author list: Agent
  family name: Plank
  given name: Michael J.
doi: 10.7717/peerj.14119
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Binny et al.
attribution name: Binny et al.

Habitat selection of black grouse in an isolated population in northern Germany—the importance of mixing dry and wet habitats
type: item
type: AcademicArticle
description: Wildlife habitats in general must provide foraging, hiding and resting places as well as sites for reproduction. Little is known about habitat selection of black grouse in the lowlands of Central Europe. We investigated habitat selection of seven radio tagged birds in an open heath and grassland area surrounded by dense pine forests in the northern German Lüneburg Heath Nature Reserve. This site carries one of the last remaining populations in the Central European lowlands. Using resource selection functions based on presence/background data, we estimated the probability of black grouse occurrence by availability of, or distance to habitat types as well as vegetation diversity indices. Black grouse preferred undisturbed and heterogeneous habitats far from dense forests with wide sand heaths, natural grasslands and intermixed bogs, diverse vegetation and food sources, low density of (loose) shrub formations and solitary trees. Wetlands were extremely important in a landscape that is dominated by dry heaths and grasslands. About 4% (9 km2) of the nature reserve was a suitable habitat for black grouse, mostly due to lack of open areas due to the amount of dense forest, and because smaller, open heaths are only partly suitable. We suggest that to improve habitat quality and quantity for the grouse, habitat patch size and connectivity must be increased, along with a mosaic of heterogeneous landscape structures in these habitat islands. Our results may be used to inform and improve black grouse habitat management in the region and elsewhere.
format: application/pdf
format: text/html
creator: Daniel Tost
creator: Tobias Ludwig
creator: Egbert Strauss
creator: Klaus Jung
creator: Ursula Siebert
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.14161
publisher: PeerJ Inc.
rights: © 2022 Tost et al.
abstract: Wildlife habitats in general must provide foraging, hiding and resting places as well as sites for reproduction. Little is known about habitat selection of black grouse in the lowlands of Central Europe. We investigated habitat selection of seven radio tagged birds in an open heath and grassland area surrounded by dense pine forests in the northern German Lüneburg Heath Nature Reserve. This site carries one of the last remaining populations in the Central European lowlands. Using resource selection functions based on presence/background data, we estimated the probability of black grouse occurrence by availability of, or distance to habitat types as well as vegetation diversity indices. Black grouse preferred undisturbed and heterogeneous habitats far from dense forests with wide sand heaths, natural grasslands and intermixed bogs, diverse vegetation and food sources, low density of (loose) shrub formations and solitary trees. Wetlands were extremely important in a landscape that is dominated by dry heaths and grasslands. About 4% (9 km2) of the nature reserve was a suitable habitat for black grouse, mostly due to lack of open areas due to the amount of dense forest, and because smaller, open heaths are only partly suitable. We suggest that to improve habitat quality and quantity for the grouse, habitat patch size and connectivity must be increased, along with a mosaic of heterogeneous landscape structures in these habitat islands. Our results may be used to inform and improve black grouse habitat management in the region and elsewhere.
bibliographic citation: Tost et al. (2022) Habitat selection of black grouse in an isolated population in northern Germany—the importance of mixing dry and wet habitats. PeerJ 10:e14161 https://doi.org/10.7717/peerj.14161
date submitted: 2022-03-09
date accepted: 2022-09-09
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tost
  given name: Daniel
author list: Agent
  family name: Ludwig
  given name: Tobias
author list: Agent
  family name: Strauss
  given name: Egbert
author list: Agent
  family name: Jung
  given name: Klaus
author list: Agent
  family name: Siebert
  given name: Ursula
doi: 10.7717/peerj.14161
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Tost et al.
attribution name: Tost et al.

Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review
type: item
type: AcademicArticle
description: Background There have been promising results published regarding the potential of stem cells in regenerative medicine. However, the vast variety of choices of techniques and the lack of a standard approach to analyse human osteoblast and osteoclast differentiation may reduce the utility of stem cells as a tool in medical applications. Therefore, this review aims to systematically evaluate the findings based on stem cell differentiation to define a standard gene expression profile approach. Methods This review was performed following the PRISMA guidelines. A systematic search of the study was conducted by retrieving articles from the electronic databases PubMed and Web of Science to identify articles focussed on gene expression and approaches for osteoblast and osteoclast differentiation. Results Six articles were included in this review; there were original articles of in vitro human stem cell differentiation into osteoblasts and osteoclasts that involved gene expression profiling. Quantitative polymerase chain reaction (qPCR) was the most used technique for gene expression to detect differentiated human osteoblasts and osteoclasts. A total of 16 genes were found to be related to differentiating osteoblast and osteoclast differentiation. Conclusion Qualitative information of gene expression provided by qPCR could become a standard technique to analyse the differentiation of human stem cells into osteoblasts and osteoclasts rather than evaluating relative gene expression. RUNX2 and CTSK could be applied to detect osteoblasts and osteoclasts, respectively, while RANKL could be applied to detect both osteoblasts and osteoclasts. This review provides future researchers with a central source of relevant information on the vast variety of gene expression approaches in analysing the differentiation of human osteoblast and osteoclast cells. In addition, these findings should enable researchers to conduct accurately and efficiently studies involving isolated human stem cell …
format: application/pdf
format: text/html
creator: Shahrul Hisham Zainal Ariffin
creator: Ker Wei Lim
creator: Rohaya Megat Abdul Wahab
creator: Zaidah Zainal Ariffin
creator: Rus Dina Rus Din
creator: Muhammad Ashraf Shahidan
creator: Anis Nabilah Johari
creator: Intan Zarina Zainol Abidin
subject: Biochemistry
subject: Biotechnology
subject: Cell Biology
subject: Developmental Biology
subject: Molecular Biology
description: doi:10.7717/peerj.14174
publisher: PeerJ Inc.
rights: © 2022 Zainal Ariffin et al.
abstract: Background There have been promising results published regarding the potential of stem cells in regenerative medicine. However, the vast variety of choices of techniques and the lack of a standard approach to analyse human osteoblast and osteoclast differentiation may reduce the utility of stem cells as a tool in medical applications. Therefore, this review aims to systematically evaluate the findings based on stem cell differentiation to define a standard gene expression profile approach. Methods This review was performed following the PRISMA guidelines. A systematic search of the study was conducted by retrieving articles from the electronic databases PubMed and Web of Science to identify articles focussed on gene expression and approaches for osteoblast and osteoclast differentiation. Results Six articles were included in this review; there were original articles of in vitro human stem cell differentiation into osteoblasts and osteoclasts that involved gene expression profiling. Quantitative polymerase chain reaction (qPCR) was the most used technique for gene expression to detect differentiated human osteoblasts and osteoclasts. A total of 16 genes were found to be related to differentiating osteoblast and osteoclast differentiation. Conclusion Qualitative information of gene expression provided by qPCR could become a standard technique to analyse the differentiation of human stem cells into osteoblasts and osteoclasts rather than evaluating relative gene expression. RUNX2 and CTSK could be applied to detect osteoblasts and osteoclasts, respectively, while RANKL could be applied to detect both osteoblasts and osteoclasts. This review provides future researchers with a central source of relevant information on the vast variety of gene expression approaches in analysing the differentiation of human osteoblast and osteoclast cells. In addition, these findings should enable researchers to conduct accurately and efficiently studies involving isolated human stem cell …
bibliographic citation: Zainal Ariffin et al. (2022) Gene expression profiles for in vitro human stem cell differentiation into osteoblasts and osteoclasts: a systematic review. PeerJ 10:e14174 https://doi.org/10.7717/peerj.14174
date submitted: 2022-04-28
date accepted: 2022-09-12
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zainal Ariffin
  given name: Shahrul Hisham
author list: Agent
  family name: Lim
  given name: Ker Wei
author list: Agent
  family name: Megat Abdul Wahab
  given name: Rohaya
author list: Agent
  family name: Zainal Ariffin
  given name: Zaidah
author list: Agent
  family name: Rus Din
  given name: Rus Dina
author list: Agent
  family name: Shahidan
  given name: Muhammad Ashraf
author list: Agent
  family name: Johari
  given name: Anis Nabilah
author list: Agent
  family name: Zainol Abidin
  given name: Intan Zarina
doi: 10.7717/peerj.14174
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Zainal Ariffin et al.
attribution name: Zainal Ariffin et al.

isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting
type: item
type: AcademicArticle
description: Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5′-end variations (5′-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)—a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5′-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5′-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5′-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5′-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5′-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p—+1, hsa-miR-192-5p—+1 and hsa-miR-148a-3p—0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer.
format: application/pdf
format: text/html
creator: Stepan Nersisyan
creator: Aleksandra Gorbonos
creator: Alexey Makhonin
creator: Anton Zhiyanov
creator: Maxim Shkurnikov
creator: Alexander Tonevitsky
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.14205
publisher: PeerJ Inc.
rights: © 2022 Nersisyan et al.
abstract: Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5′-end variations (5′-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)—a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5′-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5′-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5′-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5′-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5′-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p—+1, hsa-miR-192-5p—+1 and hsa-miR-148a-3p—0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer.
bibliographic citation: Nersisyan et al. (2022) isomiRTar: a comprehensive portal of pan-cancer 5′-isomiR targeting. PeerJ 10:e14205 https://doi.org/10.7717/peerj.14205
date submitted: 2022-07-28
date accepted: 2022-09-19
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nersisyan
  given name: Stepan
author list: Agent
  family name: Gorbonos
  given name: Aleksandra
author list: Agent
  family name: Makhonin
  given name: Alexey
author list: Agent
  family name: Zhiyanov
  given name: Anton
author list: Agent
  family name: Shkurnikov
  given name: Maxim
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.14205
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Nersisyan et al.
attribution name: Nersisyan et al.

Signal peptidase 21 suppresses cell proliferation, migration, and invasion via the PTEN-PI3K/Akt signaling pathway in lung adenocarcinoma
type: item
type: AcademicArticle
description: Background In a previous study, a total of 568 differentially expressed proteins including the signal peptidase SPC21 were identified from lung adenocarcinoma (LUAD) and paired normal lung tissues. In this study, the role of SPC21 in LUAD progression was investigated. Methods The relationships and protein-protein interaction network of proteins differentially expressed between paired LUAD samples and adjacent normal tissues samples were identified via the String and Pajek software, respectively. The expression levels of the hub protein SPC21 were analyzed in 84 LUAD-normal paired tissues via immunohistochemistry. The prognostic value of SPC21 mRNA was investigated in 478 LUAD patients from TCGA and GTEx datasets. siRNAs were used in A549 and NCI-H1299 cells to knockdown SPC21. The SPC21 biological function was evaluated using the CCK-8, EdU, plate colony formation, transwell, wound healing, and adhesion assays. Results Patients with lower SPC21 mRNA levels tended to have worse prognosis (overall survival) than those with higher mRNA levels. SPC21 expression was significantly downregulated in LUAD tumor tissues compared with that in paired normal tissues (P < 0.001). Functionally, SPC21 knockdown promoted cell growth, migration, and invasion. Further analyses showed that SPC21 inactivated Akt signaling, and the Akt inhibitor MK-2206 blocked the tumor-promoting effects of SPC21 knockdown. Conclusions SPC21 plays a tumor suppressor role in LUAD cells by targeting the PTEN-PI3K/Akt axis and might be used as a prognostic indicator and therapeutic target in LUAD patients.
format: application/pdf
format: text/html
creator: Na Zhang
creator: Shiguang Cao
creator: Ruiying Sun
creator: Yibei Wang
creator: Luna Liu
creator: Wei Wang
creator: Xia Meng
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.14206
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background In a previous study, a total of 568 differentially expressed proteins including the signal peptidase SPC21 were identified from lung adenocarcinoma (LUAD) and paired normal lung tissues. In this study, the role of SPC21 in LUAD progression was investigated. Methods The relationships and protein-protein interaction network of proteins differentially expressed between paired LUAD samples and adjacent normal tissues samples were identified via the String and Pajek software, respectively. The expression levels of the hub protein SPC21 were analyzed in 84 LUAD-normal paired tissues via immunohistochemistry. The prognostic value of SPC21 mRNA was investigated in 478 LUAD patients from TCGA and GTEx datasets. siRNAs were used in A549 and NCI-H1299 cells to knockdown SPC21. The SPC21 biological function was evaluated using the CCK-8, EdU, plate colony formation, transwell, wound healing, and adhesion assays. Results Patients with lower SPC21 mRNA levels tended to have worse prognosis (overall survival) than those with higher mRNA levels. SPC21 expression was significantly downregulated in LUAD tumor tissues compared with that in paired normal tissues (P < 0.001). Functionally, SPC21 knockdown promoted cell growth, migration, and invasion. Further analyses showed that SPC21 inactivated Akt signaling, and the Akt inhibitor MK-2206 blocked the tumor-promoting effects of SPC21 knockdown. Conclusions SPC21 plays a tumor suppressor role in LUAD cells by targeting the PTEN-PI3K/Akt axis and might be used as a prognostic indicator and therapeutic target in LUAD patients.
bibliographic citation: Zhang et al. (2022) Signal peptidase 21 suppresses cell proliferation, migration, and invasion via the PTEN-PI3K/Akt signaling pathway in lung adenocarcinoma. PeerJ 10:e14206 https://doi.org/10.7717/peerj.14206
date submitted: 2022-07-05
date accepted: 2022-09-19
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Cao
  given name: Shiguang
author list: Agent
  family name: Sun
  given name: Ruiying
author list: Agent
  family name: Wang
  given name: Yibei
author list: Agent
  family name: Liu
  given name: Luna
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Meng
  given name: Xia
doi: 10.7717/peerj.14206
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Hand port-site infection after hand-assisted laparoscopic donor nephrectomy for living-donor kidney transplantation: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Hand-assisted laparoscopic donor nephrectomy (HALDN) is widely performed to minimize burden on living kidney donors. However, hand port-site infections after HALDN may occur. This study aimed to assess the impact of donor characteristics including preoperative comorbidities and operative factors on hand port-site infection after HALDN. Methods In this single-center, retrospective cohort study, 1,260 consecutive HALDNs for living-donor kidney transplantation performed between January 2008 and December 2021 were evaluated. All living donors met the living kidney donor guidelines in Japan. Hand port-site infections were identified in 88 HALDN cases (7.0%). To investigate risk factors for hand port-site infection, donor characteristics including preoperative comorbidities such as hypertension, glucose intolerance, dyslipidemia, obesity, and operative factors such as operative duration, blood loss, preoperative antibiotic prophylaxis, and prophylactic subcutaneous suction drain placement at the hand port-site were analyzed using logistic regression analysis. Results In the multivariate analysis, significant differences were identified regarding sex (P = 0.021; odds ratio [OR], 1.971; 95% confidence interval [CI], 1.108–3.507), preoperative antibiotic prophylaxis (P < 0.001; OR, 0.037; 95% CI [0.011–0.127]), and prophylactic subcutaneous suction drain placement at the hand port-site (P = 0.041; OR, 2.005; 95% CI [1.029–3.907]). However, a significant difference was not identified regarding glucose intolerance (P = 0.572; OR, 1.148; 95% CI [0.711–1.856]). Preoperative comorbidities may not cause hand port-site infections within the donors who meet the living kidney donor guidelines. Preoperative antibiotic prophylaxis is crucial in preventing hand port-site infection, whereas prophylactic subcutaneous suction drain placement may increase the risk of hand port-site infection.
format: application/pdf
format: text/html
creator: Takahisa Hiramitsu
creator: Toshihide Tomosugi
creator: Kenta Futamura
creator: Manabu Okada
creator: Norihiko Goto
creator: Toshihiro Ichimori
creator: Shunji Narumi
creator: Kazuharu Uchida
creator: Yoshihiko Watarai
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Nephrology
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.14215
publisher: PeerJ Inc.
rights: © 2022 Hiramitsu et al.
abstract: Background Hand-assisted laparoscopic donor nephrectomy (HALDN) is widely performed to minimize burden on living kidney donors. However, hand port-site infections after HALDN may occur. This study aimed to assess the impact of donor characteristics including preoperative comorbidities and operative factors on hand port-site infection after HALDN. Methods In this single-center, retrospective cohort study, 1,260 consecutive HALDNs for living-donor kidney transplantation performed between January 2008 and December 2021 were evaluated. All living donors met the living kidney donor guidelines in Japan. Hand port-site infections were identified in 88 HALDN cases (7.0%). To investigate risk factors for hand port-site infection, donor characteristics including preoperative comorbidities such as hypertension, glucose intolerance, dyslipidemia, obesity, and operative factors such as operative duration, blood loss, preoperative antibiotic prophylaxis, and prophylactic subcutaneous suction drain placement at the hand port-site were analyzed using logistic regression analysis. Results In the multivariate analysis, significant differences were identified regarding sex (P = 0.021; odds ratio [OR], 1.971; 95% confidence interval [CI], 1.108–3.507), preoperative antibiotic prophylaxis (P < 0.001; OR, 0.037; 95% CI [0.011–0.127]), and prophylactic subcutaneous suction drain placement at the hand port-site (P = 0.041; OR, 2.005; 95% CI [1.029–3.907]). However, a significant difference was not identified regarding glucose intolerance (P = 0.572; OR, 1.148; 95% CI [0.711–1.856]). Preoperative comorbidities may not cause hand port-site infections within the donors who meet the living kidney donor guidelines. Preoperative antibiotic prophylaxis is crucial in preventing hand port-site infection, whereas prophylactic subcutaneous suction drain placement may increase the risk of hand port-site infection.
bibliographic citation: Hiramitsu et al. (2022) Hand port-site infection after hand-assisted laparoscopic donor nephrectomy for living-donor kidney transplantation: a retrospective cohort study. PeerJ 10:e14215 https://doi.org/10.7717/peerj.14215
date submitted: 2022-06-17
date accepted: 2022-09-19
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hiramitsu
  given name: Takahisa
author list: Agent
  family name: Tomosugi
  given name: Toshihide
author list: Agent
  family name: Futamura
  given name: Kenta
author list: Agent
  family name: Okada
  given name: Manabu
author list: Agent
  family name: Goto
  given name: Norihiko
author list: Agent
  family name: Ichimori
  given name: Toshihiro
author list: Agent
  family name: Narumi
  given name: Shunji
author list: Agent
  family name: Uchida
  given name: Kazuharu
author list: Agent
  family name: Watarai
  given name: Yoshihiko
doi: 10.7717/peerj.14215
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Hiramitsu et al.
attribution name: Hiramitsu et al.

Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms
type: item
type: AcademicArticle
description: Real-time quantitative PCR (RT-qPCR) is a widely applied technique for relative quantification of gene expression. In this context, the selection of a suitable reference gene (RG) is an essential step for obtaining reliable and biologically relevant RT-qPCR results. The present study aimed to determine the expression stability of commonly used RGs in mouse skeletal muscle tissue. The expression pattern of eight RGs (ACTB, GAPDH, HPRT, YWHAZ, B2M, PPIA, TUBA and 18S) were evaluated by RT-qPCR in different sample groups classified based on genetic background, muscle tissue type, and growth stage, as well as in a C2C12 myoblast cell line model. Five computational programs were included in the study (comparative ΔCq value, NormFinder, BestKeeper, geNorm, RefFinder) to evaluate the expression stability of RGs. Furthermore, the normalization effects of RGs in soleus (SOL) and gastrocnemius (GAS) muscle tissue were evaluated. Collectively, ACTB, HPRT and YWHAZ were shown to be the most stable RGs, while GADPH and 18S were the least stable. Therefore, the combined use of ACTB, HPRT and YWHAZ is recommended for the normalization of gene expression results in experiments with murine skeletal muscle. The results discussed herein provide a foundation for gene expression analysis by RT-qPCR in mammalian skeletal muscle.
format: application/pdf
format: text/html
creator: Jianfeng Ma
creator: Jingyun Chen
creator: Mailin Gan
creator: Lei Chen
creator: Ye Zhao
creator: Lili Niu
creator: Yan Zhu
creator: Shunhua Zhang
creator: Xuewei Li
creator: Zongyi Guo
creator: Jinyong Wang
creator: Li Zhu
creator: Linyuan Shen
subject: Biochemistry
subject: Cell Biology
subject: Developmental Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.14221
publisher: PeerJ Inc.
rights: © 2022 Ma et al.
abstract: Real-time quantitative PCR (RT-qPCR) is a widely applied technique for relative quantification of gene expression. In this context, the selection of a suitable reference gene (RG) is an essential step for obtaining reliable and biologically relevant RT-qPCR results. The present study aimed to determine the expression stability of commonly used RGs in mouse skeletal muscle tissue. The expression pattern of eight RGs (ACTB, GAPDH, HPRT, YWHAZ, B2M, PPIA, TUBA and 18S) were evaluated by RT-qPCR in different sample groups classified based on genetic background, muscle tissue type, and growth stage, as well as in a C2C12 myoblast cell line model. Five computational programs were included in the study (comparative ΔCq value, NormFinder, BestKeeper, geNorm, RefFinder) to evaluate the expression stability of RGs. Furthermore, the normalization effects of RGs in soleus (SOL) and gastrocnemius (GAS) muscle tissue were evaluated. Collectively, ACTB, HPRT and YWHAZ were shown to be the most stable RGs, while GADPH and 18S were the least stable. Therefore, the combined use of ACTB, HPRT and YWHAZ is recommended for the normalization of gene expression results in experiments with murine skeletal muscle. The results discussed herein provide a foundation for gene expression analysis by RT-qPCR in mammalian skeletal muscle.
bibliographic citation: Ma et al. (2022) Comparison of reference gene expression stability in mouse skeletal muscle via five algorithms. PeerJ 10:e14221 https://doi.org/10.7717/peerj.14221
date submitted: 2022-07-11
date accepted: 2022-09-20
issued: 2022-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jianfeng
author list: Agent
  family name: Chen
  given name: Jingyun
author list: Agent
  family name: Gan
  given name: Mailin
author list: Agent
  family name: Chen
  given name: Lei
author list: Agent
  family name: Zhao
  given name: Ye
author list: Agent
  family name: Niu
  given name: Lili
author list: Agent
  family name: Zhu
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Shunhua
author list: Agent
  family name: Li
  given name: Xuewei
author list: Agent
  family name: Guo
  given name: Zongyi
author list: Agent
  family name: Wang
  given name: Jinyong
author list: Agent
  family name: Zhu
  given name: Li
author list: Agent
  family name: Shen
  given name: Linyuan
doi: 10.7717/peerj.14221
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-17
copyright: ©2022 Ma et al.
attribution name: Ma et al.

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