PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Hub gene associated with prognosis in bladder cancer is a novel therapeutic target
items: Antifungal effects of eugenol on Candida albicans adherence to denture polymers
items: Life-expectancy changes during the COVID-19 pandemic from 2019–2021: estimates from Japan, a country with low pandemic impact
items: Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
items: LIDER: cell embedding based deep neural network classifier for supervised cell type identification
items: Effects of post-activation protocols based on slow tempo bodyweight squat and isometric activity on vertical jump height enhancement in trained males: a randomized controlled trial
items: Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids
items: Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings
items: Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma
items: Repetition velocity as a measure of loading intensity in the free weight and Smith machine Bulgarian split squat

Hub gene associated with prognosis in bladder cancer is a novel therapeutic target
type: item
type: AcademicArticle
description: Objective Bladder cancer is a clinical and social conundrum due to its high incidence and recurrence rate. It is urgent to find new targets for the diagnosis and treatment of bladder cancer and improve the prognosis and survival rate of bladder cancer patients. We sought a prognosis-related gene, built related models of evaluated bladder cancer and identified the function of the hub gene in bladder cancer. Methods We downloaded the data of bladder cancer patients from the TCGA database, and used differentially expressed genes (DEGs), copy number variation (CNV) and survival analysis to scan the hub genes associated with prognosis in bladder cancer. Then, multi-factor cox regression was used to obtain the bladder cancer prognosis correlation model. Then, we analyzed the relationship between the expression of hub gene and immune microenvironment of bladder cancer. The relationship between the expression of hub gene and prognosis in bladder cancer patients was verified by immunohistochemistry. Cell proliferation assay and drug sensitivity test in vivo were used to verify the inhibition of bladder cancer by targeted inhibitors. Results In bladder cancer, we screened seven hub genes (ACLY, CNP, NKIRAS2, P3H4, PDIA6, VPS25 and XPO1) associated with survival. Moreover, the multifactor regression model constructed with hub gene can well distinguish the prognosis of bladder cancer. Hub gene is mostly associated with immune microenvironment. Immunohistochemical results basically confirmed the importance of XPO1 in bladder cancer. Selinexor (an inhibitor of XPO1) could effectively inhibit the proliferation of bladder cancer in the cell proliferation experiments by CCK-8 assays and it could suppress the growth of bladder cancer in mouse bladder cancer model. Conclusions In this study, a prognostic model with seven hub genes has provided great help for the prognosis prediction of bladder cancer patients. And XPO1 is an important target affecting the prognosis of bladder cancer, …
format: application/pdf
format: text/html
creator: Dengpan Fang
creator: Yuanqiao He
creator: Yun Yi
creator: Jiaqi Mei
creator: Cundong Liu
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.15670
publisher: PeerJ Inc.
rights: © 2023 Fang et al.
abstract: Objective Bladder cancer is a clinical and social conundrum due to its high incidence and recurrence rate. It is urgent to find new targets for the diagnosis and treatment of bladder cancer and improve the prognosis and survival rate of bladder cancer patients. We sought a prognosis-related gene, built related models of evaluated bladder cancer and identified the function of the hub gene in bladder cancer. Methods We downloaded the data of bladder cancer patients from the TCGA database, and used differentially expressed genes (DEGs), copy number variation (CNV) and survival analysis to scan the hub genes associated with prognosis in bladder cancer. Then, multi-factor cox regression was used to obtain the bladder cancer prognosis correlation model. Then, we analyzed the relationship between the expression of hub gene and immune microenvironment of bladder cancer. The relationship between the expression of hub gene and prognosis in bladder cancer patients was verified by immunohistochemistry. Cell proliferation assay and drug sensitivity test in vivo were used to verify the inhibition of bladder cancer by targeted inhibitors. Results In bladder cancer, we screened seven hub genes (ACLY, CNP, NKIRAS2, P3H4, PDIA6, VPS25 and XPO1) associated with survival. Moreover, the multifactor regression model constructed with hub gene can well distinguish the prognosis of bladder cancer. Hub gene is mostly associated with immune microenvironment. Immunohistochemical results basically confirmed the importance of XPO1 in bladder cancer. Selinexor (an inhibitor of XPO1) could effectively inhibit the proliferation of bladder cancer in the cell proliferation experiments by CCK-8 assays and it could suppress the growth of bladder cancer in mouse bladder cancer model. Conclusions In this study, a prognostic model with seven hub genes has provided great help for the prognosis prediction of bladder cancer patients. And XPO1 is an important target affecting the prognosis of bladder cancer, …
bibliographic citation: Fang et al. (2023) Hub gene associated with prognosis in bladder cancer is a novel therapeutic target. PeerJ 11:e15670 https://doi.org/10.7717/peerj.15670
date submitted: 2023-03-27
date accepted: 2023-06-09
issued: 2023-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Dengpan
author list: Agent
  family name: He
  given name: Yuanqiao
author list: Agent
  family name: Yi
  given name: Yun
author list: Agent
  family name: Mei
  given name: Jiaqi
author list: Agent
  family name: Liu
  given name: Cundong
doi: 10.7717/peerj.15670
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-16
copyright: ©2023 Fang et al.
attribution name: Fang et al.

Antifungal effects of eugenol on Candida albicans adherence to denture polymers
type: item
type: AcademicArticle
description: Background The study’s objective is to assess the adherence of C. albicans in different types of denture polymers and the effectiveness of eugenol and commercialized denture cleansers in the removal of C. albicans. Three types of denture base polymers (Lucitone® 199 (High-Impact PMMA), Impact® (conventional PMMA) and Eclipse® (UDMA)) and two hard denture reline materials (Kooliner® and Tokuyama® Rebase II Fast) were used in this study. Methods Three hundred samples were prepared (6 × 2 mm disc shape) and divided into five groups of denture polymers (n = 60) and further subjected into five treatment groups (Polident®, Steradent, distilled water, eugenol 5-minutes, and eugenol 10-min). Three samples were extracted from each treatment group for baseline data (n = 12). Baseline data were used to calculate the initial number of C. albicans adherence. A 0.5 ml immersion solution from each specimen was cultured on YPD agar and incubated for 48 h at 37 °C. Visible colonies were counted using a colony counter machine (ROCKER Galaxy 230). Results The result showed that the denture base polymer significantly affected the initial adherence (p = 0.007). The removal of C. albicans was also considerably affected by the denture base polymers and denture cleansers (p < 0.05). Lucitone®, Tokuyama®, and Kooliner® denture base polymers immersed for 3 min in eugenol showed the best results of removal. Discussion This study’s overall results showed that all denture polymers used as denture bases had an effect on C. albicans initial adherence and removal from the denture base, and eugenol is comparable to commercialised denture cleansers in reducing the number of attached C. albicans on denture base polymers.
format: application/pdf
format: text/html
creator: Zubaidah Zanul Abidin
creator: Nosizana Mohd Salleh
creator: Wan Harun Himratul-Aznita
creator: Siti Fauzza Ahmad
creator: Ghee Seong Lim
creator: Noorhayati Raja Mohd
creator: Nabihah Dziaruddin
subject: Biochemistry
subject: Microbiology
subject: Mycology
subject: Dentistry
description: doi:10.7717/peerj.15750
publisher: PeerJ Inc.
rights: © 2023 Zanul Abidin et al.
abstract: Background The study’s objective is to assess the adherence of C. albicans in different types of denture polymers and the effectiveness of eugenol and commercialized denture cleansers in the removal of C. albicans. Three types of denture base polymers (Lucitone® 199 (High-Impact PMMA), Impact® (conventional PMMA) and Eclipse® (UDMA)) and two hard denture reline materials (Kooliner® and Tokuyama® Rebase II Fast) were used in this study. Methods Three hundred samples were prepared (6 × 2 mm disc shape) and divided into five groups of denture polymers (n = 60) and further subjected into five treatment groups (Polident®, Steradent, distilled water, eugenol 5-minutes, and eugenol 10-min). Three samples were extracted from each treatment group for baseline data (n = 12). Baseline data were used to calculate the initial number of C. albicans adherence. A 0.5 ml immersion solution from each specimen was cultured on YPD agar and incubated for 48 h at 37 °C. Visible colonies were counted using a colony counter machine (ROCKER Galaxy 230). Results The result showed that the denture base polymer significantly affected the initial adherence (p = 0.007). The removal of C. albicans was also considerably affected by the denture base polymers and denture cleansers (p < 0.05). Lucitone®, Tokuyama®, and Kooliner® denture base polymers immersed for 3 min in eugenol showed the best results of removal. Discussion This study’s overall results showed that all denture polymers used as denture bases had an effect on C. albicans initial adherence and removal from the denture base, and eugenol is comparable to commercialised denture cleansers in reducing the number of attached C. albicans on denture base polymers.
bibliographic citation: Zanul Abidin et al. (2023) Antifungal effects of eugenol on Candida albicans adherence to denture polymers. PeerJ 11:e15750 https://doi.org/10.7717/peerj.15750
date submitted: 2022-12-01
date accepted: 2023-06-22
issued: 2023-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zanul Abidin
  given name: Zubaidah
author list: Agent
  family name: Mohd Salleh
  given name: Nosizana
author list: Agent
  family name: Himratul-Aznita
  given name: Wan Harun
author list: Agent
  family name: Ahmad
  given name: Siti Fauzza
author list: Agent
  family name: Lim
  given name: Ghee Seong
author list: Agent
  family name: Raja Mohd
  given name: Noorhayati
author list: Agent
  family name: Dziaruddin
  given name: Nabihah
doi: 10.7717/peerj.15750
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-16
copyright: ©2023 Zanul Abidin et al.
attribution name: Zanul Abidin et al.

Life-expectancy changes during the COVID-19 pandemic from 2019–2021: estimates from Japan, a country with low pandemic impact
type: item
type: AcademicArticle
description: Background The COVID-19 pandemic had a low impact on Japan in 2020, but the size of the epidemic increased considerably there in 2021. This study made a statistical analysis of life expectancy changes up to the end of 2021 in Japan. Objective We aimed to estimate changes in life expectancy from 2019 to 2021 associated with the COVID-19 pandemic. To do so, we decomposed the life expectancy changes from 2020–2021 into age-specific and cause of death-specific contributions. Methods We used the absolute number of deaths by age and prefecture in Japan to calculate life expectancy from 2019–21 at both national and prefectural levels, and also examined the correlation between life expectancy gap and annual number of COVID-19 cases, total person-days spent in intensive care, and documented deaths due to COVID-19. We used the Arriaga decomposition method to decompose national life expectancy changes from 2020 to 2021 into age and cause of death components. Results From 2019–2020, Japan’s national level life expectancy across the entire population was extended by 0.24 years. From 2020–2021, it shortened by 0.15 years. The life expectancy shortened more among women (0.15 years) than men (0.12 years). There was significant heterogeneity in life expectancy changes from 2020–2021 by prefecture. It ranged from the maximum shortening of 0.57 years in Tottori prefecture to the maximum extension of 0.23 years in Fukui. The regression analysis revealed the negative correlation between the life expectancy change and burden of COVID-19 at prefectural level. The decomposition of life expectancy changes at birth from 2020–2021 showed that losses in life expectancy were largely attributable to the mortality of the population over 70 years old. Changes in life expectancy among infants and working-age adults mostly contributed to lengthening overall life expectancy. Among leading major causes of death, deaths due to neoplastic tumor and cardiovascular diseases contributed to shortening life …
format: application/pdf
format: text/html
creator: Mst Sirajum Munira
creator: Yuta Okada
creator: Hiroshi Nishiura
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.15784
publisher: PeerJ Inc.
rights: © 2023 Mst Sirajum Munira et al.
abstract: Background The COVID-19 pandemic had a low impact on Japan in 2020, but the size of the epidemic increased considerably there in 2021. This study made a statistical analysis of life expectancy changes up to the end of 2021 in Japan. Objective We aimed to estimate changes in life expectancy from 2019 to 2021 associated with the COVID-19 pandemic. To do so, we decomposed the life expectancy changes from 2020–2021 into age-specific and cause of death-specific contributions. Methods We used the absolute number of deaths by age and prefecture in Japan to calculate life expectancy from 2019–21 at both national and prefectural levels, and also examined the correlation between life expectancy gap and annual number of COVID-19 cases, total person-days spent in intensive care, and documented deaths due to COVID-19. We used the Arriaga decomposition method to decompose national life expectancy changes from 2020 to 2021 into age and cause of death components. Results From 2019–2020, Japan’s national level life expectancy across the entire population was extended by 0.24 years. From 2020–2021, it shortened by 0.15 years. The life expectancy shortened more among women (0.15 years) than men (0.12 years). There was significant heterogeneity in life expectancy changes from 2020–2021 by prefecture. It ranged from the maximum shortening of 0.57 years in Tottori prefecture to the maximum extension of 0.23 years in Fukui. The regression analysis revealed the negative correlation between the life expectancy change and burden of COVID-19 at prefectural level. The decomposition of life expectancy changes at birth from 2020–2021 showed that losses in life expectancy were largely attributable to the mortality of the population over 70 years old. Changes in life expectancy among infants and working-age adults mostly contributed to lengthening overall life expectancy. Among leading major causes of death, deaths due to neoplastic tumor and cardiovascular diseases contributed to shortening life …
bibliographic citation: Munira et al. (2023) Life-expectancy changes during the COVID-19 pandemic from 2019–2021: estimates from Japan, a country with low pandemic impact. PeerJ 11:e15784 https://doi.org/10.7717/peerj.15784
date submitted: 2023-03-23
date accepted: 2023-07-03
issued: 2023-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Munira
  given name: Mst Sirajum
author list: Agent
  family name: Okada
  given name: Yuta
author list: Agent
  family name: Nishiura
  given name: Hiroshi
doi: 10.7717/peerj.15784
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-16
copyright: © 2023 Mst Sirajum Munira et al.
attribution name: Mst Sirajum Munira et al.

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
type: item
type: AcademicArticle
description: Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
format: application/pdf
format: text/html
creator: Johan Rollin
creator: Rachelle Bester
creator: Yves Brostaux
creator: Kadriye Caglayan
creator: Kris De Jonghe
creator: Ales Eichmeier
creator: Yoika Foucart
creator: Annelies Haegeman
creator: Igor Koloniuk
creator: Petr Kominek
creator: Hans Maree
creator: Serkan Onder
creator: Susana Posada Céspedes
creator: Vahid Roumi
creator: Dana Šafářová
creator: Olivier Schumpp
creator: Cigdem Ulubas Serce
creator: Merike Sõmera
creator: Lucie Tamisier
creator: Eeva Vainio
creator: Rene AA van der Vlugt
creator: Sebastien Massart
subject: Bioinformatics
subject: Genomics
subject: Plant Science
subject: Virology
description: doi:10.7717/peerj.15816
publisher: PeerJ Inc.
rights: © 2023 Rollin et al.
abstract: Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
bibliographic citation: Rollin et al. (2023) Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies. PeerJ 11:e15816 https://doi.org/10.7717/peerj.15816
date submitted: 2023-02-20
date accepted: 2023-07-10
issued: 2023-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rollin
  given name: Johan
author list: Agent
  family name: Bester
  given name: Rachelle
author list: Agent
  family name: Brostaux
  given name: Yves
author list: Agent
  family name: Caglayan
  given name: Kadriye
author list: Agent
  family name: De Jonghe
  given name: Kris
author list: Agent
  family name: Eichmeier
  given name: Ales
author list: Agent
  family name: Foucart
  given name: Yoika
author list: Agent
  family name: Haegeman
  given name: Annelies
author list: Agent
  family name: Koloniuk
  given name: Igor
author list: Agent
  family name: Kominek
  given name: Petr
author list: Agent
  family name: Maree
  given name: Hans
author list: Agent
  family name: Onder
  given name: Serkan
author list: Agent
  family name: Posada Céspedes
  given name: Susana
author list: Agent
  family name: Roumi
  given name: Vahid
author list: Agent
  family name: Šafářová
  given name: Dana
author list: Agent
  family name: Schumpp
  given name: Olivier
author list: Agent
  family name: Ulubas Serce
  given name: Cigdem
author list: Agent
  family name: Sõmera
  given name: Merike
author list: Agent
  family name: Tamisier
  given name: Lucie
author list: Agent
  family name: Vainio
  given name: Eeva
author list: Agent
  family name: van der Vlugt
  given name: Rene AA
author list: Agent
  family name: Massart
  given name: Sebastien
doi: 10.7717/peerj.15816
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-16
copyright: © 2023 Rollin et al.
attribution name: Rollin et al.

LIDER: cell embedding based deep neural network classifier for supervised cell type identification
type: item
type: AcademicArticle
description: Background Automatic cell type identification has been an urgent task for the rapid development of single-cell RNA-seq techniques. Generally, the current approach for cell type identification is to generate cell clusters by unsupervised clustering and later assign labels to each cell cluster with manual annotation. Methods Here, we introduce LIDER (celL embeddIng based Deep nEural netwoRk classifier), a deep supervised learning method that combines cell embedding and deep neural network classifier for automatic cell type identification. Based on a stacked denoising autoencoder with a tailored and reconstructed loss function, LIDER identifies cell embedding and predicts cell types with a deep neural network classifier. LIDER was developed upon a stacked denoising autoencoder to learn encoder-decoder structures for identifying cell embedding. Results LIDER accurately identifies cell types by using stacked denoising autoencoder. Benchmarking against state-of-the-art methods across eight types of single-cell data, LIDER achieves comparable or even superior enhancement performance. Moreover, LIDER suggests comparable robust to batch effects. Our results show a potential in deep supervised learning for automatic cell type identification of single-cell RNA-seq data. The LIDER codes are available at https://github.com/ShiMGLab/LIDER.
format: application/pdf
format: text/html
creator: Yachen Tang
creator: Xuefeng Li
creator: Mingguang Shi
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
description: doi:10.7717/peerj.15862
publisher: PeerJ Inc.
rights: © 2023 Tang et al.
abstract: Background Automatic cell type identification has been an urgent task for the rapid development of single-cell RNA-seq techniques. Generally, the current approach for cell type identification is to generate cell clusters by unsupervised clustering and later assign labels to each cell cluster with manual annotation. Methods Here, we introduce LIDER (celL embeddIng based Deep nEural netwoRk classifier), a deep supervised learning method that combines cell embedding and deep neural network classifier for automatic cell type identification. Based on a stacked denoising autoencoder with a tailored and reconstructed loss function, LIDER identifies cell embedding and predicts cell types with a deep neural network classifier. LIDER was developed upon a stacked denoising autoencoder to learn encoder-decoder structures for identifying cell embedding. Results LIDER accurately identifies cell types by using stacked denoising autoencoder. Benchmarking against state-of-the-art methods across eight types of single-cell data, LIDER achieves comparable or even superior enhancement performance. Moreover, LIDER suggests comparable robust to batch effects. Our results show a potential in deep supervised learning for automatic cell type identification of single-cell RNA-seq data. The LIDER codes are available at https://github.com/ShiMGLab/LIDER.
bibliographic citation: Tang et al. (2023) LIDER: cell embedding based deep neural network classifier for supervised cell type identification. PeerJ 11:e15862 https://doi.org/10.7717/peerj.15862
date submitted: 2023-04-14
date accepted: 2023-07-17
issued: 2023-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Yachen
author list: Agent
  family name: Li
  given name: Xuefeng
author list: Agent
  family name: Shi
  given name: Mingguang
doi: 10.7717/peerj.15862
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-16
copyright: ©2023 Tang et al.
attribution name: Tang et al.

Effects of post-activation protocols based on slow tempo bodyweight squat and isometric activity on vertical jump height enhancement in trained males: a randomized controlled trial
type: item
type: AcademicArticle
description: This study aimed to establish the effectiveness of slow tempo bodyweight squat combined with an isometric squat (ST-ISO), and an isometric squat alone (ISO), as a post-activation performance enhancement protocol (PAPE) for jump height improvement. The study sample consisted of 41 trained men aged 18–24. The ST-ISO group (n = 17) performed three five-second sets of the maximal voluntary back squat while pushing on an immovable bar and two sets of five repetitions of a slow-tempo (5-0-5-0) body squat immediately after isometry with a 2-m rest interval. The ISO (n = 14) group only performed isometric squats, and the control group (CG; n = 10) performed a 5-min treadmill run at 6 km/h. The countermovement jump (CMJ) height results were analyzed from the baseline and then at 3, 5, 7, and 9 min after the PAPE protocols. The statistical significance was set at p < 0.05. RM-ANOVA revealed differences in the group-minute interaction (F = 2.70; p = 0.0083; η2 = 0.1243), and post-hoc tests demonstrated a significant decrease in CMJ after 5 min in the ISO group (p < 0.0446). The performance of the ST-ISO group markedly decreased in the 3rd and 7th min after PAPE (p = 0.0137; p = 0.0424, respectively), though it improved significantly in the final minute (p < 0.0030). Chi-squared analysis revealed that the ST-ISO group peaked more frequently in the 9th min (X2 = 17.97; p = 0.0214). However, CMJ height improvement did not differ between the PAPE protocols, thus it was close to statistical significance (t = −1.82; p = 0.07; ES = 0.7). The ST-ISO protocol provided jump enhancement, though the deterioration observed in the first minutes after the protocols suggest the rest period after activity requires attention, and the methods need to be individualized.
format: application/pdf
format: text/html
creator: Dawid Koźlenia
creator: Jarosław Domaradzki
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.15753
publisher: PeerJ Inc.
rights: © 2023 Koźlenia and Domaradzki
abstract: This study aimed to establish the effectiveness of slow tempo bodyweight squat combined with an isometric squat (ST-ISO), and an isometric squat alone (ISO), as a post-activation performance enhancement protocol (PAPE) for jump height improvement. The study sample consisted of 41 trained men aged 18–24. The ST-ISO group (n = 17) performed three five-second sets of the maximal voluntary back squat while pushing on an immovable bar and two sets of five repetitions of a slow-tempo (5-0-5-0) body squat immediately after isometry with a 2-m rest interval. The ISO (n = 14) group only performed isometric squats, and the control group (CG; n = 10) performed a 5-min treadmill run at 6 km/h. The countermovement jump (CMJ) height results were analyzed from the baseline and then at 3, 5, 7, and 9 min after the PAPE protocols. The statistical significance was set at p < 0.05. RM-ANOVA revealed differences in the group-minute interaction (F = 2.70; p = 0.0083; η2 = 0.1243), and post-hoc tests demonstrated a significant decrease in CMJ after 5 min in the ISO group (p < 0.0446). The performance of the ST-ISO group markedly decreased in the 3rd and 7th min after PAPE (p = 0.0137; p = 0.0424, respectively), though it improved significantly in the final minute (p < 0.0030). Chi-squared analysis revealed that the ST-ISO group peaked more frequently in the 9th min (X2 = 17.97; p = 0.0214). However, CMJ height improvement did not differ between the PAPE protocols, thus it was close to statistical significance (t = −1.82; p = 0.07; ES = 0.7). The ST-ISO protocol provided jump enhancement, though the deterioration observed in the first minutes after the protocols suggest the rest period after activity requires attention, and the methods need to be individualized.
bibliographic citation: Koźlenia et al. (2023) Effects of post-activation protocols based on slow tempo bodyweight squat and isometric activity on vertical jump height enhancement in trained males: a randomized controlled trial. PeerJ 11:e15753 https://doi.org/10.7717/peerj.15753
date submitted: 2023-03-20
date accepted: 2023-06-23
issued: 2023-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koźlenia
  given name: Dawid
author list: Agent
  family name: Domaradzki
  given name: Jarosław
doi: 10.7717/peerj.15753
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-15
copyright: © 2023 Koźlenia and Domaradzki
attribution name: Koźlenia and Domaradzki

Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids
type: item
type: AcademicArticle
description: Background The Australian citrus industry remains one of the few in the world to be unaffected by the African and the Asian citrus psyllids, Trioza erytreae Del Guercio and Diaphorina citri Kuwayama, respectively, and the diseases their vectored bacteria can cause. Surveillance, early detection, and strict quarantine measures are therefore fundamental to safeguard Australian citrus. However, long-term targeted surveillance for exotic citrus pests can be a time-consuming and expensive activity, often relying on manually screening large numbers of trap samples and morphological identification of specimens, which requires a high level of taxonomic knowledge. Methods Here we evaluated the use of non-destructive insect metabarcoding for exotic pest surveillance in citrus orchards. We conducted an 11-week field trial, between the months of December and February, at a horticultural research farm (SuniTAFE Smart Farm) in the Northwest of Victoria, Australia, and processed more than 250 samples collected from three types of invertebrate traps across four sites. Results The whole-community metabarcoding data enabled comparisons between different trapping methods, demonstrated the spatial variation of insect diversity across the same orchard, and highlighted how comprehensive assessment of insect biodiversity requires use of multiple complimentary trapping methods. In addition to revealing the diversity of native psyllid species in citrus orchards, the non-targeted metabarcoding approach identified a diversity of other pest and beneficial insects and arachnids within the trap bycatch, and recorded the presence of the triozid Casuarinicola cf warrigalensis for the first time in Victoria. Ultimately, this work highlights how a non-targeted surveillance approach for insect monitoring coupled with non-destructive DNA metabarcoding can provide accurate and high-throughput species identification for biosecurity and biodiversity monitoring.
format: application/pdf
format: text/html
creator: Francesco Martoni
creator: Reannon Smith
creator: Alexander M. Piper
creator: Jessica Lye
creator: Conrad Trollip
creator: Brendan C. Rodoni
creator: Mark J. Blacket
subject: Agricultural Science
subject: Biodiversity
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15831
publisher: PeerJ Inc.
rights: © 2023 Martoni et al.
abstract: Background The Australian citrus industry remains one of the few in the world to be unaffected by the African and the Asian citrus psyllids, Trioza erytreae Del Guercio and Diaphorina citri Kuwayama, respectively, and the diseases their vectored bacteria can cause. Surveillance, early detection, and strict quarantine measures are therefore fundamental to safeguard Australian citrus. However, long-term targeted surveillance for exotic citrus pests can be a time-consuming and expensive activity, often relying on manually screening large numbers of trap samples and morphological identification of specimens, which requires a high level of taxonomic knowledge. Methods Here we evaluated the use of non-destructive insect metabarcoding for exotic pest surveillance in citrus orchards. We conducted an 11-week field trial, between the months of December and February, at a horticultural research farm (SuniTAFE Smart Farm) in the Northwest of Victoria, Australia, and processed more than 250 samples collected from three types of invertebrate traps across four sites. Results The whole-community metabarcoding data enabled comparisons between different trapping methods, demonstrated the spatial variation of insect diversity across the same orchard, and highlighted how comprehensive assessment of insect biodiversity requires use of multiple complimentary trapping methods. In addition to revealing the diversity of native psyllid species in citrus orchards, the non-targeted metabarcoding approach identified a diversity of other pest and beneficial insects and arachnids within the trap bycatch, and recorded the presence of the triozid Casuarinicola cf warrigalensis for the first time in Victoria. Ultimately, this work highlights how a non-targeted surveillance approach for insect monitoring coupled with non-destructive DNA metabarcoding can provide accurate and high-throughput species identification for biosecurity and biodiversity monitoring.
bibliographic citation: Martoni et al. (2023) Non-destructive insect metabarcoding for surveillance and biosecurity in citrus orchards: recording the good, the bad and the psyllids. PeerJ 11:e15831 https://doi.org/10.7717/peerj.15831
date submitted: 2023-05-02
date accepted: 2023-07-11
issued: 2023-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martoni
  given name: Francesco
author list: Agent
  family name: Smith
  given name: Reannon
author list: Agent
  family name: Piper
  given name: Alexander M.
author list: Agent
  family name: Lye
  given name: Jessica
author list: Agent
  family name: Trollip
  given name: Conrad
author list: Agent
  family name: Rodoni
  given name: Brendan C.
author list: Agent
  family name: Blacket
  given name: Mark J.
doi: 10.7717/peerj.15831
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-15
copyright: © 2023 Martoni et al.
attribution name: Martoni et al.

Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings
type: item
type: AcademicArticle
description: Transmission of Chlamydia pecorum between koalas is a potential risk in field capture or rehabilitation settings, where koalas are held in proximity to each other, or equipment is shared between animals. Given the impact of C. pecorum on koala welfare and population viability it is surprising that quarantine and disinfection protocols in a koala rehabilitation facility or capture settings have not previously been evaluated. This study aimed to evaluate an approach, based on the detection of chlamydial DNA and cell viability, to determine the degree of environmental contamination within a koala care facility. Various fomite sites associated with koala care at a koala rehabilitation facility in New South Wales, Australia were identified as potential sources of chlamydial contamination, following exposure to koalas known to be infected with C. pecorum. Fomite sites were swabbed following exposure, and again after decontamination procedures were carried out. Samples were tested for the presence of chlamydial DNA using qPCR and viability using both RT-qPCR and cell culture. From a total of 239 sampling events, 30 tested qPCR positive for chlamydial DNA, with 19 and 11 samples corresponding to pre-decontamination and post-decontamination events respectively. Detection of chlamydial DNA appeared to be most common in the examination room, especially on fomite sites in direct contact with koalas. Physical removal of chlamydial DNA, or its degradation by the elements, appeared to be more common on outdoor enclosures, clothing, and hands. Based on the cell culture assay, of the pre-decontamination samples with chlamydial DNA, eight had viable chlamydial cells, two of these at low levels. Of the post-decontamination samples with chlamydial DNA, one had a moderate number, and one had a very low number of viable chlamydial cells. RT-qPCR was unsuccessful in determining cell viability due to low yields of RNA and high levels of contaminants from the environmental samples. The outc…
format: application/pdf
format: text/html
creator: Andrea Casteriano
creator: Astrid Robin Van Aggelen
creator: Shali Fischer
creator: Cheyne Flanagan
creator: Caroline Marschner
creator: Hannah Nugent
creator: Wilhelmina Huston
creator: Damien P. Higgins
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.15842
publisher: PeerJ Inc.
rights: © 2023 Casteriano et al.
abstract: Transmission of Chlamydia pecorum between koalas is a potential risk in field capture or rehabilitation settings, where koalas are held in proximity to each other, or equipment is shared between animals. Given the impact of C. pecorum on koala welfare and population viability it is surprising that quarantine and disinfection protocols in a koala rehabilitation facility or capture settings have not previously been evaluated. This study aimed to evaluate an approach, based on the detection of chlamydial DNA and cell viability, to determine the degree of environmental contamination within a koala care facility. Various fomite sites associated with koala care at a koala rehabilitation facility in New South Wales, Australia were identified as potential sources of chlamydial contamination, following exposure to koalas known to be infected with C. pecorum. Fomite sites were swabbed following exposure, and again after decontamination procedures were carried out. Samples were tested for the presence of chlamydial DNA using qPCR and viability using both RT-qPCR and cell culture. From a total of 239 sampling events, 30 tested qPCR positive for chlamydial DNA, with 19 and 11 samples corresponding to pre-decontamination and post-decontamination events respectively. Detection of chlamydial DNA appeared to be most common in the examination room, especially on fomite sites in direct contact with koalas. Physical removal of chlamydial DNA, or its degradation by the elements, appeared to be more common on outdoor enclosures, clothing, and hands. Based on the cell culture assay, of the pre-decontamination samples with chlamydial DNA, eight had viable chlamydial cells, two of these at low levels. Of the post-decontamination samples with chlamydial DNA, one had a moderate number, and one had a very low number of viable chlamydial cells. RT-qPCR was unsuccessful in determining cell viability due to low yields of RNA and high levels of contaminants from the environmental samples. The outc…
bibliographic citation: Casteriano et al. (2023) Evaluation of a biosecurity survey approach for contamination by Chlamydia pecorum in koala rehabilitation, field capture, and captive settings. PeerJ 11:e15842 https://doi.org/10.7717/peerj.15842
date submitted: 2023-03-26
date accepted: 2023-07-12
issued: 2023-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Casteriano
  given name: Andrea
author list: Agent
  family name: Van Aggelen
  given name: Astrid Robin
author list: Agent
  family name: Fischer
  given name: Shali
author list: Agent
  family name: Flanagan
  given name: Cheyne
author list: Agent
  family name: Marschner
  given name: Caroline
author list: Agent
  family name: Nugent
  given name: Hannah
author list: Agent
  family name: Huston
  given name: Wilhelmina
author list: Agent
  family name: Higgins
  given name: Damien P.
doi: 10.7717/peerj.15842
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-15
copyright: © 2023 Casteriano et al.
attribution name: Casteriano et al.

Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma
type: item
type: AcademicArticle
description: Background Sexual selection and conflicts within and between sexes promote morphological diversity of reproductive traits within species. Variation in the morphology of diagnostic reproductive characters within species offer an excellent opportunity to study these evolutionary processes as drivers of species diversification. The African monarch, Danaus chrysippus (Linnaeus, 1758), is widespread across Africa. The species is polytypic, with the respective geographical ranges of the four colour morphs only overlapping in East Africa. Furthermore, some of the populations host an endosymbiotic bacterium, Spiroplasma, which induces son-killing and distorts the local host population sex-ratio, creating sexual conflicts between the females seeking to optimize their fecundity and the limited mating capacity of the rare males. Methods We dissected females from Kenya, Rwanda and South Africa, where Spiroplasma vary in presence and prevalence (high, variable and absent, respectively), and conducted microscopy imaging of their reproductive organs. We then characterized the effect of population, female body size, and female mating status, on the size and shape of different genitalia characters of the D. chrysippus female butterflies. Results We showed that although the general morphology of the organs is conserved in D. chrysippus, female genitalia vary in size and shape between and within populations. The virgin females have smaller organs, while the same organs were expanded in mated females. Females from highly female-biased populations, where the male-killing Spiroplasma is prevalent, also have a larger area of their corpus bursae covered with signa structures. However, this pattern occurs because a larger proportion of the females remains virgin in the female-biased populations rather than because of male depletion due to the symbiont, as males from sex-ratio distorted populations did not produce significantly smaller nutritious spermatophores.
format: application/pdf
format: text/html
creator: Jenny Malmberg
creator: Simon H. Martin
creator: Ian J. Gordon
creator: Pasi Sihvonen
creator: Anne Duplouy
subject: Entomology
subject: Evolutionary Studies
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15853
publisher: PeerJ Inc.
rights: © 2023 Malmberg et al.
abstract: Background Sexual selection and conflicts within and between sexes promote morphological diversity of reproductive traits within species. Variation in the morphology of diagnostic reproductive characters within species offer an excellent opportunity to study these evolutionary processes as drivers of species diversification. The African monarch, Danaus chrysippus (Linnaeus, 1758), is widespread across Africa. The species is polytypic, with the respective geographical ranges of the four colour morphs only overlapping in East Africa. Furthermore, some of the populations host an endosymbiotic bacterium, Spiroplasma, which induces son-killing and distorts the local host population sex-ratio, creating sexual conflicts between the females seeking to optimize their fecundity and the limited mating capacity of the rare males. Methods We dissected females from Kenya, Rwanda and South Africa, where Spiroplasma vary in presence and prevalence (high, variable and absent, respectively), and conducted microscopy imaging of their reproductive organs. We then characterized the effect of population, female body size, and female mating status, on the size and shape of different genitalia characters of the D. chrysippus female butterflies. Results We showed that although the general morphology of the organs is conserved in D. chrysippus, female genitalia vary in size and shape between and within populations. The virgin females have smaller organs, while the same organs were expanded in mated females. Females from highly female-biased populations, where the male-killing Spiroplasma is prevalent, also have a larger area of their corpus bursae covered with signa structures. However, this pattern occurs because a larger proportion of the females remains virgin in the female-biased populations rather than because of male depletion due to the symbiont, as males from sex-ratio distorted populations did not produce significantly smaller nutritious spermatophores.
bibliographic citation: Malmberg et al. (2023) Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma. PeerJ 11:e15853 https://doi.org/10.7717/peerj.15853
date submitted: 2023-03-17
date accepted: 2023-07-16
issued: 2023-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malmberg
  given name: Jenny
author list: Agent
  family name: Martin
  given name: Simon H.
author list: Agent
  family name: Gordon
  given name: Ian J.
author list: Agent
  family name: Sihvonen
  given name: Pasi
author list: Agent
  family name: Duplouy
  given name: Anne
doi: 10.7717/peerj.15853
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-15
copyright: © 2023 Malmberg et al.
attribution name: Malmberg et al.

Repetition velocity as a measure of loading intensity in the free weight and Smith machine Bulgarian split squat
type: item
type: AcademicArticle
description: This study investigated the grouped and individualized load-velocity profile (GLVP vs. ILVP) in Bulgarian split squat using Smith machine and free weight. Seventy five recreational male lifters completed two incremental loading tests of Bulgarian split squat. Mean velocity was measured by a linear-position transducer (GymAware). Linear regression equation was applied to construct the GLVP and ILVP. The agreement of predicted %1RM and measured %1RM was assessed by a combination of intraclass correlation coefficient (ICC), coefficient of variation (CV), standard error of measurement (SEM) and Bland-Altman analysis. Acceptable validity was defined as ICC > 0.75, CV ≤ 10% and p ≥ 0.05 (a paired Wilcoxon signed-rank test). A very high level of inverse load-velocity relationships were demonstrated in Bulgarian split squat (r = − 0.92) with free weights and a Smith machine. ILVP (ICC ≥ 0.98, CV ≤ 8.73%, p ≥ 0.56) was valid enough to predict the %1RM, but GLVP of both limbs revealed large CVs in free weights (CV: 15.4%,15.63%) and a Smith machine (CV: 11.24%, 12.25%). Cross-validation between the actual %1RM and predicted %1RM using free weights and a Smith machine ILVP was not acceptable (p ≤ 0.03, CV ≥ 14.07%). A very high level of inverse relationship were observed between %1RM and MV in Bulgarian split squat using free weights and a Smith machine, indicating individualized load velocity properties, and the ILVP showed high between-devices variability in both scenarios. Using velocity as a measure of loading intensity in Bulgarian split squat needs to consider the individualized load velocity properties, and difference between free weights and a Smith machine.
format: application/pdf
format: text/html
creator: Kaifang Liao
creator: Chao Bian
creator: Zhili Chen
creator: Zhihang Yuan
creator: Chris Bishop
creator: Mengyuan Han
creator: Yongming Li
creator: Yong Zheng
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.15863
publisher: PeerJ Inc.
rights: © 2023 Liao et al.
abstract: This study investigated the grouped and individualized load-velocity profile (GLVP vs. ILVP) in Bulgarian split squat using Smith machine and free weight. Seventy five recreational male lifters completed two incremental loading tests of Bulgarian split squat. Mean velocity was measured by a linear-position transducer (GymAware). Linear regression equation was applied to construct the GLVP and ILVP. The agreement of predicted %1RM and measured %1RM was assessed by a combination of intraclass correlation coefficient (ICC), coefficient of variation (CV), standard error of measurement (SEM) and Bland-Altman analysis. Acceptable validity was defined as ICC > 0.75, CV ≤ 10% and p ≥ 0.05 (a paired Wilcoxon signed-rank test). A very high level of inverse load-velocity relationships were demonstrated in Bulgarian split squat (r = − 0.92) with free weights and a Smith machine. ILVP (ICC ≥ 0.98, CV ≤ 8.73%, p ≥ 0.56) was valid enough to predict the %1RM, but GLVP of both limbs revealed large CVs in free weights (CV: 15.4%,15.63%) and a Smith machine (CV: 11.24%, 12.25%). Cross-validation between the actual %1RM and predicted %1RM using free weights and a Smith machine ILVP was not acceptable (p ≤ 0.03, CV ≥ 14.07%). A very high level of inverse relationship were observed between %1RM and MV in Bulgarian split squat using free weights and a Smith machine, indicating individualized load velocity properties, and the ILVP showed high between-devices variability in both scenarios. Using velocity as a measure of loading intensity in Bulgarian split squat needs to consider the individualized load velocity properties, and difference between free weights and a Smith machine.
bibliographic citation: Liao et al. (2023) Repetition velocity as a measure of loading intensity in the free weight and Smith machine Bulgarian split squat. PeerJ 11:e15863 https://doi.org/10.7717/peerj.15863
date submitted: 2023-02-10
date accepted: 2023-07-17
issued: 2023-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Kaifang
author list: Agent
  family name: Bian
  given name: Chao
author list: Agent
  family name: Chen
  given name: Zhili
author list: Agent
  family name: Yuan
  given name: Zhihang
author list: Agent
  family name: Bishop
  given name: Chris
author list: Agent
  family name: Han
  given name: Mengyuan
author list: Agent
  family name: Li
  given name: Yongming
author list: Agent
  family name: Zheng
  given name: Yong
doi: 10.7717/peerj.15863
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-15
copyright: ©2023 Liao et al.
attribution name: Liao et al.

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