PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
items: Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica
items: Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies
items: Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)
items: Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region
items: Radar remote sensing-based inversion model of soil salt content at different depths under vegetation
items: Analysis of professional soccer players in competitive match play based on submaximum intensity periods
items: Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL
items: Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake
items: Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods

Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules
type: item
type: AcademicArticle
description: The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
format: application/pdf
format: text/html
creator: Stepan Nersisyan
creator: Anton Zhiyanov
creator: Maria Zakharova
creator: Irina Ishina
creator: Inna Kurbatskaia
creator: Azad Mamedov
creator: Alexei Galatenko
creator: Maxim Shkurnikov
creator: Alexander Gabibov
creator: Alexander Tonevitsky
subject: Bioinformatics
subject: Cell Biology
subject: Virology
description: doi:10.7717/peerj.13354
publisher: PeerJ Inc.
rights: © 2022 Nersisyan et al.
abstract: The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
bibliographic citation: Nersisyan et al. (2022) Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 10:e13354 https://doi.org/10.7717/peerj.13354
date submitted: 2022-03-01
date accepted: 2022-04-08
issued: 2022-04-27
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: Zhiyanov
  given name: Anton
author list: Agent
  family name: Zakharova
  given name: Maria
author list: Agent
  family name: Ishina
  given name: Irina
author list: Agent
  family name: Kurbatskaia
  given name: Inna
author list: Agent
  family name: Mamedov
  given name: Azad
author list: Agent
  family name: Galatenko
  given name: Alexei
author list: Agent
  family name: Shkurnikov
  given name: Maxim
author list: Agent
  family name: Gabibov
  given name: Alexander
author list: Agent
  family name: Tonevitsky
  given name: Alexander
doi: 10.7717/peerj.13354
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-27
copyright: © 2022 Nersisyan et al.
attribution name: Nersisyan et al.

Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica
type: item
type: AcademicArticle
description: Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to a…
format: application/pdf
format: text/html
creator: Janie L. Reavis
creator: Daniela Rojas-Cañizales
creator: Carmen Mejías-Balsalobre
creator: Isabel Naranjo
creator: Randall Arauz
creator: Jesse F. Senko
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.12925
publisher: PeerJ Inc.
rights: © 2022 Reavis et al.
abstract: Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to a…
bibliographic citation: Reavis et al. (2022) Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica. PeerJ 10:e12925 https://doi.org/10.7717/peerj.12925
date submitted: 2021-08-12
date accepted: 2022-01-20
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reavis
  given name: Janie L.
author list: Agent
  family name: Rojas-Cañizales
  given name: Daniela
author list: Agent
  family name: Mejías-Balsalobre
  given name: Carmen
author list: Agent
  family name: Naranjo
  given name: Isabel
author list: Agent
  family name: Arauz
  given name: Randall
author list: Agent
  family name: Senko
  given name: Jesse F.
doi: 10.7717/peerj.12925
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Reavis et al.
attribution name: Reavis et al.

Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies
type: item
type: AcademicArticle
description: Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies.
format: application/pdf
format: text/html
creator: Yixin Shi
creator: Bingrun Qiu
creator: Linyang Huang
creator: Jie Lin
creator: Yiling Li
creator: Yiting Ze
creator: Chenglong Huang
creator: Yang Yao
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.13238
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies.
bibliographic citation: Shi et al. (2022) Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies. PeerJ 10:e13238 https://doi.org/10.7717/peerj.13238
date submitted: 2021-12-15
date accepted: 2022-03-18
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yixin
author list: Agent
  family name: Qiu
  given name: Bingrun
author list: Agent
  family name: Huang
  given name: Linyang
author list: Agent
  family name: Lin
  given name: Jie
author list: Agent
  family name: Li
  given name: Yiling
author list: Agent
  family name: Ze
  given name: Yiting
author list: Agent
  family name: Huang
  given name: Chenglong
author list: Agent
  family name: Yao
  given name: Yang
doi: 10.7717/peerj.13238
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Shi et al.
attribution name: Shi et al.

Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta)
type: item
type: AcademicArticle
description: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the d…
format: application/pdf
format: text/html
creator: Vladimir E. Fedosov
creator: Anna V. Shkurko
creator: Alina V. Fedorova
creator: Elena A. Ignatova
creator: Evgeniya N. Solovyeva
creator: John C. Brinda
creator: Michael S. Ignatov
creator: Jan Kučera
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.13260
publisher: PeerJ Inc.
rights: © 2022 Fedosov et al.
abstract: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the d…
bibliographic citation: Fedosov et al. (2022) Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta). PeerJ 10:e13260 https://doi.org/10.7717/peerj.13260
date submitted: 2021-11-10
date accepted: 2022-03-22
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fedosov
  given name: Vladimir E.
author list: Agent
  family name: Shkurko
  given name: Anna V.
author list: Agent
  family name: Fedorova
  given name: Alina V.
author list: Agent
  family name: Ignatova
  given name: Elena A.
author list: Agent
  family name: Solovyeva
  given name: Evgeniya N.
author list: Agent
  family name: Brinda
  given name: John C.
author list: Agent
  family name: Ignatov
  given name: Michael S.
author list: Agent
  family name: Kučera
  given name: Jan
doi: 10.7717/peerj.13260
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Fedosov et al.
attribution name: Fedosov et al.

Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region
type: item
type: AcademicArticle
description: Background The Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species. Methods The diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses. Results We recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatron Fischer & Fisher, 2013 and P. spinosa Forel, 1891 stat. nov. Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabrior Forel, 1891 syn. nov., P. picata Forel, 1891 syn. nov., P. picata gietleni Forel, 1905 syn. nov., P. picata bernhardae Emery, 1915 syn. nov., and P. decepticon Fischer & Fisher, 2013 syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst i…
format: application/pdf
format: text/html
creator: Sebastian Salata
creator: Brian L. Fisher
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.13263
publisher: PeerJ Inc.
rights: © 2022 Salata and Fisher
abstract: Background The Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species. Methods The diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses. Results We recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatron Fischer & Fisher, 2013 and P. spinosa Forel, 1891 stat. nov. Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabrior Forel, 1891 syn. nov., P. picata Forel, 1891 syn. nov., P. picata gietleni Forel, 1905 syn. nov., P. picata bernhardae Emery, 1915 syn. nov., and P. decepticon Fischer & Fisher, 2013 syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst i…
bibliographic citation: Salata et al. (2022) Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region. PeerJ 10:e13263 https://doi.org/10.7717/peerj.13263
date submitted: 2021-12-09
date accepted: 2022-03-22
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salata
  given name: Sebastian
author list: Agent
  family name: Fisher
  given name: Brian L.
doi: 10.7717/peerj.13263
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: ©2022 Salata and Fisher
attribution name: Salata and Fisher

Radar remote sensing-based inversion model of soil salt content at different depths under vegetation
type: item
type: AcademicArticle
description: Excessive soil salt content (SSC) seriously affects the crop growth and economic benefits in the agricultural production area. Prior research mainly focused on estimating the salinity in the top bare soil rather than in deep soil that is vital to crop growth. For this end, an experiment was carried out in the Hetao Irrigation District, Inner Mongolia, China. In the experiment, the SSC at different depths under vegetation was measured, and the Sentinel-1 radar images were obtained synchronously. The radar backscattering coefficients (VV and VH) were combined to construct multiple indices, whose sensitivity was then analyzed using the best subset selection (BSS). Meanwhile, four most commonly used algorithms, partial least squares regression (PLSR), quantile regression (QR), support vector machine (SVM), and extreme learning machine (ELM), were utilized to construct estimation models of salinity at the depths of 0–10, 10–20, 0–20, 20–40, 0–40, 40–60 and 0–60 cm before and after BSS, respectively. The results showed: (a) radar remote sensing can be used to estimate the salinity in the root zone of vegetation (0-30 cm); (b) after BSS, the correlation coefficients and estimation accuracy of the four monitoring models were all improved significantly; (c) the estimation accuracy of the four regression models was: SVM > QR > ELM > PLSR; and (d) among the seven sampling depths, 10–20 cm was the optimal inversion depth for all the four models, followed by 20–40 and 0–40 cm. Among the four models, SVM was higher in accuracy than the other three at 10–20 cm (RP2 = 0.67, RMSEP = 0.12%). These findings can provide valuable guidance for soil salinity monitoring and agricultural production in the arid or semi-arid areas under vegetation.
format: application/pdf
format: text/html
creator: Yinwen Chen
creator: Yuyan Du
creator: Haoyuan Yin
creator: Huiyun Wang
creator: Haiying Chen
creator: Xianwen Li
creator: Zhitao Zhang
creator: Junying Chen
subject: Agricultural Science
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.13306
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Excessive soil salt content (SSC) seriously affects the crop growth and economic benefits in the agricultural production area. Prior research mainly focused on estimating the salinity in the top bare soil rather than in deep soil that is vital to crop growth. For this end, an experiment was carried out in the Hetao Irrigation District, Inner Mongolia, China. In the experiment, the SSC at different depths under vegetation was measured, and the Sentinel-1 radar images were obtained synchronously. The radar backscattering coefficients (VV and VH) were combined to construct multiple indices, whose sensitivity was then analyzed using the best subset selection (BSS). Meanwhile, four most commonly used algorithms, partial least squares regression (PLSR), quantile regression (QR), support vector machine (SVM), and extreme learning machine (ELM), were utilized to construct estimation models of salinity at the depths of 0–10, 10–20, 0–20, 20–40, 0–40, 40–60 and 0–60 cm before and after BSS, respectively. The results showed: (a) radar remote sensing can be used to estimate the salinity in the root zone of vegetation (0-30 cm); (b) after BSS, the correlation coefficients and estimation accuracy of the four monitoring models were all improved significantly; (c) the estimation accuracy of the four regression models was: SVM > QR > ELM > PLSR; and (d) among the seven sampling depths, 10–20 cm was the optimal inversion depth for all the four models, followed by 20–40 and 0–40 cm. Among the four models, SVM was higher in accuracy than the other three at 10–20 cm (RP2 = 0.67, RMSEP = 0.12%). These findings can provide valuable guidance for soil salinity monitoring and agricultural production in the arid or semi-arid areas under vegetation.
bibliographic citation: Chen et al. (2022) Radar remote sensing-based inversion model of soil salt content at different depths under vegetation. PeerJ 10:e13306 https://doi.org/10.7717/peerj.13306
date submitted: 2021-10-13
date accepted: 2022-03-30
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yinwen
author list: Agent
  family name: Du
  given name: Yuyan
author list: Agent
  family name: Yin
  given name: Haoyuan
author list: Agent
  family name: Wang
  given name: Huiyun
author list: Agent
  family name: Chen
  given name: Haiying
author list: Agent
  family name: Li
  given name: Xianwen
author list: Agent
  family name: Zhang
  given name: Zhitao
author list: Agent
  family name: Chen
  given name: Junying
doi: 10.7717/peerj.13306
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Analysis of professional soccer players in competitive match play based on submaximum intensity periods
type: item
type: AcademicArticle
description: The main objective of this study is to analyse sub-maximum intensity periods (SubMIP’s) manifested by professional soccer players during official matches (number of events and time spent in each event), according to the player position, match halve and match, and also to group the players according to their SubMip values during the competition. Methods We collected a total of 247 individual records of 14 players using Global Positioning System (GPS) during 15 official league matches (Azerbaijan Premier League 2019–2020). We calculated both the number of SubMIPs events and the time each player spent in the SubMIPs zone (threshold of 85% MIP). We analysed the possible independence of the variables with the Kruskal–Wallis test and the possible specific relationships between the groups using a post-hoc analysis with Dunn’s test. In order to explore the possible distribution of physical demands in homogeneous groups, a cluster analysis was performed. Results The statistical analysis showed significant differences between the individual variables in the number of events and in the time spent by the player above the threshold in distance covered at speed >19.8 km/h (HSR), distance covered at speed >25.2 km/h (Sprint), acceleration density (AccDens), mean metabolic power (MetPow), metres per minute (Mmin) and high metabolic load distance >25.5 W/kg (HMLD). Differences were also found according to the playing position in MetPow, Mmin and between halves in AccDens, MetPow, Mmin. In the clustering based on the time spent by the player in SubMIPs, three main groups were described: (1) the centroid was located in lower values in each of the variables; (2) there were an accentuation of the AccDens variable; (3) all the variables, except AccDens, were accentuated. Conclusions The main differences with regard to SubMIPs were related to the player’s individual physical performance and not to position. However, the player’s position could act as an attractor and show significant diff…
format: application/pdf
format: text/html
creator: Eduardo Caro
creator: Miguel Ángel Campos-Vázquez
creator: Manuel Lapuente-Sagarra
creator: Toni Caparrós
subject: Anatomy and Physiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.13309
publisher: PeerJ Inc.
rights: © 2022 Caro et al.
abstract: The main objective of this study is to analyse sub-maximum intensity periods (SubMIP’s) manifested by professional soccer players during official matches (number of events and time spent in each event), according to the player position, match halve and match, and also to group the players according to their SubMip values during the competition. Methods We collected a total of 247 individual records of 14 players using Global Positioning System (GPS) during 15 official league matches (Azerbaijan Premier League 2019–2020). We calculated both the number of SubMIPs events and the time each player spent in the SubMIPs zone (threshold of 85% MIP). We analysed the possible independence of the variables with the Kruskal–Wallis test and the possible specific relationships between the groups using a post-hoc analysis with Dunn’s test. In order to explore the possible distribution of physical demands in homogeneous groups, a cluster analysis was performed. Results The statistical analysis showed significant differences between the individual variables in the number of events and in the time spent by the player above the threshold in distance covered at speed >19.8 km/h (HSR), distance covered at speed >25.2 km/h (Sprint), acceleration density (AccDens), mean metabolic power (MetPow), metres per minute (Mmin) and high metabolic load distance >25.5 W/kg (HMLD). Differences were also found according to the playing position in MetPow, Mmin and between halves in AccDens, MetPow, Mmin. In the clustering based on the time spent by the player in SubMIPs, three main groups were described: (1) the centroid was located in lower values in each of the variables; (2) there were an accentuation of the AccDens variable; (3) all the variables, except AccDens, were accentuated. Conclusions The main differences with regard to SubMIPs were related to the player’s individual physical performance and not to position. However, the player’s position could act as an attractor and show significant diff…
bibliographic citation: Caro et al. (2022) Analysis of professional soccer players in competitive match play based on submaximum intensity periods. PeerJ 10:e13309 https://doi.org/10.7717/peerj.13309
date submitted: 2021-12-01
date accepted: 2022-03-30
issued: 2022-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caro
  given name: Eduardo
author list: Agent
  family name: Campos-Vázquez
  given name: Miguel Ángel
author list: Agent
  family name: Lapuente-Sagarra
  given name: Manuel
author list: Agent
  family name: Caparrós
  given name: Toni
doi: 10.7717/peerj.13309
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-26
copyright: © 2022 Caro et al.
attribution name: Caro et al.

Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL
type: item
type: AcademicArticle
description: Background Antisense noncoding RNA in the INK4 locus (ANRIL) is located on human chromosome 9p21, and modulation of ANRIL expression mediates susceptibility to some important human disease, including atherosclerosis (AS) and tumors, by affecting the cell cycle circANRIL and linear ANRIL are isoforms of ANRIL. However, it remains unclear whether these isoforms have distinct functions. In our research, we constructed a circANRIL overexpression plasmid, transfected it into HEK-293T cell line, and explored potential core genes and signaling pathways related to the important differential mechanisms between the circANRIL-overexpressing cell line and control cells through bioinformatics analysis. Methods Stable circANRIL-overexpressing (circANRIL-OE) HEK-293T cells and control cells were generated by infection with the circANRIL-OE lentiviral vector or a negative control vector, and successful transfection was confirmed by conventional flurescence microscopy and quantitative real-time PCR (qRT-PCR). Next, differentially expressed genes (DEGs) between circANRIL-OE cells and control cells were detected. Subsequently, Gene Ontology (GO) biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the principal functions of the significant DEGs. A protein–protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were constructed in Cytoscape to determine circularRNA (circRNA)- microRNA(miRNA)-messenger RNA (mRNA) interactions and hub genes, and qRT-PCR was used to verify changes in the expression of these identified target genes. Results The successful construction of circANRIL-OE cells was confirmed by plasmid sequencing, visualization with fluorescence microscopy and qRT-PCR. A total of 1745 DEGs between the circANRIL-OE group and control were identified, GO BP analysis showed that these genes were mostly related to RNA biosynthesis and processing, regulation of transcription and signal …
format: application/pdf
format: text/html
creator: Qiuyan Qin
creator: Pengfei Zheng
creator: Ronghui Tu
creator: Jiegang Huang
creator: Xiaoli Cao
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
description: doi:10.7717/peerj.13135
publisher: PeerJ Inc.
rights: © 2022 Qin et al.
abstract: Background Antisense noncoding RNA in the INK4 locus (ANRIL) is located on human chromosome 9p21, and modulation of ANRIL expression mediates susceptibility to some important human disease, including atherosclerosis (AS) and tumors, by affecting the cell cycle circANRIL and linear ANRIL are isoforms of ANRIL. However, it remains unclear whether these isoforms have distinct functions. In our research, we constructed a circANRIL overexpression plasmid, transfected it into HEK-293T cell line, and explored potential core genes and signaling pathways related to the important differential mechanisms between the circANRIL-overexpressing cell line and control cells through bioinformatics analysis. Methods Stable circANRIL-overexpressing (circANRIL-OE) HEK-293T cells and control cells were generated by infection with the circANRIL-OE lentiviral vector or a negative control vector, and successful transfection was confirmed by conventional flurescence microscopy and quantitative real-time PCR (qRT-PCR). Next, differentially expressed genes (DEGs) between circANRIL-OE cells and control cells were detected. Subsequently, Gene Ontology (GO) biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the principal functions of the significant DEGs. A protein–protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were constructed in Cytoscape to determine circularRNA (circRNA)- microRNA(miRNA)-messenger RNA (mRNA) interactions and hub genes, and qRT-PCR was used to verify changes in the expression of these identified target genes. Results The successful construction of circANRIL-OE cells was confirmed by plasmid sequencing, visualization with fluorescence microscopy and qRT-PCR. A total of 1745 DEGs between the circANRIL-OE group and control were identified, GO BP analysis showed that these genes were mostly related to RNA biosynthesis and processing, regulation of transcription and signal …
bibliographic citation: Qin et al. (2022) Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL. PeerJ 10:e13135 https://doi.org/10.7717/peerj.13135
date submitted: 2021-08-20
date accepted: 2022-02-27
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Qiuyan
author list: Agent
  family name: Zheng
  given name: Pengfei
author list: Agent
  family name: Tu
  given name: Ronghui
author list: Agent
  family name: Huang
  given name: Jiegang
author list: Agent
  family name: Cao
  given name: Xiaoli
doi: 10.7717/peerj.13135
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: ©2022 Qin et al.
attribution name: Qin et al.

Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake
type: item
type: AcademicArticle
description: Background The percentages of heart rate (%HRR) or oxygen uptake (%V̇O2R) reserve are used interchangeably for prescribing aerobic exercise intensity due to their assumed 1:1 relationship, although its validity is debated. This study aimed to assess if %HRR and %V̇O2R show a 1:1 relationship during steady-state exercise (SSE) and if exercise intensity and duration affect their relationship. Methods Eight physically active males (age 22.6 ± 1.2 years) were enrolled. Pre-exercise and maximal HR and V̇O2 were assessed on the first day. In the following 4 days, different SSEs were performed (running) combining the following randomly assigned durations and intensities: 15 min, 45 min, 60% HRR, 80% HRR. Post-exercise maximal HR and V̇O2 were assessed after each SSE. Using pre-exercise and post-exercise maximal values, the average HR and V̇O2 of the last 5 min of each SSE were converted into percentages of the reserves (%RES), which were computed in a 3-way RM-ANOVA (α = 0.05) to assess if they were affected by the prescription parameter (HRR or V̇O2R), exercise intensity (60% or 80% HRR), and duration (15 or 45 min). Results The %RES values were not affected by the prescription parameter (p = 0.056) or its interactions with intensity (p = 0.319) or duration and intensity (p = 0.117), while parameter and duration interaction was significant (p = 0.009). %HRRs and %V̇O2Rs did not differ in the 15-min SSEs (mean difference [MD] = 0.7 percentage points, p = 0.717), whereas %HRR was higher than %V̇O2R in the 45-min SSEs (MD = 6.7 percentage points, p = 0.009). Conclusion SSE duration affects the %HRR-%V̇O2R relationship, with %HRRs higher than %V̇O2Rs in SSEs of longer duration.
format: application/pdf
format: text/html
creator: Carlo Ferri Marini
creator: Ario Federici
creator: James S. Skinner
creator: Giovanni Piccoli
creator: Vilberto Stocchi
creator: Luca Zoffoli
creator: Luca Correale
creator: Stefano Dell’Anna
creator: Carlo Alberto Naldini
creator: Matteo Vandoni
creator: Francesco Lucertini
subject: Anatomy and Physiology
subject: Cardiology
subject: Kinesiology
description: doi:10.7717/peerj.13190
publisher: PeerJ Inc.
rights: © 2022 Ferri Marini et al.
abstract: Background The percentages of heart rate (%HRR) or oxygen uptake (%V̇O2R) reserve are used interchangeably for prescribing aerobic exercise intensity due to their assumed 1:1 relationship, although its validity is debated. This study aimed to assess if %HRR and %V̇O2R show a 1:1 relationship during steady-state exercise (SSE) and if exercise intensity and duration affect their relationship. Methods Eight physically active males (age 22.6 ± 1.2 years) were enrolled. Pre-exercise and maximal HR and V̇O2 were assessed on the first day. In the following 4 days, different SSEs were performed (running) combining the following randomly assigned durations and intensities: 15 min, 45 min, 60% HRR, 80% HRR. Post-exercise maximal HR and V̇O2 were assessed after each SSE. Using pre-exercise and post-exercise maximal values, the average HR and V̇O2 of the last 5 min of each SSE were converted into percentages of the reserves (%RES), which were computed in a 3-way RM-ANOVA (α = 0.05) to assess if they were affected by the prescription parameter (HRR or V̇O2R), exercise intensity (60% or 80% HRR), and duration (15 or 45 min). Results The %RES values were not affected by the prescription parameter (p = 0.056) or its interactions with intensity (p = 0.319) or duration and intensity (p = 0.117), while parameter and duration interaction was significant (p = 0.009). %HRRs and %V̇O2Rs did not differ in the 15-min SSEs (mean difference [MD] = 0.7 percentage points, p = 0.717), whereas %HRR was higher than %V̇O2R in the 45-min SSEs (MD = 6.7 percentage points, p = 0.009). Conclusion SSE duration affects the %HRR-%V̇O2R relationship, with %HRRs higher than %V̇O2Rs in SSEs of longer duration.
bibliographic citation: Ferri Marini et al. (2022) Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake. PeerJ 10:e13190 https://doi.org/10.7717/peerj.13190
date submitted: 2022-01-19
date accepted: 2022-03-08
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferri Marini
  given name: Carlo
author list: Agent
  family name: Federici
  given name: Ario
author list: Agent
  family name: Skinner
  given name: James S.
author list: Agent
  family name: Piccoli
  given name: Giovanni
author list: Agent
  family name: Stocchi
  given name: Vilberto
author list: Agent
  family name: Zoffoli
  given name: Luca
author list: Agent
  family name: Correale
  given name: Luca
author list: Agent
  family name: Dell’Anna
  given name: Stefano
author list: Agent
  family name: Naldini
  given name: Carlo Alberto
author list: Agent
  family name: Vandoni
  given name: Matteo
author list: Agent
  family name: Lucertini
  given name: Francesco
doi: 10.7717/peerj.13190
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: ©2022 Ferri Marini et al.
attribution name: Ferri Marini et al.

Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods
type: item
type: AcademicArticle
description: The tremendous boost in next generation sequencing and in the “omics” technologies makes it possible to characterize the human gut microbiome—the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn’s disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extre…
format: application/pdf
format: text/html
creator: Burcu Bakir-Gungor
creator: Hilal Hacılar
creator: Amhar Jabeer
creator: Ozkan Ufuk Nalbantoglu
creator: Oya Aran
creator: Malik Yousef
subject: Bioinformatics
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13205
publisher: PeerJ Inc.
rights: © 2022 Bakir-Gungor et al.
abstract: The tremendous boost in next generation sequencing and in the “omics” technologies makes it possible to characterize the human gut microbiome—the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn’s disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extre…
bibliographic citation: Bakir-Gungor et al. (2022) Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ 10:e13205 https://doi.org/10.7717/peerj.13205
date submitted: 2021-02-03
date accepted: 2022-03-10
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bakir-Gungor
  given name: Burcu
author list: Agent
  family name: Hacılar
  given name: Hilal
author list: Agent
  family name: Jabeer
  given name: Amhar
author list: Agent
  family name: Nalbantoglu
  given name: Ozkan Ufuk
author list: Agent
  family name: Aran
  given name: Oya
author list: Agent
  family name: Yousef
  given name: Malik
doi: 10.7717/peerj.13205
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: ©2022 Bakir-Gungor et al.
attribution name: Bakir-Gungor et al.

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