PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis
items: Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections
items: The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation
items: Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022
items: High variability in the attractiveness of municipally-planted decorative plants to insects

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.

Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis
type: item
type: AcademicArticle
description: Background Phragmites australis is a common foundation species found in inland and brackish estuarine ecosystems. P. australis stands provide a wide range of habitats for wetland organisms and perform essential functions, such as nutrient cycling, pollutant filtration, wave energy reduction, and soil stabilization. However, excessive growth of P. australis can degrade the quality of wetland habitats, thereby reducing the functions of restored wetlands. Methods In this study, we investigated the effectiveness of vegetation management techniques, such as aboveground cutting and temporal inundation with varying depth and periodicity, in controlling the growth performance of P. australis and adjacent vegetation, Bolboschoenus planiculmis. Differences in growth responses to manipulated inundation stress between P. australis and B. planiculmis were measured. Results Inundation stress of 10–50 cm caused significantly greater inhibition of growth performance in B. planiculmis compared to P. australis. The combination of aboveground-cutting and inundation treatments resulted in a significant inhibitory effect on the growth performance and survival rate of P. australis. The growth performance of P. australis, including stem volume and biomass, decreased and its mortality rate increased. Our manipulated experiment suggests a combined treatment approach of moderate inundation, such as 5–10 cm for 20–30 days, and aboveground cutting to manage the overgrowth of P. australis in restored brackish wetlands.
format: application/pdf
format: text/html
creator: Hee-Sun Park
creator: Ji Yoon Kim
creator: Gu-Yeon Kim
creator: Hyunbin Jo
creator: Gea-Jae Joo
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.18402
publisher: PeerJ Inc.
rights: © 2024 Park et al.
abstract: Background Phragmites australis is a common foundation species found in inland and brackish estuarine ecosystems. P. australis stands provide a wide range of habitats for wetland organisms and perform essential functions, such as nutrient cycling, pollutant filtration, wave energy reduction, and soil stabilization. However, excessive growth of P. australis can degrade the quality of wetland habitats, thereby reducing the functions of restored wetlands. Methods In this study, we investigated the effectiveness of vegetation management techniques, such as aboveground cutting and temporal inundation with varying depth and periodicity, in controlling the growth performance of P. australis and adjacent vegetation, Bolboschoenus planiculmis. Differences in growth responses to manipulated inundation stress between P. australis and B. planiculmis were measured. Results Inundation stress of 10–50 cm caused significantly greater inhibition of growth performance in B. planiculmis compared to P. australis. The combination of aboveground-cutting and inundation treatments resulted in a significant inhibitory effect on the growth performance and survival rate of P. australis. The growth performance of P. australis, including stem volume and biomass, decreased and its mortality rate increased. Our manipulated experiment suggests a combined treatment approach of moderate inundation, such as 5–10 cm for 20–30 days, and aboveground cutting to manage the overgrowth of P. australis in restored brackish wetlands.
bibliographic citation: Park et al. (2024) Combined effect of temporal inundation and aboveground-cutting on the growth performance of two emergent wetland plants, Phragmites australis and Bolboschoenus planiculmis. PeerJ 12:e18402 https://doi.org/10.7717/peerj.18402
date submitted: 2024-02-28
date accepted: 2024-10-04
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Park
  given name: Hee-Sun
author list: Agent
  family name: Kim
  given name: Ji Yoon
author list: Agent
  family name: Kim
  given name: Gu-Yeon
author list: Agent
  family name: Jo
  given name: Hyunbin
author list: Agent
  family name: Joo
  given name: Gea-Jae
doi: 10.7717/peerj.18402
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: © 2024 Park et al.
attribution name: Park et al.

Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections
type: item
type: AcademicArticle
description: Background Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses. Methods In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology. Results A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively. Conclusion Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood culture…
format: application/pdf
format: text/html
creator: Xinyuan Liu
creator: Zhitao Gan
creator: Zengshun Lin
creator: Xiaojun Lin
creator: Jianying Yuan
creator: Lili Rong
creator: Jiachang Chen
creator: Jun Liu
creator: Yingzhen Li
creator: Chaohui Hu
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Hematology
subject: Infectious Diseases
description: doi:10.7717/peerj.18471
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses. Methods In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology. Results A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively. Conclusion Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood culture…
bibliographic citation: Liu et al. (2024) Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections. PeerJ 12:e18471 https://doi.org/10.7717/peerj.18471
date submitted: 2024-04-11
date accepted: 2024-10-15
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xinyuan
author list: Agent
  family name: Gan
  given name: Zhitao
author list: Agent
  family name: Lin
  given name: Zengshun
author list: Agent
  family name: Lin
  given name: Xiaojun
author list: Agent
  family name: Yuan
  given name: Jianying
author list: Agent
  family name: Rong
  given name: Lili
author list: Agent
  family name: Chen
  given name: Jiachang
author list: Agent
  family name: Liu
  given name: Jun
author list: Agent
  family name: Li
  given name: Yingzhen
author list: Agent
  family name: Hu
  given name: Chaohui
doi: 10.7717/peerj.18471
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: ©2024 Liu et al.
attribution name: Liu et al.

The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation
type: item
type: AcademicArticle
description: Background Breast cancer (BC) is one of most frequent female malignancies that poses multiple challenges in treatment and prevention. This study aimed to explore the role of miRNAs and their target genes during the BC progression. Methods Based on the BC data (113 normal and 1,118 tumor samples) from the TCGA-BRCA dataset, a single-sample gene set enrichment analysis (ssGSEA) was applied to calculate the cancer migration scores, and weighted gene co-expression network analysis (WGCNA) were performed using the WGCNA R package, with a focus on the set of genes associated with cancer migration. Key modules and hub genes related to cell migration and signaling pathways were identified. Survival analysis of hub genes was conducted using the survminer R package, and prediction of regulatory miRNAs were performed to analyze their impact on BC prognosis. In addition, the BC cell lines MCF-7 and MDA-MB-231 were used to further explore the effect of hsa-miR-1972 mimics on the gene expression and angiogenic factor regulation. Results The study classified important modules (MEblue, MEmagenta, MEpink, and MEfloralwhite) associated with cell migration and identified three hub genes, namely, MRPL20, COL4A1 and VWF. Survival analysis showed that certain hub genes with a low expression were related to a poor prognosis, whereas low-expressed COL4A1 and VWF were related to better survival outcomes. We also found that hsa-miR-1972 mimics significantly downregulated critical genes involved in BC metastasis and angiogenesis and effectively inhibited the proliferation of BC cell lines, showing a strong therapeutic potential. Manipulation of VWF expression in cells overexpressing hsa-miR-1972 had significant effects on the malignant markers and angiogenic factors, suggesting a novel therapeutic direction for BC treatment. Conclusion Our study highlighted the complex interplay of genetic factors in BC progression as well as the therapeutic potential of targeting specific miRNAs and their re…
format: application/pdf
format: text/html
creator: Changjiang Yu
creator: Tao Zhang
creator: Fan Chen
creator: Zhenyang Yu
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.18476
publisher: PeerJ Inc.
rights: © 2024 Yu et al.
abstract: Background Breast cancer (BC) is one of most frequent female malignancies that poses multiple challenges in treatment and prevention. This study aimed to explore the role of miRNAs and their target genes during the BC progression. Methods Based on the BC data (113 normal and 1,118 tumor samples) from the TCGA-BRCA dataset, a single-sample gene set enrichment analysis (ssGSEA) was applied to calculate the cancer migration scores, and weighted gene co-expression network analysis (WGCNA) were performed using the WGCNA R package, with a focus on the set of genes associated with cancer migration. Key modules and hub genes related to cell migration and signaling pathways were identified. Survival analysis of hub genes was conducted using the survminer R package, and prediction of regulatory miRNAs were performed to analyze their impact on BC prognosis. In addition, the BC cell lines MCF-7 and MDA-MB-231 were used to further explore the effect of hsa-miR-1972 mimics on the gene expression and angiogenic factor regulation. Results The study classified important modules (MEblue, MEmagenta, MEpink, and MEfloralwhite) associated with cell migration and identified three hub genes, namely, MRPL20, COL4A1 and VWF. Survival analysis showed that certain hub genes with a low expression were related to a poor prognosis, whereas low-expressed COL4A1 and VWF were related to better survival outcomes. We also found that hsa-miR-1972 mimics significantly downregulated critical genes involved in BC metastasis and angiogenesis and effectively inhibited the proliferation of BC cell lines, showing a strong therapeutic potential. Manipulation of VWF expression in cells overexpressing hsa-miR-1972 had significant effects on the malignant markers and angiogenic factors, suggesting a novel therapeutic direction for BC treatment. Conclusion Our study highlighted the complex interplay of genetic factors in BC progression as well as the therapeutic potential of targeting specific miRNAs and their re…
bibliographic citation: Yu et al. (2024) The impact of hsa-miR-1972 on the expression of von Willebrand factor in breast cancer progression regulation. PeerJ 12:e18476 https://doi.org/10.7717/peerj.18476
date submitted: 2024-06-27
date accepted: 2024-10-16
issued: 2024-11-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Changjiang
author list: Agent
  family name: Zhang
  given name: Tao
author list: Agent
  family name: Chen
  given name: Fan
author list: Agent
  family name: Yu
  given name: Zhenyang
doi: 10.7717/peerj.18476
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-08
copyright: © 2024 Yu et al.
attribution name: Yu et al.

Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022
type: item
type: AcademicArticle
description: Black carbon (BC) is a pollutant produced by the combustion of fossil fuels and biomass fuels, which has a huge impact on regional climate, atmospheric environment, and human health. In this study, based on MERRA-2 reanalysis data and ground-based observation data, the Mann-Kendall (MK) test and random forest (RF) model were used to explore the spatiotemporal variation characteristics of atmospheric BC concentration in Xinjiang, China and its correlation with meteorological and environmental covariates in 2010–2022. The results showed that the use of MERRA-2 reanalysis data to explore the spatiotemporal variation characteristics of BC concentration in Xinjiang had high reliability (relative average deviation (RAD) = 0.65). From 2010 to 2022, the annual average concentration of atmospheric BC in Xinjiang was 195.40 ± 15.55 ng/m3, and the multi-year average change rate was −0.05%. The winter season had the highest atmospheric BC concentration (145.52 ± 39.31 ng/m3), followed by autumn (124.95 ± 28.82 ng/m3), spring (74.05 ± 9.96 ng/m3), and summer (73.41 ± 5.69 ng/m3). The atmospheric BC concentration had a significant spatial variation, showing two high-BC-concentration areas on the northern slope of the Tianshan Mountains (centered on Urumqi-Changji-Shihezi region) and the urban agglomeration around the Tarim Basin (centered on Kashgar). The RF model analysis showed that meteorological factors including snow depth, surface temperature, and humidity as well as environmental factors including NO2, PM10, and SO2 were the main factors affecting the BC concentration. This work is of great significance for clarifying the accumulation and spatial distribution characteristics of atmospheric BC in northwest China and the factors influencing the atmospheric BC concentration, and helps to raise public attention to the increasingly serious climate change and public health problems caused by BC.
format: application/pdf
format: text/html
creator: Xiang Xie
creator: Zhujun Zhao
creator: Shuting Li
creator: Zhongqi Lu
creator: Lijuan Chen
creator: Jiangjiang Cai
subject: Atmospheric Chemistry
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.18187
publisher: PeerJ Inc.
rights: © 2024 Xie et al.
abstract: Black carbon (BC) is a pollutant produced by the combustion of fossil fuels and biomass fuels, which has a huge impact on regional climate, atmospheric environment, and human health. In this study, based on MERRA-2 reanalysis data and ground-based observation data, the Mann-Kendall (MK) test and random forest (RF) model were used to explore the spatiotemporal variation characteristics of atmospheric BC concentration in Xinjiang, China and its correlation with meteorological and environmental covariates in 2010–2022. The results showed that the use of MERRA-2 reanalysis data to explore the spatiotemporal variation characteristics of BC concentration in Xinjiang had high reliability (relative average deviation (RAD) = 0.65). From 2010 to 2022, the annual average concentration of atmospheric BC in Xinjiang was 195.40 ± 15.55 ng/m3, and the multi-year average change rate was −0.05%. The winter season had the highest atmospheric BC concentration (145.52 ± 39.31 ng/m3), followed by autumn (124.95 ± 28.82 ng/m3), spring (74.05 ± 9.96 ng/m3), and summer (73.41 ± 5.69 ng/m3). The atmospheric BC concentration had a significant spatial variation, showing two high-BC-concentration areas on the northern slope of the Tianshan Mountains (centered on Urumqi-Changji-Shihezi region) and the urban agglomeration around the Tarim Basin (centered on Kashgar). The RF model analysis showed that meteorological factors including snow depth, surface temperature, and humidity as well as environmental factors including NO2, PM10, and SO2 were the main factors affecting the BC concentration. This work is of great significance for clarifying the accumulation and spatial distribution characteristics of atmospheric BC in northwest China and the factors influencing the atmospheric BC concentration, and helps to raise public attention to the increasingly serious climate change and public health problems caused by BC.
bibliographic citation: Xie et al. (2024) Spatiotemporal variations of atmospheric black carbon concentration and its correlation with meteorological and environmental factors in Xinjiang, China, from 2010 to 2022. PeerJ 12:e18187 https://doi.org/10.7717/peerj.18187
date submitted: 2024-02-26
date accepted: 2024-09-06
issued: 2024-11-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Xiang
author list: Agent
  family name: Zhao
  given name: Zhujun
author list: Agent
  family name: Li
  given name: Shuting
author list: Agent
  family name: Lu
  given name: Zhongqi
author list: Agent
  family name: Chen
  given name: Lijuan
author list: Agent
  family name: Cai
  given name: Jiangjiang
doi: 10.7717/peerj.18187
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-07
copyright: ©2024 Xie et al.
attribution name: Xie et al.

High variability in the attractiveness of municipally-planted decorative plants to insects
type: item
type: AcademicArticle
description: Insect populations are declining globally. A major driver of this decline is land use change, including urbanisation. However, urban environments can also offer a wide range of floral resources to pollinators, through ornamental plantings, but these can vary widely in their attractiveness to insects. Often, the largest single planter of ornamental plants in an urban area is the municipality. Here we evaluated the decorative plantings carried out by the city municipality of Regensburg, Germany, by systematically surveying insect visitations on different plant types in late summer, when forage is often limited for pollinators. We found a 130-fold difference from the least to the most attractive plants, and high variation in which insect groups were attracted to which plants. While honey bees, which are not a conservation concern, were the most common insect visitors, some decorative plants attracted a very large proportion of wild bees, flies, and wasps. Our results demonstrate that there is great scope for increasing the supply of urban forage to pollinators in general, and specific groups in particular, without requiring new decorative plant types to be sourced or planted. We argue that providing local evidence-based guidance to municipalities offers a quick and potentially cost-neutral method for supporting urban insect populations.
format: application/pdf
format: text/html
creator: Tomer J. Czaczkes
creator: Carsten Breuss
creator: Christoph Kurze
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.17762
publisher: PeerJ Inc.
rights: © 2024 Czaczkes et al.
abstract: Insect populations are declining globally. A major driver of this decline is land use change, including urbanisation. However, urban environments can also offer a wide range of floral resources to pollinators, through ornamental plantings, but these can vary widely in their attractiveness to insects. Often, the largest single planter of ornamental plants in an urban area is the municipality. Here we evaluated the decorative plantings carried out by the city municipality of Regensburg, Germany, by systematically surveying insect visitations on different plant types in late summer, when forage is often limited for pollinators. We found a 130-fold difference from the least to the most attractive plants, and high variation in which insect groups were attracted to which plants. While honey bees, which are not a conservation concern, were the most common insect visitors, some decorative plants attracted a very large proportion of wild bees, flies, and wasps. Our results demonstrate that there is great scope for increasing the supply of urban forage to pollinators in general, and specific groups in particular, without requiring new decorative plant types to be sourced or planted. We argue that providing local evidence-based guidance to municipalities offers a quick and potentially cost-neutral method for supporting urban insect populations.
bibliographic citation: Czaczkes et al. (2024) High variability in the attractiveness of municipally-planted decorative plants to insects. PeerJ 12:e17762 https://doi.org/10.7717/peerj.17762
date submitted: 2024-02-02
date accepted: 2024-06-26
issued: 2024-11-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Czaczkes
  given name: Tomer J.
author list: Agent
  family name: Breuss
  given name: Carsten
author list: Agent
  family name: Kurze
  given name: Christoph
doi: 10.7717/peerj.17762
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-06
copyright: © 2024 Czaczkes et al.
attribution name: Czaczkes et al.

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