PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: A DNA barcode survey of insect biodiversity in Pakistan
items: Spatial variability of microzooplankton grazing on phytoplankton in coastal southern Florida, USA
items: Association between laryngopharyngeal reflux and obstructive sleep apnea in adults
items: Do patterns of insect mortality in temperate and tropical zones have broader implications for insect ecology and pest management?

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.

A DNA barcode survey of insect biodiversity in Pakistan
type: item
type: AcademicArticle
description: Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010–2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
format: application/pdf
format: text/html
creator: Muhammad Ashfaq
creator: Arif M. Khan
creator: Akhtar Rasool
creator: Saleem Akhtar
creator: Naila Nazir
creator: Nazeer Ahmed
creator: Farkhanda Manzoor
creator: Jayme Sones
creator: Kate Perez
creator: Ghulam Sarwar
creator: Azhar A. Khan
creator: Muhammad Akhter
creator: Shafqat Saeed
creator: Riffat Sultana
creator: Hafiz Muhammad Tahir
creator: Muhammad A. Rafi
creator: Romana Iftikhar
creator: Muhammad Tayyib Naseem
creator: Mariyam Masood
creator: Muhammad Tufail
creator: Santosh Kumar
creator: Sabila Afzal
creator: Jaclyn McKeown
creator: Ahmed Ali Samejo
creator: Imran Khaliq
creator: Michelle L. D’Souza
creator: Shahid Mansoor
creator: Paul D. N. Hebert
subject: Ecology
subject: Entomology
subject: Genetics
subject: Taxonomy
subject: Population Biology
description: doi:10.7717/peerj.13267
publisher: PeerJ Inc.
rights: © 2022 Ashfaq et al.
abstract: Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010–2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library.
bibliographic citation: Ashfaq et al. (2022) A DNA barcode survey of insect biodiversity in Pakistan. PeerJ 10:e13267 https://doi.org/10.7717/peerj.13267
date submitted: 2021-12-30
date accepted: 2022-03-23
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ashfaq
  given name: Muhammad
author list: Agent
  family name: Khan
  given name: Arif M.
author list: Agent
  family name: Rasool
  given name: Akhtar
author list: Agent
  family name: Akhtar
  given name: Saleem
author list: Agent
  family name: Nazir
  given name: Naila
author list: Agent
  family name: Ahmed
  given name: Nazeer
author list: Agent
  family name: Manzoor
  given name: Farkhanda
author list: Agent
  family name: Sones
  given name: Jayme
author list: Agent
  family name: Perez
  given name: Kate
author list: Agent
  family name: Sarwar
  given name: Ghulam
author list: Agent
  family name: Khan
  given name: Azhar A.
author list: Agent
  family name: Akhter
  given name: Muhammad
author list: Agent
  family name: Saeed
  given name: Shafqat
author list: Agent
  family name: Sultana
  given name: Riffat
author list: Agent
  family name: Tahir
  given name: Hafiz Muhammad
author list: Agent
  family name: Rafi
  given name: Muhammad A.
author list: Agent
  family name: Iftikhar
  given name: Romana
author list: Agent
  family name: Naseem
  given name: Muhammad Tayyib
author list: Agent
  family name: Masood
  given name: Mariyam
author list: Agent
  family name: Tufail
  given name: Muhammad
author list: Agent
  family name: Kumar
  given name: Santosh
author list: Agent
  family name: Afzal
  given name: Sabila
author list: Agent
  family name: McKeown
  given name: Jaclyn
author list: Agent
  family name: Samejo
  given name: Ahmed Ali
author list: Agent
  family name: Khaliq
  given name: Imran
doi: 10.7717/peerj.13267
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: © 2022 Ashfaq et al.
attribution name: Ashfaq et al.

Spatial variability of microzooplankton grazing on phytoplankton in coastal southern Florida, USA
type: item
type: AcademicArticle
description: Microzooplankton are considered the primary consumers of phytoplankton in marine environments. Microzooplankton grazing rates on phytoplankton have been studied across the globe, but there are still large regions of the ocean that are understudied, such as sub-tropical coastal oceans. One of these regions is the coastal area around south Florida, USA. We measured microzooplankton grazing rates in two distinct environments around south Florida; the oligotrophic Florida Keys and the mesotrophic outflow from the Everglades. For 2-years from January 2018 to January 2020, we set up 55 dilution and light-dark bottle experiments at five stations to estimate the microzooplankton community grazing rate, instantaneous phytoplankton growth rate, and primary production. Our results suggest that microzooplankton are consuming a higher proportion of the primary production near the Everglades outflow compared to the Florida Keys. We also found that changes in phytoplankton growth rates are disconnected from changes in the microzooplankton grazing rates in the Florida Keys. Overall, the data from the Everglades outflow is what would be expected based on global patterns, but factors other than microzooplankton grazing are more important in controlling phytoplankton biomass in the Florida Keys.
format: application/pdf
format: text/html
creator: Nicole Millette
creator: Christopher Kelble
creator: Ian Smith
creator: Kelly Montenero
creator: Elizabeth Harvey
subject: Ecosystem Science
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.13291
publisher: PeerJ Inc.
rights: © 2022 Millette et al.
abstract: Microzooplankton are considered the primary consumers of phytoplankton in marine environments. Microzooplankton grazing rates on phytoplankton have been studied across the globe, but there are still large regions of the ocean that are understudied, such as sub-tropical coastal oceans. One of these regions is the coastal area around south Florida, USA. We measured microzooplankton grazing rates in two distinct environments around south Florida; the oligotrophic Florida Keys and the mesotrophic outflow from the Everglades. For 2-years from January 2018 to January 2020, we set up 55 dilution and light-dark bottle experiments at five stations to estimate the microzooplankton community grazing rate, instantaneous phytoplankton growth rate, and primary production. Our results suggest that microzooplankton are consuming a higher proportion of the primary production near the Everglades outflow compared to the Florida Keys. We also found that changes in phytoplankton growth rates are disconnected from changes in the microzooplankton grazing rates in the Florida Keys. Overall, the data from the Everglades outflow is what would be expected based on global patterns, but factors other than microzooplankton grazing are more important in controlling phytoplankton biomass in the Florida Keys.
bibliographic citation: Millette et al. (2022) Spatial variability of microzooplankton grazing on phytoplankton in coastal southern Florida, USA. PeerJ 10:e13291 https://doi.org/10.7717/peerj.13291
date submitted: 2021-12-14
date accepted: 2022-03-28
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Millette
  given name: Nicole
author list: Agent
  family name: Kelble
  given name: Christopher
author list: Agent
  family name: Smith
  given name: Ian
author list: Agent
  family name: Montenero
  given name: Kelly
author list: Agent
  family name: Harvey
  given name: Elizabeth
doi: 10.7717/peerj.13291
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: © 2022 Millette et al.
attribution name: Millette et al.

Association between laryngopharyngeal reflux and obstructive sleep apnea in adults
type: item
type: AcademicArticle
description: Background Obstructive sleep apnea syndrome (OSAS) and laryngopharyngeal reflux (LPR) have been found to coexist in the population. OSAS and LPR also share obesity as an important risk factor. However, the relationship between LPR and OSAS remains unclear. This study aimed to correlate LPR as measured by the Reflux Symptom Index (RSI) and the Reflux Finding Score (RFS) with OSAS. Methods This cross-sectional study included sixty-four subjects who underwent anamnesis to complete the RSI and the Epworth Sleeping Scale (ESS). The subjects were then divided into the OSAS and non-OSAS groups based on the Apnea-Hypopnea Index (AHI) obtained through a polysomnography examination. Both groups underwent a flexible fiberoptic nasopharyngolaryngoscopy examination to determine the RFS. LPR was identified based on the RSI and RFS. Results The mean BMI of the OSAS group significantly was higher than the non-OSAS group (p < 0.05). Most of the subjects in the OSAS group exhibited mild-moderate OSAS (AHI 10–29), and severe OSAS occurred in only seven subjects. The mean RSI and RFS values in the OSAS group did not differ significantly from the non-OSAS group (p = 0.34 and p = 0.36, respectively). The proportion of LPR between the mild-moderate OSAS group, the severe OSAS group, and the non-OSAS group did not differ significantly (p = 1.00). RSI and RFS did not significantly correlate with AHI. Based on RSI, the proportion of LPR between the ESS (+) and ESS (-) groups did not significantly differ (adjusted p = 0.062). The proportion of LPR based on RFS was almost equal between the ESS (+) and ESS (-) groups (p = 0.817). Conclusions The BMI of the OSAS group was significantly higher than the non-OSAS group. There was no significant difference in RSI and RFS between the OSAS and non-OSAS groups. There was no significant correlation between RSI and AHI, or between RFS and AHI. There was no significant difference in the proportion of RSI between the ESS (+) and the ESS (-) groups.
format: application/pdf
format: text/html
creator: Susyana Tamin
creator: Dumasari Siregar
creator: Syahrial Marsinta Hutauruk
creator: Ratna Dwi Restuti
creator: Elvie Zulka Kautzia Rachmawati
creator: Saptawati Bardosono
subject: Gastroenterology and Hepatology
subject: Otorhinolaryngology
subject: Respiratory Medicine
subject: Obesity
description: doi:10.7717/peerj.13303
publisher: PeerJ Inc.
rights: © 2022 Tamin et al.
abstract: Background Obstructive sleep apnea syndrome (OSAS) and laryngopharyngeal reflux (LPR) have been found to coexist in the population. OSAS and LPR also share obesity as an important risk factor. However, the relationship between LPR and OSAS remains unclear. This study aimed to correlate LPR as measured by the Reflux Symptom Index (RSI) and the Reflux Finding Score (RFS) with OSAS. Methods This cross-sectional study included sixty-four subjects who underwent anamnesis to complete the RSI and the Epworth Sleeping Scale (ESS). The subjects were then divided into the OSAS and non-OSAS groups based on the Apnea-Hypopnea Index (AHI) obtained through a polysomnography examination. Both groups underwent a flexible fiberoptic nasopharyngolaryngoscopy examination to determine the RFS. LPR was identified based on the RSI and RFS. Results The mean BMI of the OSAS group significantly was higher than the non-OSAS group (p < 0.05). Most of the subjects in the OSAS group exhibited mild-moderate OSAS (AHI 10–29), and severe OSAS occurred in only seven subjects. The mean RSI and RFS values in the OSAS group did not differ significantly from the non-OSAS group (p = 0.34 and p = 0.36, respectively). The proportion of LPR between the mild-moderate OSAS group, the severe OSAS group, and the non-OSAS group did not differ significantly (p = 1.00). RSI and RFS did not significantly correlate with AHI. Based on RSI, the proportion of LPR between the ESS (+) and ESS (-) groups did not significantly differ (adjusted p = 0.062). The proportion of LPR based on RFS was almost equal between the ESS (+) and ESS (-) groups (p = 0.817). Conclusions The BMI of the OSAS group was significantly higher than the non-OSAS group. There was no significant difference in RSI and RFS between the OSAS and non-OSAS groups. There was no significant correlation between RSI and AHI, or between RFS and AHI. There was no significant difference in the proportion of RSI between the ESS (+) and the ESS (-) groups.
bibliographic citation: Tamin et al. (2022) Association between laryngopharyngeal reflux and obstructive sleep apnea in adults. PeerJ 10:e13303 https://doi.org/10.7717/peerj.13303
date submitted: 2022-01-03
date accepted: 2022-03-29
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tamin
  given name: Susyana
author list: Agent
  family name: Siregar
  given name: Dumasari
author list: Agent
  family name: Hutauruk
  given name: Syahrial Marsinta
author list: Agent
  family name: Restuti
  given name: Ratna Dwi
author list: Agent
  family name: Rachmawati
  given name: Elvie Zulka Kautzia
author list: Agent
  family name: Bardosono
  given name: Saptawati
doi: 10.7717/peerj.13303
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: ©2022 Tamin et al.
attribution name: Tamin et al.

Do patterns of insect mortality in temperate and tropical zones have broader implications for insect ecology and pest management?
type: item
type: AcademicArticle
description: Background Understanding how biotic and abiotic factors affect insect mortality is crucial for both fundamental knowledge of population ecology and for successful pest management. However, because these factors are difficult to quantify and interpret, patterns and dynamics of insect mortality remain unclear, especially comparative mortality across climate zones. Life table analysis provides robust information for quantifying population mortality and population parameters. Methods In this study, we estimated cause-of-death probabilities and irreplaceable mortality (the portion of mortality that cannot be replaced by another cause or combination of causes) using a Multiple Decrement Life Table (MDLT) analysis of 268 insect life tables from 107 peer-reviewed journal articles. In particular, we analyzed insect mortality between temperate and tropical climate zones. Results Surprisingly, our results suggest that non-natural enemy factors (abiotic) were the major source of insect mortality in both temperate and tropical zones. In addition, we observed that irreplaceable mortality from predators in tropical zones was 3.7-fold greater than in temperate zones. In contrast, irreplaceable mortality from parasitoids and pathogens was low and not different between temperate and tropical zones. Surprisingly, we did not observe differences in natural enemy and non-natural enemy factors based on whether the insect species was native or non-native. We suggest that characterizing predation should be a high priority in tropical conditions. Furthermore, because mortality from parasitoids was low in both tropical and temperate zones, this mortality needs to be better understood, especially as it relates to biological control and integrated pest management.
format: application/pdf
format: text/html
creator: José R. L. Pinto
creator: Odair A. Fernandes
creator: Leon G. Higley
creator: Robert K. D. Peterson
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.13340
publisher: PeerJ Inc.
rights: © 2022 Pinto et al.
abstract: Background Understanding how biotic and abiotic factors affect insect mortality is crucial for both fundamental knowledge of population ecology and for successful pest management. However, because these factors are difficult to quantify and interpret, patterns and dynamics of insect mortality remain unclear, especially comparative mortality across climate zones. Life table analysis provides robust information for quantifying population mortality and population parameters. Methods In this study, we estimated cause-of-death probabilities and irreplaceable mortality (the portion of mortality that cannot be replaced by another cause or combination of causes) using a Multiple Decrement Life Table (MDLT) analysis of 268 insect life tables from 107 peer-reviewed journal articles. In particular, we analyzed insect mortality between temperate and tropical climate zones. Results Surprisingly, our results suggest that non-natural enemy factors (abiotic) were the major source of insect mortality in both temperate and tropical zones. In addition, we observed that irreplaceable mortality from predators in tropical zones was 3.7-fold greater than in temperate zones. In contrast, irreplaceable mortality from parasitoids and pathogens was low and not different between temperate and tropical zones. Surprisingly, we did not observe differences in natural enemy and non-natural enemy factors based on whether the insect species was native or non-native. We suggest that characterizing predation should be a high priority in tropical conditions. Furthermore, because mortality from parasitoids was low in both tropical and temperate zones, this mortality needs to be better understood, especially as it relates to biological control and integrated pest management.
bibliographic citation: Pinto et al. (2022) Do patterns of insect mortality in temperate and tropical zones have broader implications for insect ecology and pest management?. PeerJ 10:e13340 https://doi.org/10.7717/peerj.13340
date submitted: 2021-12-09
date accepted: 2022-04-05
issued: 2022-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pinto
  given name: José R. L.
author list: Agent
  family name: Fernandes
  given name: Odair A.
author list: Agent
  family name: Higley
  given name: Leon G.
author list: Agent
  family name: Peterson
  given name: Robert K. D.
doi: 10.7717/peerj.13340
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-25
copyright: © 2022 Pinto et al.
attribution name: Pinto et al.

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

Agent
family name: D’Souza
given name: Michelle L.

Agent
family name: Mansoor
given name: Shahid

Agent
family name: Hebert
given name: Paul D. N.