PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps
items: A cholesterogenic gene signature for predicting the prognosis of young breast cancer patients
items: Levels and correlates of knowledge of teething among Saudi Arabian families
items: Exploring the anticancer and antioxidant properties of Vicia faba L. pods extracts, a promising source of nutraceuticals
items: Growth promotion and mycorrhizal colonization of Argan (Argania spinosa (L.) Skeels) inoculated with the edible desert truffle Tirmania nivea (Desf.) Trappe
items: Phosphate solubilizing microorganisms isolated from medicinal plants improve growth of mint
items: Acute effects of variable resistance training on force, velocity, and power measures: a systematic review and meta-analysis
items: Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (NaV1.5)
items: Aluminum phosphate sludge as a phosphorus source for maize production under low soil phosphorus availability
items: The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders

Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps
type: item
type: AcademicArticle
description: We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.
format: application/pdf
format: text/html
creator: Bjørn Tore Kopperud
creator: Scott Lidgard
creator: Lee Hsiang Liow
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13921
publisher: PeerJ Inc.
rights: © 2022 Kopperud et al.
abstract: We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.
bibliographic citation: Kopperud et al. (2022) Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps. PeerJ 10:e13921 https://doi.org/10.7717/peerj.13921
date submitted: 2022-04-22
date accepted: 2022-07-29
issued: 2022-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kopperud
  given name: Bjørn Tore
author list: Agent
  family name: Lidgard
  given name: Scott
author list: Agent
  family name: Liow
  given name: Lee Hsiang
doi: 10.7717/peerj.13921
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-18
copyright: © 2022 Kopperud et al.
attribution name: Kopperud et al.

A cholesterogenic gene signature for predicting the prognosis of young breast cancer patients
type: item
type: AcademicArticle
description: Purpose We aimed to establish a cholesterogenic gene signature to predict the prognosis of young breast cancer (BC) patients and then verified it using cell line experiments. Methods In the bioinformatic section, transcriptional data and corresponding clinical data of young BC patients (age ≤ 45 years) were downloaded from The Cancer Genome Atlas (TCGA) database for training set. Differentially expressed genes (DEGs) were compared between tumour tissue (n = 183) and normal tissue (n = 30). By using univariate Cox regression and multi COX regression, a five-cholesterogenic-gene signature was established to predict prognosis. Subgroup analysis and external validations of GSE131769 from the Gene Expression Omnibus (GEO) were performed to verify the signature. Subsequently, in experiment part, cell experiments were performed to further verify the biological roles of the five cholesterogenic genes in BC. Results In the bioinformatic section, a total of 97 upregulated genes and 124 downregulated cholesterogenic genes were screened as DEGs in the TCGA for training the model. A risk scoring signature contained five cholesterogenic genes (risk score = −1.169 × GRAMD1C −0.992 × NFKBIA + 0.432 × INHBA + 0.261 × CD24 −0.839 × ACSS2) was established, which could differentiate the prognosis of young BC patients between high-risk and low-risk group (<0.001). The prediction value of chelesterogenic gene signature in excellent with AUC was 0.810 in TCGA dataset. Then the prediction value of the signature was verified in GSE131769 with P = 0.033. In experiment part, although the downregulation of CD24, GRAMD1C and ACSS2 did not significantly affect cell viability, NFKBIA downregulation promoted the viability, colony forming ability and invasion capability of BC cells, while INHBA downregulation had the opposite effects. Conclusion The five-cholesterogenic-gene signature had independent prognostic value and robust reliability in predicting the prognosis of young BC patients. The cell …
format: application/pdf
format: text/html
creator: Xiaoping Li
creator: Chaorong Zhou
creator: Chaoran Qiu
creator: Weiwen Li
creator: Qihe Yu
creator: Hui Huang
creator: Yiwen Zhang
creator: Xin Zhang
creator: Liangliang Ren
creator: Xin Huang
creator: Qinghua Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.13922
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Purpose We aimed to establish a cholesterogenic gene signature to predict the prognosis of young breast cancer (BC) patients and then verified it using cell line experiments. Methods In the bioinformatic section, transcriptional data and corresponding clinical data of young BC patients (age ≤ 45 years) were downloaded from The Cancer Genome Atlas (TCGA) database for training set. Differentially expressed genes (DEGs) were compared between tumour tissue (n = 183) and normal tissue (n = 30). By using univariate Cox regression and multi COX regression, a five-cholesterogenic-gene signature was established to predict prognosis. Subgroup analysis and external validations of GSE131769 from the Gene Expression Omnibus (GEO) were performed to verify the signature. Subsequently, in experiment part, cell experiments were performed to further verify the biological roles of the five cholesterogenic genes in BC. Results In the bioinformatic section, a total of 97 upregulated genes and 124 downregulated cholesterogenic genes were screened as DEGs in the TCGA for training the model. A risk scoring signature contained five cholesterogenic genes (risk score = −1.169 × GRAMD1C −0.992 × NFKBIA + 0.432 × INHBA + 0.261 × CD24 −0.839 × ACSS2) was established, which could differentiate the prognosis of young BC patients between high-risk and low-risk group (<0.001). The prediction value of chelesterogenic gene signature in excellent with AUC was 0.810 in TCGA dataset. Then the prediction value of the signature was verified in GSE131769 with P = 0.033. In experiment part, although the downregulation of CD24, GRAMD1C and ACSS2 did not significantly affect cell viability, NFKBIA downregulation promoted the viability, colony forming ability and invasion capability of BC cells, while INHBA downregulation had the opposite effects. Conclusion The five-cholesterogenic-gene signature had independent prognostic value and robust reliability in predicting the prognosis of young BC patients. The cell …
bibliographic citation: Li et al. (2022) A cholesterogenic gene signature for predicting the prognosis of young breast cancer patients. PeerJ 10:e13922 https://doi.org/10.7717/peerj.13922
date submitted: 2022-05-31
date accepted: 2022-07-29
issued: 2022-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xiaoping
author list: Agent
  family name: Zhou
  given name: Chaorong
author list: Agent
  family name: Qiu
  given name: Chaoran
author list: Agent
  family name: Li
  given name: Weiwen
author list: Agent
  family name: Yu
  given name: Qihe
author list: Agent
  family name: Huang
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Yiwen
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Ren
  given name: Liangliang
author list: Agent
  family name: Huang
  given name: Xin
author list: Agent
  family name: Zhou
  given name: Qinghua
doi: 10.7717/peerj.13922
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-18
copyright: ©2022 Li et al.
attribution name: Li et al.

Levels and correlates of knowledge of teething among Saudi Arabian families
type: item
type: AcademicArticle
description: Background Parental knowledge of teething has been repeatedly investigated; however, little emphasis has been made on the associated sociodemographic factors with good knowledge of the parents and whether or not good knowledge is translated into adopting proper pain-relieving practices. The present study aims to firstly assess the knowledge level and practices of Saudi parents regarding teething and then explore associated sociodemographic variables with good knowledge of teething to determine the relation between parents’ knowledge of teething and their adoption of pain-relieving practices. Methods This cross-sectional study recruited parents from the social networking sites Facebook, Twitter, Instagram, and WhatsApp, and they were asked to answer a pretested three-part internationally accepted questionnaire. Data were examined using descriptive statistics, chi-square analysis, multivariate logistic regression analysis, and Spearman rank-order correlation coefficient analysis. Results One thousand four hundred ninety-nine parents responded and returned completed questionnaires. Of those, only 11.2% had good knowledge of teething. The majority of parents did not have basic knowledge of the teething period as well as believed that teething was associated with a runny nose (87.5%), diarrhea (77.9%), and sleep disturbance (72%). The results of multivariate logistic regression analysis indicated that parents with no primary school education (Odds Ratio: 0.29), or those who had an intermediate or secondary education level (OR: 0.55 and 0.78) were less likely to have good knowledge compared with parents who had a university degree. However, parents who earned intermediate monthly income (OR: 6.63) were more likely to have good knowledge of teething. With regards to practices used to relieve teething pain, inappropriate practices were observed regarding bottle feeding at night to soothe the child’s pain (72%) and applying topical analgesics to rub the gum (72.4%). A signif…
format: application/pdf
format: text/html
creator: Dina A. Alkhozaim
creator: Sanaa N. Al-Haj Ali
creator: Ra’fat I. Farah
subject: Dentistry
subject: Pediatrics
description: doi:10.7717/peerj.13948
publisher: PeerJ Inc.
rights: © 2022 Alkhozaim et al.
abstract: Background Parental knowledge of teething has been repeatedly investigated; however, little emphasis has been made on the associated sociodemographic factors with good knowledge of the parents and whether or not good knowledge is translated into adopting proper pain-relieving practices. The present study aims to firstly assess the knowledge level and practices of Saudi parents regarding teething and then explore associated sociodemographic variables with good knowledge of teething to determine the relation between parents’ knowledge of teething and their adoption of pain-relieving practices. Methods This cross-sectional study recruited parents from the social networking sites Facebook, Twitter, Instagram, and WhatsApp, and they were asked to answer a pretested three-part internationally accepted questionnaire. Data were examined using descriptive statistics, chi-square analysis, multivariate logistic regression analysis, and Spearman rank-order correlation coefficient analysis. Results One thousand four hundred ninety-nine parents responded and returned completed questionnaires. Of those, only 11.2% had good knowledge of teething. The majority of parents did not have basic knowledge of the teething period as well as believed that teething was associated with a runny nose (87.5%), diarrhea (77.9%), and sleep disturbance (72%). The results of multivariate logistic regression analysis indicated that parents with no primary school education (Odds Ratio: 0.29), or those who had an intermediate or secondary education level (OR: 0.55 and 0.78) were less likely to have good knowledge compared with parents who had a university degree. However, parents who earned intermediate monthly income (OR: 6.63) were more likely to have good knowledge of teething. With regards to practices used to relieve teething pain, inappropriate practices were observed regarding bottle feeding at night to soothe the child’s pain (72%) and applying topical analgesics to rub the gum (72.4%). A signif…
bibliographic citation: Alkhozaim et al. (2022) Levels and correlates of knowledge of teething among Saudi Arabian families. PeerJ 10:e13948 https://doi.org/10.7717/peerj.13948
date submitted: 2022-03-16
date accepted: 2022-08-03
issued: 2022-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alkhozaim
  given name: Dina A.
author list: Agent
  family name: Al-Haj Ali
  given name: Sanaa N.
author list: Agent
  family name: Farah
  given name: Ra’fat I.
doi: 10.7717/peerj.13948
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-18
copyright: © 2022 Alkhozaim et al.
attribution name: Alkhozaim et al.

Exploring the anticancer and antioxidant properties of Vicia faba L. pods extracts, a promising source of nutraceuticals
type: item
type: AcademicArticle
description: Background Pulse crops are considered the major sources of proteins, dietary fiber, micronutrients, and bioactive phytochemicals. Among the numerous pulse crops, broad beans (Vicia faba L.) have received particular attention due to their nutraceutical, functional and economic importance. Our attention was mainly focused on the broad bean pods (VFs), which are the primary by-product of the domestic and industrial processing of broad beans and an attractive source of valuable ingredients. Methods In order to investigate the VFs properties, the flours from broad beans of three different harvest periods were extracted with acetone, methanol and 70% aqueous ethanol and the dried extracts were analyzed, qualitatively and quantitatively, and tested for their antioxidant through DPPH and ABTS assay and anticancer activities using the MTT assay and immunofluorescence analysis. Results The VF extracts demonstrated a good in vitro radical scavenging activity from the first stage of collection of all the V. faba L. extracts. Additionally, the extracts were tested for their cytotoxicity against a panel of cancer and normal cells and the outcomes indicated the ethanol extract as the most active against the melanoma cell line Sk-Mel-28, without affecting the viability of the normal cells. Finally, we found out that the ethanol extract interfered with the microtubules organization, leading to the cancer cells death by apoptosis.
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format: text/html
creator: Jessica Ceramella
creator: Chiara La Torre
creator: Michele De Luca
creator: Domenico Iacopetta
creator: Alessia Fazio
creator: Alessia Catalano
creator: Gaetano Ragno
creator: Pasquale Longo
creator: Maria Stefania Sinicropi
creator: Camillo Rosano
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
subject: Drugs and Devices
description: doi:10.7717/peerj.13683
publisher: PeerJ Inc.
rights: © 2022 Ceramella et al.
abstract: Background Pulse crops are considered the major sources of proteins, dietary fiber, micronutrients, and bioactive phytochemicals. Among the numerous pulse crops, broad beans (Vicia faba L.) have received particular attention due to their nutraceutical, functional and economic importance. Our attention was mainly focused on the broad bean pods (VFs), which are the primary by-product of the domestic and industrial processing of broad beans and an attractive source of valuable ingredients. Methods In order to investigate the VFs properties, the flours from broad beans of three different harvest periods were extracted with acetone, methanol and 70% aqueous ethanol and the dried extracts were analyzed, qualitatively and quantitatively, and tested for their antioxidant through DPPH and ABTS assay and anticancer activities using the MTT assay and immunofluorescence analysis. Results The VF extracts demonstrated a good in vitro radical scavenging activity from the first stage of collection of all the V. faba L. extracts. Additionally, the extracts were tested for their cytotoxicity against a panel of cancer and normal cells and the outcomes indicated the ethanol extract as the most active against the melanoma cell line Sk-Mel-28, without affecting the viability of the normal cells. Finally, we found out that the ethanol extract interfered with the microtubules organization, leading to the cancer cells death by apoptosis.
bibliographic citation: Ceramella et al. (2022) Exploring the anticancer and antioxidant properties of Vicia faba L. pods extracts, a promising source of nutraceuticals. PeerJ 10:e13683 https://doi.org/10.7717/peerj.13683
date submitted: 2022-02-22
date accepted: 2022-06-14
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ceramella
  given name: Jessica
author list: Agent
  family name: La Torre
  given name: Chiara
author list: Agent
  family name: De Luca
  given name: Michele
author list: Agent
  family name: Iacopetta
  given name: Domenico
author list: Agent
  family name: Fazio
  given name: Alessia
author list: Agent
  family name: Catalano
  given name: Alessia
author list: Agent
  family name: Ragno
  given name: Gaetano
author list: Agent
  family name: Longo
  given name: Pasquale
author list: Agent
  family name: Sinicropi
  given name: Maria Stefania
author list: Agent
  family name: Rosano
  given name: Camillo
doi: 10.7717/peerj.13683
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: © 2022 Ceramella et al.
attribution name: Ceramella et al.

Growth promotion and mycorrhizal colonization of Argan (Argania spinosa (L.) Skeels) inoculated with the edible desert truffle Tirmania nivea (Desf.) Trappe
type: item
type: AcademicArticle
description: This study presents the first evidence of the mycorrhizal compatibility between the edible desert truffle Tirmania nivea and the valuable fruit tree Argania spinosa. Seed germination trials demonstrated that soaking pre-treatment of argan seeds in hydrogen peroxide (9%) for five days combined with the application of a fungicide treatment on an inert sowing material maximized the seed germination of this tree species. The mycorrhizal synthesis was conducted under greenhouse conditions by inoculating, in vivo, the host plant seedlings with spores of T. nivea. The growth and mycorrhizal status of A. spinosa was assessed 15.5 months after inoculation. The desert truffle mycorrhization significantly promoted all the investigated morphological parameters of growth and improved the physiological performances of the host plant through enhancing plant water status and chlorophyll concentration. The mycorrhizal symbiosis led to the formation of typical desert truffle endomycorrhizae with intracellular coils. The resistance of A. spinosa to the harsh environmental conditions of desert habitats makes it a potential candidate for cultivation of desert truffles.
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creator: Ahlem Khrizi
creator: Fatima El-Houaria Zitouni-Haouar
creator: Zohra Fortas
subject: Agricultural Science
subject: Biotechnology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13769
publisher: PeerJ Inc.
rights: © 2022 Khrizi et al.
abstract: This study presents the first evidence of the mycorrhizal compatibility between the edible desert truffle Tirmania nivea and the valuable fruit tree Argania spinosa. Seed germination trials demonstrated that soaking pre-treatment of argan seeds in hydrogen peroxide (9%) for five days combined with the application of a fungicide treatment on an inert sowing material maximized the seed germination of this tree species. The mycorrhizal synthesis was conducted under greenhouse conditions by inoculating, in vivo, the host plant seedlings with spores of T. nivea. The growth and mycorrhizal status of A. spinosa was assessed 15.5 months after inoculation. The desert truffle mycorrhization significantly promoted all the investigated morphological parameters of growth and improved the physiological performances of the host plant through enhancing plant water status and chlorophyll concentration. The mycorrhizal symbiosis led to the formation of typical desert truffle endomycorrhizae with intracellular coils. The resistance of A. spinosa to the harsh environmental conditions of desert habitats makes it a potential candidate for cultivation of desert truffles.
bibliographic citation: Khrizi et al. (2022) Growth promotion and mycorrhizal colonization of Argan (Argania spinosa (L.) Skeels) inoculated with the edible desert truffle Tirmania nivea (Desf.) Trappe. PeerJ 10:e13769 https://doi.org/10.7717/peerj.13769
date submitted: 2022-01-19
date accepted: 2022-07-01
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khrizi
  given name: Ahlem
author list: Agent
  family name: Zitouni-Haouar
  given name: Fatima El-Houaria
author list: Agent
  family name: Fortas
  given name: Zohra
doi: 10.7717/peerj.13769
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: ©2022 Khrizi et al.
attribution name: Khrizi et al.

Phosphate solubilizing microorganisms isolated from medicinal plants improve growth of mint
type: item
type: AcademicArticle
description: The current research project involves isolation and characterization of PSM (phosphate solubilizing microorganisms) from the rhizospheric soil of certain medicinal plants and to determine their effect on plant growth. Medicinal plants, Aloe vera, Bauhinia variegata, Cannabis sativa, Lantana camara and Mentha viridis were selected for the isolation of PSMs. Soil status of the selected medicinal plants was also checked. Phosphate solubilizing bacteria (PSB) were observed under stereomicroscope for their morphological characteristics and Gram’s staining. Phosphate solubilizing fungi (PSF) were also identified microscopically. Colony diameter, halo zone diameter and solubilization index were determined on PVK agar plates. TLC results indicated that citric acid was the most common acid produced by PSM strains. All strains were found to be non-pathogenic in pathogenicity test. A positive plant growth response to PSM inoculation was observed in all studies. In study 1, individual inoculation of PSM showed a significant increased effect on plant growth parameter i.e., fresh and dry weight, plant height and root and shoot length as compared to control. In study2, composite inoculation of PSM along with different P sources revealed that rock phosphate (RP) with PSM increased growth of plants significantly. The present study suggests that PSM inoculation along with RP amendment can be used as biofertilizer.
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format: text/html
creator: Muhammad Rizwan Tariq
creator: Fouzia Shaheen
creator: Sharmeen Mustafa
creator: Sajid ALI
creator: Ammara Fatima
creator: Muhammad Shafiq
creator: Waseem Safdar
creator: Muhammad Naveed Sheas
creator: Amna Hameed
creator: Muhammad Adnan Nasir
subject: Agricultural Science
subject: Biochemistry
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13782
publisher: PeerJ Inc.
rights: © 2022 Tariq et al.
abstract: The current research project involves isolation and characterization of PSM (phosphate solubilizing microorganisms) from the rhizospheric soil of certain medicinal plants and to determine their effect on plant growth. Medicinal plants, Aloe vera, Bauhinia variegata, Cannabis sativa, Lantana camara and Mentha viridis were selected for the isolation of PSMs. Soil status of the selected medicinal plants was also checked. Phosphate solubilizing bacteria (PSB) were observed under stereomicroscope for their morphological characteristics and Gram’s staining. Phosphate solubilizing fungi (PSF) were also identified microscopically. Colony diameter, halo zone diameter and solubilization index were determined on PVK agar plates. TLC results indicated that citric acid was the most common acid produced by PSM strains. All strains were found to be non-pathogenic in pathogenicity test. A positive plant growth response to PSM inoculation was observed in all studies. In study 1, individual inoculation of PSM showed a significant increased effect on plant growth parameter i.e., fresh and dry weight, plant height and root and shoot length as compared to control. In study2, composite inoculation of PSM along with different P sources revealed that rock phosphate (RP) with PSM increased growth of plants significantly. The present study suggests that PSM inoculation along with RP amendment can be used as biofertilizer.
bibliographic citation: Tariq et al. (2022) Phosphate solubilizing microorganisms isolated from medicinal plants improve growth of mint. PeerJ 10:e13782 https://doi.org/10.7717/peerj.13782
date submitted: 2022-04-01
date accepted: 2022-07-05
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tariq
  given name: Muhammad Rizwan
author list: Agent
  family name: Shaheen
  given name: Fouzia
author list: Agent
  family name: Mustafa
  given name: Sharmeen
author list: Agent
  family name: ALI
  given name: Sajid
author list: Agent
  family name: Fatima
  given name: Ammara
author list: Agent
  family name: Shafiq
  given name: Muhammad
author list: Agent
  family name: Safdar
  given name: Waseem
author list: Agent
  family name: Sheas
  given name: Muhammad Naveed
author list: Agent
  family name: Hameed
  given name: Amna
author list: Agent
  family name: Nasir
  given name: Muhammad Adnan
doi: 10.7717/peerj.13782
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: ©2022 Tariq et al.
attribution name: Tariq et al.

Acute effects of variable resistance training on force, velocity, and power measures: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objective Acute effects of variable resistance training (VRT) and constant resistance training (CRT) on neuromuscular performance are still equivocal. We aimed to determine the differences between VRT and CRT in terms of force, velocity, and power outcomes. Methods We searched PubMed, Web of Science, and SPORTDiscus electronic databases for articles until June 2021. Crossover design studies comparing force, velocity, and power outcomes while performing VRT and CRT were included. Two reviewers independently applied the modified version of the Cochrane Collaboration’s tool to assess the risk of bias. A three-level random effects meta-analyses and meta-regressions were used to compute standardized mean differences (SMDs) and 95% confidence intervals. Results We included 16 studies with 207 participants in the quantitative synthesis. Based on the pooled results, VRT generated greater mean velocity (SMD = 0.675; moderate Grading of Recommendations Assessment, Development and Evaluation (GRADE) quality evidence) and mean power (SMD = 1.022; low) than CRT. Subgroup analyses revealed that VRT considerably increased the mean velocity (SMD = 0.903; moderate) and mean power (SMD = 1.456; moderate) in the equated loading scheme and the mean velocity (SMD = 0.712; low) in the CRT higher loading scheme. However, VRT marginally significantly reduced peak velocity (SMD = −0.481; low) in the VRT higher loading scheme. Based on the meta-regression analysis, it was found that mean power (p = 0.014–0.043) was positively moderated by the contribution of variable resistance and peak velocity (p = 0.018) and peak power (p = 0.001–0.004) and RFD (p = 0.003) were positively moderated by variable resistance equipment, favoring elastic bands. Conclusions VRT provides practitioners with the means of emphasizing specific force, velocity, and power outcomes. Different strategies should be considered in context of an individual’s needs. Systematic review registration: PROSPERO CRD42021259205.
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creator: Lin Shi
creator: Zhidong Cai
creator: Sitong Chen
creator: Dong Han
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.13870
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Objective Acute effects of variable resistance training (VRT) and constant resistance training (CRT) on neuromuscular performance are still equivocal. We aimed to determine the differences between VRT and CRT in terms of force, velocity, and power outcomes. Methods We searched PubMed, Web of Science, and SPORTDiscus electronic databases for articles until June 2021. Crossover design studies comparing force, velocity, and power outcomes while performing VRT and CRT were included. Two reviewers independently applied the modified version of the Cochrane Collaboration’s tool to assess the risk of bias. A three-level random effects meta-analyses and meta-regressions were used to compute standardized mean differences (SMDs) and 95% confidence intervals. Results We included 16 studies with 207 participants in the quantitative synthesis. Based on the pooled results, VRT generated greater mean velocity (SMD = 0.675; moderate Grading of Recommendations Assessment, Development and Evaluation (GRADE) quality evidence) and mean power (SMD = 1.022; low) than CRT. Subgroup analyses revealed that VRT considerably increased the mean velocity (SMD = 0.903; moderate) and mean power (SMD = 1.456; moderate) in the equated loading scheme and the mean velocity (SMD = 0.712; low) in the CRT higher loading scheme. However, VRT marginally significantly reduced peak velocity (SMD = −0.481; low) in the VRT higher loading scheme. Based on the meta-regression analysis, it was found that mean power (p = 0.014–0.043) was positively moderated by the contribution of variable resistance and peak velocity (p = 0.018) and peak power (p = 0.001–0.004) and RFD (p = 0.003) were positively moderated by variable resistance equipment, favoring elastic bands. Conclusions VRT provides practitioners with the means of emphasizing specific force, velocity, and power outcomes. Different strategies should be considered in context of an individual’s needs. Systematic review registration: PROSPERO CRD42021259205.
bibliographic citation: Shi et al. (2022) Acute effects of variable resistance training on force, velocity, and power measures: a systematic review and meta-analysis. PeerJ 10:e13870 https://doi.org/10.7717/peerj.13870
date submitted: 2022-04-14
date accepted: 2022-07-19
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Lin
author list: Agent
  family name: Cai
  given name: Zhidong
author list: Agent
  family name: Chen
  given name: Sitong
author list: Agent
  family name: Han
  given name: Dong
doi: 10.7717/peerj.13870
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: ©2022 Shi et al.
attribution name: Shi et al.

Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (NaV1.5)
type: item
type: AcademicArticle
description: Common genetic polymorphisms may modify the phenotypic outcome when co-occurring with a disease-causing variant, and therefore understanding their modulating role in health and disease is of great importance. The polymorphic p.His558Arg variant of the sodium voltage-gated channel alpha subunit 5 (NaV1.5) encoded by the SCN5A gene is a case in point, as several studies have shown it can modify the clinical phenotype in a number of cardiac diseases. To evaluate the genetic backgrounds associated with this modulating effect, we reanalysed previous electrophysiological findings regarding the p.His558Arg variant and further assessed its patterns of genetic diversity in human populations. The NaV1.5 p.His558Arg variant was found to be in linkage disequilibrium with six other polymorphic variants that previously were also associated with cardiac traits in GWAS analyses. On account of this, incongruent reports that Arg558 allele can compensate, aggravate or have no effect on NaV1.5, likely might have arose due to a role of p.His558Arg depending on the additional linked variants. Altogether, these results indicate a major influence of the epistatic interactions between SCN5A variants, revealing also that phenotypic severity may depend on the polymorphic background associated to each individual genome.
format: application/pdf
format: text/html
creator: Monica Lopes-Marques
creator: Raquel Silva
creator: Catarina Serrano
creator: Verónica Gomes
creator: Ana Cardoso
creator: Maria João Prata
creator: Antonio Amorim
creator: Luisa Azevedo
subject: Genomics
subject: Molecular Biology
subject: Cardiology
subject: Medical Genetics
description: doi:10.7717/peerj.13913
publisher: PeerJ Inc.
rights: © 2022 Lopes-Marques et al.
abstract: Common genetic polymorphisms may modify the phenotypic outcome when co-occurring with a disease-causing variant, and therefore understanding their modulating role in health and disease is of great importance. The polymorphic p.His558Arg variant of the sodium voltage-gated channel alpha subunit 5 (NaV1.5) encoded by the SCN5A gene is a case in point, as several studies have shown it can modify the clinical phenotype in a number of cardiac diseases. To evaluate the genetic backgrounds associated with this modulating effect, we reanalysed previous electrophysiological findings regarding the p.His558Arg variant and further assessed its patterns of genetic diversity in human populations. The NaV1.5 p.His558Arg variant was found to be in linkage disequilibrium with six other polymorphic variants that previously were also associated with cardiac traits in GWAS analyses. On account of this, incongruent reports that Arg558 allele can compensate, aggravate or have no effect on NaV1.5, likely might have arose due to a role of p.His558Arg depending on the additional linked variants. Altogether, these results indicate a major influence of the epistatic interactions between SCN5A variants, revealing also that phenotypic severity may depend on the polymorphic background associated to each individual genome.
bibliographic citation: Lopes-Marques et al. (2022) Complex interactions between p.His558Arg and linked variants in the sodium voltage-gated channel alpha subunit 5 (NaV1.5). PeerJ 10:e13913 https://doi.org/10.7717/peerj.13913
date submitted: 2022-02-24
date accepted: 2022-07-27
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lopes-Marques
  given name: Monica
author list: Agent
  family name: Silva
  given name: Raquel
author list: Agent
  family name: Serrano
  given name: Catarina
author list: Agent
  family name: Gomes
  given name: Verónica
author list: Agent
  family name: Cardoso
  given name: Ana
author list: Agent
  family name: Prata
  given name: Maria João
author list: Agent
  family name: Amorim
  given name: Antonio
author list: Agent
  family name: Azevedo
  given name: Luisa
doi: 10.7717/peerj.13913
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: © 2022 Lopes-Marques et al.
attribution name: Lopes-Marques et al.

Aluminum phosphate sludge as a phosphorus source for maize production under low soil phosphorus availability
type: item
type: AcademicArticle
description: Background With increasing food demand as a consequence of the growing world population, there is a corresponding demand for additional sources of phosphorus (P). Alum-phosphate (Al-P) sludge is a by-product of wastewater treatment and can be a good source of P. In this study, the response of maize (Zea mays L.) to Al-P sludge was tested. Maize was chosen as the test crop due to its prevalent use as human and animal food and as a source of biofuel. The objective of the study was to investigate Al-P sludge as a source of P compared to a commercial fertilizer (monoammonium phosphate, MAP). Methods A growth chamber assay was conducted over four cropping cycles (45 d each). The application rate was 9.7, 19.4, 29.1 and 38.8 mg P kg−1 dry soil. Amendments were applied once at the start of the first cropping cycle. Plants were harvested after each cycle and pots were re-seeded. Dry matter yield (DMY), total P uptake, Al-P uptake, soil total P and Olsen-P concentrations, pH, and EC were measured. Results DMY was significantly greater in pots amended with Al-P sludge than in pots treated with MAP. There was a significant rate × cropping cycle interaction effect on DMY with the differences among rates in cycle 1 different from those in cycle 4. Phosphorus uptake depended on cropping cycle, P source and P application rate. With sludge uptake higher than MAP in all cycles, the highest P uptake was observed at the highest application rate except for cycle 2 where this was observed at the rate of 29.1 mg kg−1. For MAP, phosphorus recovery efficiency (PRE) at the highest rate was significantly greater than that at the lowest rate whereas PRE in cycle 1 was significantly higher than that in cycle 4. In the first two cycles, aluminum uptake was negligible in both MAP and Al-P sludge treatments; however, in cycles 3 and 4, there was significantly more Al in maize from sludge amended pots. Our results show that Al-P sludge was as effective as MAP in supplying enough P for biomass yiel…
format: application/pdf
format: text/html
creator: Ayaobu Tolofari
creator: Theresa Adesanya
creator: Francis Zvomuya
creator: Qiuyan Yuan
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.13885
publisher: PeerJ Inc.
rights: © 2022 Tolofari et al.
abstract: Background With increasing food demand as a consequence of the growing world population, there is a corresponding demand for additional sources of phosphorus (P). Alum-phosphate (Al-P) sludge is a by-product of wastewater treatment and can be a good source of P. In this study, the response of maize (Zea mays L.) to Al-P sludge was tested. Maize was chosen as the test crop due to its prevalent use as human and animal food and as a source of biofuel. The objective of the study was to investigate Al-P sludge as a source of P compared to a commercial fertilizer (monoammonium phosphate, MAP). Methods A growth chamber assay was conducted over four cropping cycles (45 d each). The application rate was 9.7, 19.4, 29.1 and 38.8 mg P kg−1 dry soil. Amendments were applied once at the start of the first cropping cycle. Plants were harvested after each cycle and pots were re-seeded. Dry matter yield (DMY), total P uptake, Al-P uptake, soil total P and Olsen-P concentrations, pH, and EC were measured. Results DMY was significantly greater in pots amended with Al-P sludge than in pots treated with MAP. There was a significant rate × cropping cycle interaction effect on DMY with the differences among rates in cycle 1 different from those in cycle 4. Phosphorus uptake depended on cropping cycle, P source and P application rate. With sludge uptake higher than MAP in all cycles, the highest P uptake was observed at the highest application rate except for cycle 2 where this was observed at the rate of 29.1 mg kg−1. For MAP, phosphorus recovery efficiency (PRE) at the highest rate was significantly greater than that at the lowest rate whereas PRE in cycle 1 was significantly higher than that in cycle 4. In the first two cycles, aluminum uptake was negligible in both MAP and Al-P sludge treatments; however, in cycles 3 and 4, there was significantly more Al in maize from sludge amended pots. Our results show that Al-P sludge was as effective as MAP in supplying enough P for biomass yiel…
bibliographic citation: Tolofari et al. (2022) Aluminum phosphate sludge as a phosphorus source for maize production under low soil phosphorus availability. PeerJ 10:e13885 https://doi.org/10.7717/peerj.13885
date submitted: 2022-02-22
date accepted: 2022-07-21
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tolofari
  given name: Ayaobu
author list: Agent
  family name: Adesanya
  given name: Theresa
author list: Agent
  family name: Zvomuya
  given name: Francis
author list: Agent
  family name: Yuan
  given name: Qiuyan
doi: 10.7717/peerj.13885
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: © 2022 Tolofari et al.
attribution name: Tolofari et al.

The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders
type: item
type: AcademicArticle
description: Background Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P < 0.05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P = 0.88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values =…
format: application/pdf
format: text/html
creator: Yunden Droma
creator: Masayuki Hanaoka
creator: Takumi Kinjo
creator: Nobumitsu Kobayashi
creator: Masanori Yasuo
creator: Yoshiaki Kitaguchi
creator: Masao Ota
subject: Genetics
subject: Medical Genetics
description: doi:10.7717/peerj.13893
publisher: PeerJ Inc.
rights: © 2022 Droma et al.
abstract: Background Sherpa highlanders demonstrate extraordinary tolerance to hypoxia at high altitudes, which may be achieved by mechanisms promoting microcirculatory blood flow and capillary density at high altitudes for restoring oxygen supply to tissues. Vascular endothelial growth factors (VEGFs) are important signaling proteins involved in vasculogenesis and angiogenesis which are stimulated by hypoxia. We hypothesize that the VEGF-A, the major member of the VEGF family, and the gene encoding VEGF-A (VEGFA) play a part in the adaptation to high-altitude hypoxia in Sherpa highlanders. Methods Fifty-one Sherpa highlanders in Namche Bazaar village at a high altitude of 3,440 meters (m) above sea level and 76 non-Sherpa lowlanders in Kathmandu city at 1,300 m in Nepal were recruited for the study. Venous blood was sampled to obtain plasma and extract DNA from each subject. The plasma VEGF-A concentrations were measured and five single-nucleotide polymorphisms (SNPs, rs699947, rs833061, rs1570360, rs2010963, and rs3025039) in the VEGFA were genotyped. The VEGF-A levels and allelic frequencies of the SNPs were compared between the two populations. Results A significant difference in oxygen saturation (SpO2) was observed between the two ethnic groups locating at different elevations (93.7 ± 0.2% in Sherpas at 3,440 m vs. 96.7 ± 0.2% in non-Sherpas at 1,300 m, P < 0.05). The plasma VEGF-A concentration in the Sherpas at high altitude was on the same level as that in the non-Sherpas at low altitude (262.8 ± 17.9 pg/ml vs. 266.8 ± 21.8 pg/ml, P = 0.88). This result suggested that the plasma VEGF-A concentration in Sherpa highlanders was stable despite a high-altitude hypoxic stimulus and that therefore the Sherpas exhibited a phenotype of blunted response to hypoxic stress. Moreover, the allele frequencies of the SNPs rs699947, rs833061, and rs2010963 in the promoter region of the VEGFA were different between the Sherpa highlanders and non-Sherpa lowlanders (corrected P values =…
bibliographic citation: Droma et al. (2022) The blunted vascular endothelial growth factor-A (VEGF-A) response to high-altitude hypoxia and genetic variants in the promoter region of the VEGFA gene in Sherpa highlanders. PeerJ 10:e13893 https://doi.org/10.7717/peerj.13893
date submitted: 2021-06-14
date accepted: 2022-07-22
issued: 2022-08-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Droma
  given name: Yunden
author list: Agent
  family name: Hanaoka
  given name: Masayuki
author list: Agent
  family name: Kinjo
  given name: Takumi
author list: Agent
  family name: Kobayashi
  given name: Nobumitsu
author list: Agent
  family name: Yasuo
  given name: Masanori
author list: Agent
  family name: Kitaguchi
  given name: Yoshiaki
author list: Agent
  family name: Ota
  given name: Masao
doi: 10.7717/peerj.13893
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-08-17
copyright: ©2022 Droma et al.
attribution name: Droma et al.

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