PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study
items: CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1
items: Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores
items: Cryophysiology of coral microfragments: effects of chilling and cryoprotectant toxicity
items: Digital competence of faculty members in health sciences measured via self-reflection: current status and contextual aspects
items: Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly
items: Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus
items: YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines
items: Stable dominance of parasitic dinoflagellates in Antarctic sponges
items: Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance

Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study
type: item
type: AcademicArticle
description: Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
format: application/pdf
format: text/html
creator: Yang Xiao
creator: Lina Han
creator: Han Wang
creator: Guorong Lyu
creator: Shilin Li
subject: Andrology
subject: Oncology
subject: Pathology
subject: Radiology and Medical Imaging
subject: Urology
description: doi:10.7717/peerj.18424
publisher: PeerJ Inc.
rights: © 2024 Xiao et al.
abstract: Background Prostate biopsies are primarily conducted using either the transrectal or transperineal approach, with the ultrasound probe positioned in the rectum to obtain a clear view of the prostate. Reports on the utilization of transperineal prostate biopsies with the ultrasound probe placed on the perineal skin are limited. Methods A retrospective investigation was conducted on 119 patients who underwent transperineal ultrasound guided transperineal prostate biopsy (TP-TPPB). Additionally, 85 patients who underwent transrectal ultrasound guided transperineal prostate biopsy (TR-TPPB) were included as controls. The prostate cancer detection rates (PCDRs) and postoperative complication rates were compared between the two groups, and their application values were also evaluated. Results The overall PCDRs were 35.3% (42/119) in the TP-TPPB and 32.9% (28/85) in the TR-TPPB group (χ2 = 0.122, p = 0.727). When categorized by PSA level, there was no significant difference between the two groups in PCDRs in any category (p > 0.05). However, the single-needle PCDRs in some regions (L4, L5, R2, and apex) showed significant differences (p < 0.05). There was no difference in postoperative complication rates between the groups. Conclusion The PCDRs and the postoperative complication rates of TP-TPPB and TR-TPPB are similar. However, TP-TPPB requires simpler equipment and does not require intestinal preparation, which is especially useful for patients with rectal contraindications, such as those with severe hemorrhoids and rectal/anal diseases.
bibliographic citation: Xiao et al. (2024) Transperineal prostate biopsy guided by which ultrasound transducer: transrectal or transperineal: a retrospective study. PeerJ 12:e18424 https://doi.org/10.7717/peerj.18424
date submitted: 2024-04-15
date accepted: 2024-10-08
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Yang
author list: Agent
  family name: Han
  given name: Lina
author list: Agent
  family name: Wang
  given name: Han
author list: Agent
  family name: Lyu
  given name: Guorong
author list: Agent
  family name: Li
  given name: Shilin
doi: 10.7717/peerj.18424
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: ©2024 Xiao et al.
attribution name: Xiao et al.

CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1
type: item
type: AcademicArticle
description: Background Cancer-associated fibroblasts (CAFs) and hepatocellular carcinoma (HCC) cells interact to promote HCC progression, but the underlying mechanisms remain unclear. Serpin family E member 1 (SERPINE1) has conflicting roles in HCC, and microRNAs (miRNAs) are known to regulate tumor progression through intercellular communication. Therefore, we investigated the potential involvement of miRNA/SERPINE1 axis in crosstalk between CAFs and HCC cells. Methods In this study, candidate miRNAs targeting SERPINE1 3′ UTR were predicted using multiple miRNA databases. The miRNAs and SERPINE1 mRNA expression in Huh7 cells was assessed after co-culture with CAFs using RT-qPCR. Huh7 cell proliferation and invasion were detected after SERPINE1 siRNA. The functions of the CAF-derived miR-642a-3p/SERPINE1 axis in HCC cells were examined using CCK-8, wound healing, transwell assays, western blot, and dual-luciferase reporter assays. Moreover, a orthotopic xenograft model was used to investigate the contribution of miR-642a-3p knockdown in HCC. Results SERPINE1 mRNA expression decreased, while miR-642a-3p expression increased in Huh7 cells co-cultured with CAFs. SERPINE1 knockdown enhanced Huh7 cell proliferation and invasion as well as miR-642a-3p expression. miR-642a-3p overexpression promoted migration, invasion, and epithelial-mesenchymal transition (EMT) in Huh7 cells by targeting SERPINE1, while miR-642a-3p knockdown yielded the opposite effect. Rescue experiments confirmed that SERPINE1 knockdown attenuated the inhibitory effects of miR-642a-3p knockdown on migration, invasion, and EMT in Huh7 cells. Importantly, miR-642a-3p knockdown suppressed growth and EMT in orthotopic liver tumors. Conclusion CAF-derived miR-642a-3p/SERPINE1 axis facilitated migration, invasion, and EMT in the HCC cells, suggesting miR-642a-3p/SERPINE1 axis can be a potential therapeutic target for HCC.
format: application/pdf
format: text/html
creator: Shuo Zhang
creator: Gang Cao
creator: Shuijie Shen
creator: Yu Wu
creator: Xiying Tan
creator: Xiaoyan Jiang
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.18428
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Cancer-associated fibroblasts (CAFs) and hepatocellular carcinoma (HCC) cells interact to promote HCC progression, but the underlying mechanisms remain unclear. Serpin family E member 1 (SERPINE1) has conflicting roles in HCC, and microRNAs (miRNAs) are known to regulate tumor progression through intercellular communication. Therefore, we investigated the potential involvement of miRNA/SERPINE1 axis in crosstalk between CAFs and HCC cells. Methods In this study, candidate miRNAs targeting SERPINE1 3′ UTR were predicted using multiple miRNA databases. The miRNAs and SERPINE1 mRNA expression in Huh7 cells was assessed after co-culture with CAFs using RT-qPCR. Huh7 cell proliferation and invasion were detected after SERPINE1 siRNA. The functions of the CAF-derived miR-642a-3p/SERPINE1 axis in HCC cells were examined using CCK-8, wound healing, transwell assays, western blot, and dual-luciferase reporter assays. Moreover, a orthotopic xenograft model was used to investigate the contribution of miR-642a-3p knockdown in HCC. Results SERPINE1 mRNA expression decreased, while miR-642a-3p expression increased in Huh7 cells co-cultured with CAFs. SERPINE1 knockdown enhanced Huh7 cell proliferation and invasion as well as miR-642a-3p expression. miR-642a-3p overexpression promoted migration, invasion, and epithelial-mesenchymal transition (EMT) in Huh7 cells by targeting SERPINE1, while miR-642a-3p knockdown yielded the opposite effect. Rescue experiments confirmed that SERPINE1 knockdown attenuated the inhibitory effects of miR-642a-3p knockdown on migration, invasion, and EMT in Huh7 cells. Importantly, miR-642a-3p knockdown suppressed growth and EMT in orthotopic liver tumors. Conclusion CAF-derived miR-642a-3p/SERPINE1 axis facilitated migration, invasion, and EMT in the HCC cells, suggesting miR-642a-3p/SERPINE1 axis can be a potential therapeutic target for HCC.
bibliographic citation: Zhang et al. (2024) CAF-derived miR-642a-3p supports migration, invasion, and EMT of hepatocellular carcinoma cells by targeting SERPINE1. PeerJ 12:e18428 https://doi.org/10.7717/peerj.18428
date submitted: 2024-06-07
date accepted: 2024-10-08
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shuo
author list: Agent
  family name: Cao
  given name: Gang
author list: Agent
  family name: Shen
  given name: Shuijie
author list: Agent
  family name: Wu
  given name: Yu
author list: Agent
  family name: Tan
  given name: Xiying
author list: Agent
  family name: Jiang
  given name: Xiaoyan
doi: 10.7717/peerj.18428
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores
type: item
type: AcademicArticle
description: The mammalian adult dentition is a non-renewable resource. Tooth attrition and disease must be accommodated by individuals using behavioral, physiological, and/or musculoskeletal shifts to minimize impact on masticatory performance. From a biomechanical perspective, the musculoskeletal system becomes less efficient at producing bite force for a given amount of muscle input force over an individual’s life, because tooth-food contact area increases as cusps wear. In this study we ask the question: does mandibular biomechanical performance show evidence of compensation with increasing tooth wear? We use representative taxa of three carnivoran ecomorphologies (meat specialist, scavenger, bone cracker) as a study system to compare morphofunctional data on tooth macrowear, jaw depth, bite mechanical efficiency, and jaw stress during biting. No significant shifts in adult mandibular corpus dimensions occurs in the sampled taxa as canine and carnassial teeth wear. In bone cracking spotted hyenas carnassial biting mechanical efficiency increases significantly with increasing tooth wear, with no significant change in mandibular stress. Analyses of the fossil carnivore Hyaenodon suggests an increase in canine biting efficiency with increased tooth wear, but this may reflect interspecific variation or phylogenetic contingency rather than a life history shift. Overall, these findings indicate that scavenging hyaenids and felid meat specialists do not exhibit morphofunctional compensation for the decreased mechanical capability of worn and dull teeth. Behavioral modifications, rather than musculoskeletal adjustments, may instead play a major role in maintaining food acquisition and processing capabilities for individuals surviving into advanced ontogenetic age and tooth wear. These observations highlight the mammalian masticatory system as having a dynamic performance profile through its useful lifespan, and encourage a more nuanced understanding of past and present carnivore gui…
format: application/pdf
format: text/html
creator: Z. Jack Tseng
creator: Larisa R. G. DeSantis
subject: Paleontology
subject: Zoology
subject: Biomechanics
description: doi:10.7717/peerj.18435
publisher: PeerJ Inc.
rights: © 2024 Tseng and DeSantis
abstract: The mammalian adult dentition is a non-renewable resource. Tooth attrition and disease must be accommodated by individuals using behavioral, physiological, and/or musculoskeletal shifts to minimize impact on masticatory performance. From a biomechanical perspective, the musculoskeletal system becomes less efficient at producing bite force for a given amount of muscle input force over an individual’s life, because tooth-food contact area increases as cusps wear. In this study we ask the question: does mandibular biomechanical performance show evidence of compensation with increasing tooth wear? We use representative taxa of three carnivoran ecomorphologies (meat specialist, scavenger, bone cracker) as a study system to compare morphofunctional data on tooth macrowear, jaw depth, bite mechanical efficiency, and jaw stress during biting. No significant shifts in adult mandibular corpus dimensions occurs in the sampled taxa as canine and carnassial teeth wear. In bone cracking spotted hyenas carnassial biting mechanical efficiency increases significantly with increasing tooth wear, with no significant change in mandibular stress. Analyses of the fossil carnivore Hyaenodon suggests an increase in canine biting efficiency with increased tooth wear, but this may reflect interspecific variation or phylogenetic contingency rather than a life history shift. Overall, these findings indicate that scavenging hyaenids and felid meat specialists do not exhibit morphofunctional compensation for the decreased mechanical capability of worn and dull teeth. Behavioral modifications, rather than musculoskeletal adjustments, may instead play a major role in maintaining food acquisition and processing capabilities for individuals surviving into advanced ontogenetic age and tooth wear. These observations highlight the mammalian masticatory system as having a dynamic performance profile through its useful lifespan, and encourage a more nuanced understanding of past and present carnivore gui…
bibliographic citation: Tseng et al. (2024) Relationship between tooth macrowear and jaw morphofunctional traits in representative hypercarnivores. PeerJ 12:e18435 https://doi.org/10.7717/peerj.18435
date submitted: 2024-08-28
date accepted: 2024-10-10
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tseng
  given name: Z. Jack
author list: Agent
  family name: DeSantis
  given name: Larisa R. G.
doi: 10.7717/peerj.18435
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Tseng and DeSantis
attribution name: Tseng and DeSantis

Cryophysiology of coral microfragments: effects of chilling and cryoprotectant toxicity
type: item
type: AcademicArticle
description: Coral reefs are being degraded at alarming rates and decisive intervention actions are urgently needed. One such intervention is coral cryopreservation. Although the cryopreservation of coral sperm and larvae has been achieved, preservation of coral fragments including both its tissue and skeleton, has not. The overarching aim of this study was to understand and assess the physiological stressors that might underlie coral fragment cryopreservation, understand the long-term consequences of these exposures to continued growth, and develop a health metrics scale for future research. Therefore, we assessed small fragments (~1 cm2) from the Hawaiian coral, Porites compressa, examining: (1) chill sensitivity; (2) chemical sensitivity to complex cryoprotectants; (3) methods to safely remove algal symbionts of coral for cryopreservation; (4) continued growth over time of coral fragments exposed to chilling and cryoprotectants; and (5) assessment of health and viability of coral fragments post the applied treatments. Corals were able to withstand chilling to 0 °C for 1 min and after 2 weeks were not significantly different from the live controls, whereas, corals exposed to complex cryoprotectants needed 3 weeks of recovery. Most importantly, it appears that once the coral fragments had surpassed this initial recovery, there was no difference in subsequent growth. Technological advances in cryo-technology promise to support successful coral fragment cryopreservation soon, and its success could help secure much of the genetic and biodiversity of reefs in the next decade.
format: application/pdf
format: text/html
creator: Claire V. A. Lager
creator: Riley Perry
creator: Jonathan Daly
creator: Christopher Page
creator: Mindy Mizobe
creator: Jessica Bouwmeester
creator: Anthony N. Consiglio
creator: Jake Carter
creator: Matthew J. Powell-Palm
creator: Mary Hagedorn
subject: Cell Biology
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.18447
publisher: PeerJ Inc.
rights: © 2024 Lager et al.
abstract: Coral reefs are being degraded at alarming rates and decisive intervention actions are urgently needed. One such intervention is coral cryopreservation. Although the cryopreservation of coral sperm and larvae has been achieved, preservation of coral fragments including both its tissue and skeleton, has not. The overarching aim of this study was to understand and assess the physiological stressors that might underlie coral fragment cryopreservation, understand the long-term consequences of these exposures to continued growth, and develop a health metrics scale for future research. Therefore, we assessed small fragments (~1 cm2) from the Hawaiian coral, Porites compressa, examining: (1) chill sensitivity; (2) chemical sensitivity to complex cryoprotectants; (3) methods to safely remove algal symbionts of coral for cryopreservation; (4) continued growth over time of coral fragments exposed to chilling and cryoprotectants; and (5) assessment of health and viability of coral fragments post the applied treatments. Corals were able to withstand chilling to 0 °C for 1 min and after 2 weeks were not significantly different from the live controls, whereas, corals exposed to complex cryoprotectants needed 3 weeks of recovery. Most importantly, it appears that once the coral fragments had surpassed this initial recovery, there was no difference in subsequent growth. Technological advances in cryo-technology promise to support successful coral fragment cryopreservation soon, and its success could help secure much of the genetic and biodiversity of reefs in the next decade.
bibliographic citation: Lager et al. (2024) Cryophysiology of coral microfragments: effects of chilling and cryoprotectant toxicity. PeerJ 12:e18447 https://doi.org/10.7717/peerj.18447
date submitted: 2024-03-22
date accepted: 2024-10-14
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lager
  given name: Claire V. A.
author list: Agent
  family name: Perry
  given name: Riley
author list: Agent
  family name: Daly
  given name: Jonathan
author list: Agent
  family name: Page
  given name: Christopher
author list: Agent
  family name: Mizobe
  given name: Mindy
author list: Agent
  family name: Bouwmeester
  given name: Jessica
author list: Agent
  family name: Consiglio
  given name: Anthony N.
author list: Agent
  family name: Carter
  given name: Jake
author list: Agent
  family name: Powell-Palm
  given name: Matthew J.
author list: Agent
  family name: Hagedorn
  given name: Mary
doi: 10.7717/peerj.18447
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Lager et al.
attribution name: Lager et al.

Digital competence of faculty members in health sciences measured via self-reflection: current status and contextual aspects
type: item
type: AcademicArticle
description: This descriptive study aims to determine the digital competence level of faculty members who teach in the health sciences, empirically considering possible contextual aspects. Two data collection instruments were used: a self-reflection questionnaire to assess digital competence, and a survey querying demographics and aspects of teaching and learning context. In total, 306 health sciences faculty members from six universities voluntarily participated the study. The results revealed that a majority of the faculty members have intermediate (integrator or expert) level of digital competence, which is described as being aware of the potential use of digital technology in teaching and having a personal repertoire for its use under various circumstances. Age, digital teaching experience, perception of work environment, and previous teaching experience in fully- or partially-online courses were identified as influencing factors for digital competence. Faculty members in health sciences were able to integrate digital technologies in their teaching practices. Health education institutions may facilitate the use of digital technologies in teaching and learning environments. Moreover, institutions or stakeholders should consider that digital competence requires practice and experience in meaningfully-designed digital environments and tools.
format: application/pdf
format: text/html
creator: Halil Ersoy
creator: Cigdem Baskici
creator: Aydan Aytar
creator: Raimonds Strods
creator: Nora Jansone Ratinika
creator: António Manuel Lopes Fernandes
creator: Hugo Neves
creator: Aurelija Blaževičienė
creator: Alina Vaškelytė
creator: Camilla Wikström-Grotell
creator: Heikki Paakkonen
creator: Anne Söderlund
creator: Johanna Fritz
creator: Sultan Kav
subject: Global Health
subject: Health Policy
subject: Nursing
subject: Science and Medical Education
description: doi:10.7717/peerj.18456
publisher: PeerJ Inc.
rights: © 2024 Ersoy et al.
abstract: This descriptive study aims to determine the digital competence level of faculty members who teach in the health sciences, empirically considering possible contextual aspects. Two data collection instruments were used: a self-reflection questionnaire to assess digital competence, and a survey querying demographics and aspects of teaching and learning context. In total, 306 health sciences faculty members from six universities voluntarily participated the study. The results revealed that a majority of the faculty members have intermediate (integrator or expert) level of digital competence, which is described as being aware of the potential use of digital technology in teaching and having a personal repertoire for its use under various circumstances. Age, digital teaching experience, perception of work environment, and previous teaching experience in fully- or partially-online courses were identified as influencing factors for digital competence. Faculty members in health sciences were able to integrate digital technologies in their teaching practices. Health education institutions may facilitate the use of digital technologies in teaching and learning environments. Moreover, institutions or stakeholders should consider that digital competence requires practice and experience in meaningfully-designed digital environments and tools.
bibliographic citation: Ersoy et al. (2024) Digital competence of faculty members in health sciences measured via self-reflection: current status and contextual aspects. PeerJ 12:e18456 https://doi.org/10.7717/peerj.18456
date submitted: 2023-09-08
date accepted: 2024-10-14
issued: 2024-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ersoy
  given name: Halil
author list: Agent
  family name: Baskici
  given name: Cigdem
author list: Agent
  family name: Aytar
  given name: Aydan
author list: Agent
  family name: Strods
  given name: Raimonds
author list: Agent
  family name: Jansone Ratinika
  given name: Nora
author list: Agent
  family name: Manuel Lopes Fernandes
  given name: António
author list: Agent
  family name: Neves
  given name: Hugo
author list: Agent
  family name: Blaževičienė
  given name: Aurelija
author list: Agent
  family name: Vaškelytė
  given name: Alina
author list: Agent
  family name: Wikström-Grotell
  given name: Camilla
author list: Agent
  family name: Paakkonen
  given name: Heikki
author list: Agent
  family name: Söderlund
  given name: Anne
author list: Agent
  family name: Fritz
  given name: Johanna
author list: Agent
  family name: Kav
  given name: Sultan
doi: 10.7717/peerj.18456
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-11
copyright: © 2024 Ersoy et al.
attribution name: Ersoy et al.

Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly
type: item
type: AcademicArticle
description: Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics–particularly coding gene content and read recruitment profiles–were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses.
format: application/pdf
format: text/html
creator: Garrett J. Smith
creator: Theo A. van Alen
creator: Maartje A.H.J. van Kessel
creator: Sebastian Lücker
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.18132
publisher: PeerJ Inc.
rights: © 2024 Smith et al.
abstract: Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics–particularly coding gene content and read recruitment profiles–were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses.
bibliographic citation: Smith et al. (2024) Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly. PeerJ 12:e18132 https://doi.org/10.7717/peerj.18132
date submitted: 2023-09-18
date accepted: 2024-08-29
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Garrett J.
author list: Agent
  family name: van Alen
  given name: Theo A.
author list: Agent
  family name: van Kessel
  given name: Maartje A.H.J.
author list: Agent
  family name: Lücker
  given name: Sebastian
doi: 10.7717/peerj.18132
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: ©2024 Smith et al.
attribution name: Smith et al.

Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus
type: item
type: AcademicArticle
description: A new species of Helicascus satunensis sp. nov. was collected on mature dead fruits of the Nypa palm in Satun Province, southern Thailand. Its morphological characteristics are similar to those of the genus Helicascus. Recently, a genus Helicascus with three species from marine habitats worldwide was studied. The morphology of this fungus was investigated and combined with multigene sequence analyzes of small subunit (SSU), large subunit (LSU), internal transcribed spacer (ITS) ribosomal DNA, translation elongation factor 1-alpha (TEF-1α) and RNA polymerase II (RPB2) genes. Morphologically, H. satunensis sp. nov. is characterized by semi-immersed, lenticular ascomata, multilocules, a bitunicate ascus and smooth, obovoid, dark brown ascospores that are one-septate and unequally two-celled. In addition, 3D visualization using synchrotron X-ray tomography was performed to investigate the interaction between fruiting body and substrata. Molecular phylogeny with multigene revealed that H. satunensis sp. nov. belongs to the family Morosphaeriaceae, order Pleosporales, class Dothideomycetes. Furthermore, H. satunensis sp. nov. forms a well-supported clade with Helicascus species described from marine habitats. Based on the unique morphological and molecular evidence, we propose this fungus, H. satunensis sp. nov., as a new species for Helicascus.
format: application/pdf
format: text/html
creator: Sita Preedanon
creator: Anupong Klaysuban
creator: Satinee Suetrong
creator: Oraphin Pracharoen
creator: Waratthaya Promchoo
creator: Tanuwong Sangtiean
creator: Catleya Rojviriya
creator: Jariya Sakayaroj
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.18341
publisher: PeerJ Inc.
rights: © 2024 Preedanon et al.
abstract: A new species of Helicascus satunensis sp. nov. was collected on mature dead fruits of the Nypa palm in Satun Province, southern Thailand. Its morphological characteristics are similar to those of the genus Helicascus. Recently, a genus Helicascus with three species from marine habitats worldwide was studied. The morphology of this fungus was investigated and combined with multigene sequence analyzes of small subunit (SSU), large subunit (LSU), internal transcribed spacer (ITS) ribosomal DNA, translation elongation factor 1-alpha (TEF-1α) and RNA polymerase II (RPB2) genes. Morphologically, H. satunensis sp. nov. is characterized by semi-immersed, lenticular ascomata, multilocules, a bitunicate ascus and smooth, obovoid, dark brown ascospores that are one-septate and unequally two-celled. In addition, 3D visualization using synchrotron X-ray tomography was performed to investigate the interaction between fruiting body and substrata. Molecular phylogeny with multigene revealed that H. satunensis sp. nov. belongs to the family Morosphaeriaceae, order Pleosporales, class Dothideomycetes. Furthermore, H. satunensis sp. nov. forms a well-supported clade with Helicascus species described from marine habitats. Based on the unique morphological and molecular evidence, we propose this fungus, H. satunensis sp. nov., as a new species for Helicascus.
bibliographic citation: Preedanon et al. (2024) Morphological, molecular and 3D synchrotron X-ray tomographic characterizations of Helicascus satunensis sp. nov., a novel mangrove fungus. PeerJ 12:e18341 https://doi.org/10.7717/peerj.18341
date submitted: 2024-07-17
date accepted: 2024-09-26
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Preedanon
  given name: Sita
author list: Agent
  family name: Klaysuban
  given name: Anupong
author list: Agent
  family name: Suetrong
  given name: Satinee
author list: Agent
  family name: Pracharoen
  given name: Oraphin
author list: Agent
  family name: Promchoo
  given name: Waratthaya
author list: Agent
  family name: Sangtiean
  given name: Tanuwong
author list: Agent
  family name: Rojviriya
  given name: Catleya
author list: Agent
  family name: Sakayaroj
  given name: Jariya
doi: 10.7717/peerj.18341
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: ©2024 Preedanon et al.
attribution name: Preedanon et al.

YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines
type: item
type: AcademicArticle
description: Background The Internet has transformed global information access, particularly through platforms like YouTube, which launched in 1995 and has since become the second largest search engine worldwide with over two billion monthly users. While YouTube offers extensive educational content, including health topics like cardiopulmonary resuscitation (CPR) and basic life support (BLS), it also poses risks due to potential misinformation. Our study focuses on evaluating the accuracy of CPR and BLS videos on YouTube according to the latest 2020 American Heart Association (AHA) guidelines. This research aims to highlight inconsistencies and provide insights into improving YouTube as a reliable educational resource for both lay rescuers and healthcare professionals. Methods In this cross-sectional observational study, English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were searched using keywords related to CPR and basic life support. Videos were assessed for their source, duration, views, use of human or mannequin models, and mean assessment scores by two emergency medicine physicians. A third physician’s opinion was sought in cases of disagreement. The first assessment evaluated video validity based on specified information criteria, while the second assessed their ability to convey advanced medical information aligned with the 2020 AHA guidelines. Results In this study, 201 English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were evaluated based on search terms related to CPR and BLS, resulting in 95 videos meeting inclusion criteria after excluding 106 due to various reasons. Most included videos were from healthcare professionals (49.5%), followed by anonymous sources (29.5%) and official medical organizations (21.1%). Video durations ranged widely from 43 to 6,019 seconds, with an average of 692 seconds. Videos featuring mannequins predominated (91.6%), followed by those using human subjects (5.3%) or both (3.2%). Healthcar…
format: application/pdf
format: text/html
creator: Merve Yazla
creator: Tuba Şafak
creator: Şakir Hakan Aksu
creator: Kadiriye Savran
creator: Rafet Fatih Aydogan
creator: Mustafa Arslan
creator: Abdullah Osman Koçak
creator: Burak Katipoğlu
subject: Emergency and Critical Care
subject: Public Health
description: doi:10.7717/peerj.18344
publisher: PeerJ Inc.
rights: © 2024 Yazla et al.
abstract: Background The Internet has transformed global information access, particularly through platforms like YouTube, which launched in 1995 and has since become the second largest search engine worldwide with over two billion monthly users. While YouTube offers extensive educational content, including health topics like cardiopulmonary resuscitation (CPR) and basic life support (BLS), it also poses risks due to potential misinformation. Our study focuses on evaluating the accuracy of CPR and BLS videos on YouTube according to the latest 2020 American Heart Association (AHA) guidelines. This research aims to highlight inconsistencies and provide insights into improving YouTube as a reliable educational resource for both lay rescuers and healthcare professionals. Methods In this cross-sectional observational study, English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were searched using keywords related to CPR and basic life support. Videos were assessed for their source, duration, views, use of human or mannequin models, and mean assessment scores by two emergency medicine physicians. A third physician’s opinion was sought in cases of disagreement. The first assessment evaluated video validity based on specified information criteria, while the second assessed their ability to convey advanced medical information aligned with the 2020 AHA guidelines. Results In this study, 201 English YouTube videos uploaded between October 21, 2020, and May 1, 2023, were evaluated based on search terms related to CPR and BLS, resulting in 95 videos meeting inclusion criteria after excluding 106 due to various reasons. Most included videos were from healthcare professionals (49.5%), followed by anonymous sources (29.5%) and official medical organizations (21.1%). Video durations ranged widely from 43 to 6,019 seconds, with an average of 692 seconds. Videos featuring mannequins predominated (91.6%), followed by those using human subjects (5.3%) or both (3.2%). Healthcar…
bibliographic citation: Yazla et al. (2024) YouTube as a source of information in cardiopulmonary resuscitation for 2020 AHA Resuscitation Guidelines. PeerJ 12:e18344 https://doi.org/10.7717/peerj.18344
date submitted: 2024-07-01
date accepted: 2024-09-26
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yazla
  given name: Merve
author list: Agent
  family name: Şafak
  given name: Tuba
author list: Agent
  family name: Aksu
  given name: Şakir Hakan
author list: Agent
  family name: Savran
  given name: Kadiriye
author list: Agent
  family name: Aydogan
  given name: Rafet Fatih
author list: Agent
  family name: Arslan
  given name: Mustafa
author list: Agent
  family name: Koçak
  given name: Abdullah Osman
author list: Agent
  family name: Katipoğlu
  given name: Burak
doi: 10.7717/peerj.18344
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: ©2024 Yazla et al.
attribution name: Yazla et al.

Stable dominance of parasitic dinoflagellates in Antarctic sponges
type: item
type: AcademicArticle
description: Background Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies. Results The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges. Conclusions The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.
format: application/pdf
format: text/html
creator: Marileyxis R. López-Rodríguez
creator: Catherine Gérikas Ribeiro
creator: Susana Rodríguez-Marconi
creator: Génesis Parada-Pozo
creator: Maria Manrique-de-la-Cuba
creator: Nicole Trefault
subject: Biodiversity
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.18365
publisher: PeerJ Inc.
rights: © 2024 López-Rodríguez et al.
abstract: Background Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies. Results The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges. Conclusions The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.
bibliographic citation: López-Rodríguez et al. (2024) Stable dominance of parasitic dinoflagellates in Antarctic sponges. PeerJ 12:e18365 https://doi.org/10.7717/peerj.18365
date submitted: 2024-06-24
date accepted: 2024-09-29
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: López-Rodríguez
  given name: Marileyxis R.
author list: Agent
  family name: Gérikas Ribeiro
  given name: Catherine
author list: Agent
  family name: Rodríguez-Marconi
  given name: Susana
author list: Agent
  family name: Parada-Pozo
  given name: Génesis
author list: Agent
  family name: Manrique-de-la-Cuba
  given name: Maria
author list: Agent
  family name: Trefault
  given name: Nicole
doi: 10.7717/peerj.18365
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: © 2024 López-Rodríguez et al.
attribution name: López-Rodríguez et al.

Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance
type: item
type: AcademicArticle
description: We investigated the convergent validity and intrasession reliability of force, velocity, and power (FVP) variables and the dynamic strength index (DSI) obtained from isometric midthigh pull (IMTP) and squat jump (SJ) testing. Fifteen male combat sports athletes (27 ± 5 years, 77 ± 9 kg, 1.76 ± 0.1 m, 14 ± 6% body fat) participated in a 2-days study. The first day involved testing familiarization, while the second was dedicated to IMTP and SJ testing. Maximal isometric force (Fiso) was obtained from IMTP, while mean force, mean velocity, jump height, and jump impulse (J) were gathered from SJ. To analyze the FVP, we calculated the linear relationship between force and velocity, which allowed us to obtain the slope of the relationship (SFV), the theoretical velocity at zero force (V0), and the theoretical maximal power (Pmax). DSI was obtained as a ratio from SJ peak force and Fiso. The convergent validity was investigated using Spearman’s ρ coefficients to assess the relationships between jump height and J with Fiso, V0, SFV, Pmax, and DSI. The intrasession reliability was assessed using intraclass correlation coefficients (ICC) and coefficient of variations (CV). All variables demonstrated acceptable reliability scores. ICC ranged from moderate to excellent, and the mean CV was <10%. We found a “very large” correlation between jump J and Pmax, while jump height was not correlated with any variable. In conclusion, the IMTP and SJ combination is a practical way to determine FVP producing capacities that can be reliably measured (intrasession). The Pmax, derived from FVP, was correlated with jump performance, which might evidence the convergent validity of the method.
format: application/pdf
format: text/html
creator: Amilton Vieira
creator: Rafael Cunha
creator: Carlos Gonçalves
creator: Juliano Dal Pupo
creator: James Tufano
subject: Kinesiology
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.18371
publisher: PeerJ Inc.
rights: © 2024 Vieira et al.
abstract: We investigated the convergent validity and intrasession reliability of force, velocity, and power (FVP) variables and the dynamic strength index (DSI) obtained from isometric midthigh pull (IMTP) and squat jump (SJ) testing. Fifteen male combat sports athletes (27 ± 5 years, 77 ± 9 kg, 1.76 ± 0.1 m, 14 ± 6% body fat) participated in a 2-days study. The first day involved testing familiarization, while the second was dedicated to IMTP and SJ testing. Maximal isometric force (Fiso) was obtained from IMTP, while mean force, mean velocity, jump height, and jump impulse (J) were gathered from SJ. To analyze the FVP, we calculated the linear relationship between force and velocity, which allowed us to obtain the slope of the relationship (SFV), the theoretical velocity at zero force (V0), and the theoretical maximal power (Pmax). DSI was obtained as a ratio from SJ peak force and Fiso. The convergent validity was investigated using Spearman’s ρ coefficients to assess the relationships between jump height and J with Fiso, V0, SFV, Pmax, and DSI. The intrasession reliability was assessed using intraclass correlation coefficients (ICC) and coefficient of variations (CV). All variables demonstrated acceptable reliability scores. ICC ranged from moderate to excellent, and the mean CV was <10%. We found a “very large” correlation between jump J and Pmax, while jump height was not correlated with any variable. In conclusion, the IMTP and SJ combination is a practical way to determine FVP producing capacities that can be reliably measured (intrasession). The Pmax, derived from FVP, was correlated with jump performance, which might evidence the convergent validity of the method.
bibliographic citation: Vieira et al. (2024) Force-velocity-power variables derived from isometric and dynamic testing: metrics reliability and the relationship with jump performance. PeerJ 12:e18371 https://doi.org/10.7717/peerj.18371
date submitted: 2024-04-24
date accepted: 2024-09-30
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Amilton
author list: Agent
  family name: Cunha
  given name: Rafael
author list: Agent
  family name: Gonçalves
  given name: Carlos
author list: Agent
  family name: Dal Pupo
  given name: Juliano
author list: Agent
  family name: Tufano
  given name: James
doi: 10.7717/peerj.18371
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: © 2024 Vieira et al.
attribution name: Vieira et al.

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