PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A multi-class classification algorithm based on hematoxylin-eosin staining for neoadjuvant therapy in rectal cancer: a retrospective study
items: Fertilizer and herbicide alter nectar and pollen quality with consequences for pollinator floral choices
items: Marine aquaculture as a source of propagules of invasive fouling species
items: Remimazolam versus propofol for procedural sedation: a meta-analysis of randomized controlled trials
items: Analysis of brain activation and wave frequencies during a sentence completion task: a paradigm used with EEG in aphasic participants
items: Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae)
items: Follow-up focused on psychological intervention initiated after intensive care unit in adult patients and informal caregivers: a systematic review and meta-analysis
items: Mineral nutrient variability of potato (Solanum tuberosum L.) tubers with different colors grown in Niksar, Kazova and Artova locations of Tokat Province, Turkey
items: Systemic effect of calcium silicate-based cements with different radiopacifiers-histopathological analysis in rats
items: Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome

A multi-class classification algorithm based on hematoxylin-eosin staining for neoadjuvant therapy in rectal cancer: a retrospective study
type: item
type: AcademicArticle
description: Neoadjuvant therapy (NAT) is a major treatment option for locally advanced rectal cancer. With recent advancement of machine/deep learning algorithms, predicting the treatment response of NAT has become possible using radiological and/or pathological images. However, programs reported thus far are limited to binary classifications, and they can only distinguish the pathological complete response (pCR). In the clinical setting, the pathological NAT responses are classified as four classes: (TRG0-3), with 0 as pCR, 1 as moderate response, 2 as minimal response and 3 as poor response. Therefore, the actual clinical need for risk stratification remains unmet. By using ResNet (Residual Neural Network), we developed a multi-class classifier based on Hematoxylin-Eosin (HE) images to divide the response to three groups (TRG0, TRG1/2, and TRG3). Overall, the model achieved the AUC 0.97 at 40× magnification and AUC 0.89 at 10× magnification. For TRG0, the model under 40× magnification achieved a precision of 0.67, a sensitivity of 0.67, and a specificity of 0.95. For TRG1/2, a precision of 0.92, a sensitivity of 0.86, and a specificity of 0.89 were achieved. For TRG3, the model obtained a precision of 0.71, a sensitivity of 0.83, and a specificity of 0.88. To find the relationship between the treatment response and pathological images, we constructed a visual heat map of tiles using Class Activation Mapping (CAM). Notably, we found that tumor nuclei and tumor-infiltrating lymphocytes appeared to be potential features of the algorithm. Taken together, this multi-class classifier represents the first of its kind to predict different NAT responses in rectal cancer.
format: application/pdf
format: text/html
creator: Yihan Wu
creator: Xiaohua Liu
creator: Fang Liu
creator: Yi Li
creator: Xiaomin Xiong
creator: Hao Sun
creator: Bo Lin
creator: Yu Li
creator: Bo Xu
subject: Computational Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.15408
publisher: PeerJ Inc.
rights: © 2023 Wu et al.
abstract: Neoadjuvant therapy (NAT) is a major treatment option for locally advanced rectal cancer. With recent advancement of machine/deep learning algorithms, predicting the treatment response of NAT has become possible using radiological and/or pathological images. However, programs reported thus far are limited to binary classifications, and they can only distinguish the pathological complete response (pCR). In the clinical setting, the pathological NAT responses are classified as four classes: (TRG0-3), with 0 as pCR, 1 as moderate response, 2 as minimal response and 3 as poor response. Therefore, the actual clinical need for risk stratification remains unmet. By using ResNet (Residual Neural Network), we developed a multi-class classifier based on Hematoxylin-Eosin (HE) images to divide the response to three groups (TRG0, TRG1/2, and TRG3). Overall, the model achieved the AUC 0.97 at 40× magnification and AUC 0.89 at 10× magnification. For TRG0, the model under 40× magnification achieved a precision of 0.67, a sensitivity of 0.67, and a specificity of 0.95. For TRG1/2, a precision of 0.92, a sensitivity of 0.86, and a specificity of 0.89 were achieved. For TRG3, the model obtained a precision of 0.71, a sensitivity of 0.83, and a specificity of 0.88. To find the relationship between the treatment response and pathological images, we constructed a visual heat map of tiles using Class Activation Mapping (CAM). Notably, we found that tumor nuclei and tumor-infiltrating lymphocytes appeared to be potential features of the algorithm. Taken together, this multi-class classifier represents the first of its kind to predict different NAT responses in rectal cancer.
bibliographic citation: Wu et al. (2023) A multi-class classification algorithm based on hematoxylin-eosin staining for neoadjuvant therapy in rectal cancer: a retrospective study. PeerJ 11:e15408 https://doi.org/10.7717/peerj.15408
date submitted: 2022-12-27
date accepted: 2023-04-21
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Yihan
author list: Agent
  family name: Liu
  given name: Xiaohua
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Li
  given name: Yi
author list: Agent
  family name: Xiong
  given name: Xiaomin
author list: Agent
  family name: Sun
  given name: Hao
author list: Agent
  family name: Lin
  given name: Bo
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Xu
  given name: Bo
doi: 10.7717/peerj.15408
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: ©2023 Wu et al.
attribution name: Wu et al.

Fertilizer and herbicide alter nectar and pollen quality with consequences for pollinator floral choices
type: item
type: AcademicArticle
description: Background Pollinating insects provide economically and ecologically valuable services, but are threatened by a variety of anthropogenic changes. The availability and quality of floral resources may be affected by anthropogenic land use. For example, flower-visiting insects in agroecosystems rely on weeds on field edges for foraging resources, but these weeds are often exposed to agrochemicals that may compromise the quality of their floral resources. Methods We conducted complementary field and greenhouse experiments to evaluate the: (1) effect of low concentrations of agrochemical exposure on nectar and pollen quality and (2) relationship between floral resource quality and insect visitation. We applied the same agrochemcial treatments (low concentrations of fertilizer, low concentrations of herbicide, a combination of both, and a control of just water) to seven plant species in the field and greenhouse. We collected data on floral visitation by insects in the field experiment for two field seasons and collected pollen and nectar from focal plants in the greenhouse to avoid interfering with insect visitation in the field. Results We found pollen amino acid concentrations were lower in plants exposed to low concentrations of herbicide, and pollen fatty acid concentrations were lower in plants exposed to low concentrations of fertilizer, while nectar amino acids were higher in plants exposed to low concentrations of either fertilizer or herbicide. Exposure to low fertilizer concentrations also increased the quantity of pollen and nectar produced per flower. The responses of plants exposed to the experimental treatments in the greenhouse helped explain insect visitation in the field study. The insect visitation rate correlated with nectar amino acids, pollen amino acids, and pollen fatty acids. An interaction between pollen protein and floral display suggested pollen amino acid concentrations drove insect preference among plant species when floral display sizes were …
format: application/pdf
format: text/html
creator: Laura Russo
creator: Fabian Ruedenauer
creator: Angela Gronert
creator: Isabelle Van de Vreken
creator: Maryse Vanderplanck
creator: Denis Michez
creator: Alexandra Klein
creator: Sara Leonhardt
creator: Jane C. Stout
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.15452
publisher: PeerJ Inc.
rights: © 2023 Russo et al.
abstract: Background Pollinating insects provide economically and ecologically valuable services, but are threatened by a variety of anthropogenic changes. The availability and quality of floral resources may be affected by anthropogenic land use. For example, flower-visiting insects in agroecosystems rely on weeds on field edges for foraging resources, but these weeds are often exposed to agrochemicals that may compromise the quality of their floral resources. Methods We conducted complementary field and greenhouse experiments to evaluate the: (1) effect of low concentrations of agrochemical exposure on nectar and pollen quality and (2) relationship between floral resource quality and insect visitation. We applied the same agrochemcial treatments (low concentrations of fertilizer, low concentrations of herbicide, a combination of both, and a control of just water) to seven plant species in the field and greenhouse. We collected data on floral visitation by insects in the field experiment for two field seasons and collected pollen and nectar from focal plants in the greenhouse to avoid interfering with insect visitation in the field. Results We found pollen amino acid concentrations were lower in plants exposed to low concentrations of herbicide, and pollen fatty acid concentrations were lower in plants exposed to low concentrations of fertilizer, while nectar amino acids were higher in plants exposed to low concentrations of either fertilizer or herbicide. Exposure to low fertilizer concentrations also increased the quantity of pollen and nectar produced per flower. The responses of plants exposed to the experimental treatments in the greenhouse helped explain insect visitation in the field study. The insect visitation rate correlated with nectar amino acids, pollen amino acids, and pollen fatty acids. An interaction between pollen protein and floral display suggested pollen amino acid concentrations drove insect preference among plant species when floral display sizes were …
bibliographic citation: Russo et al. (2023) Fertilizer and herbicide alter nectar and pollen quality with consequences for pollinator floral choices. PeerJ 11:e15452 https://doi.org/10.7717/peerj.15452
date submitted: 2023-01-18
date accepted: 2023-05-03
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Russo
  given name: Laura
author list: Agent
  family name: Ruedenauer
  given name: Fabian
author list: Agent
  family name: Gronert
  given name: Angela
author list: Agent
  family name: Van de Vreken
  given name: Isabelle
author list: Agent
  family name: Vanderplanck
  given name: Maryse
author list: Agent
  family name: Michez
  given name: Denis
author list: Agent
  family name: Klein
  given name: Alexandra
author list: Agent
  family name: Leonhardt
  given name: Sara
author list: Agent
  family name: Stout
  given name: Jane C.
doi: 10.7717/peerj.15452
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: ©2023 Russo et al.
attribution name: Russo et al.

Marine aquaculture as a source of propagules of invasive fouling species
type: item
type: AcademicArticle
description: Non-indigenous species tend to colonize aquaculture installations, especially when they are near international ports. In addition to the local environmental hazard that colonizing non-indigenous species pose, they can also take advantage of local transport opportunities to spread elsewhere. In this study, we examined the risk of the spread of eight invasive fouling species that are found in mussel farms in southern Brazil. We used ensemble niche models based on worldwide occurrences of these species, and environmental variables (ocean temperature and salinity) to predict suitable areas for each species with three algorithms (Maxent, Random Forest, and Support Vector Machine). As a proxy for propagule pressure, we used the tonnage transported by container ships from Santa Catarina (the main mariculture region) that travel to other Brazilian ports. We found that ports in the tropical states of Pernambuco, Ceará, and Bahia received the largest tonnage, although far from Santa Catarina and in a different ecoregion. The ascidians Aplidium accarense and Didemnum perlucidum are known from Bahia, with a high risk of invasion in the other states. The bryozoan Watersipora subtorquata also has a high risk of establishment in Pernambuco, while the ascidian Botrylloides giganteus has a medium risk in Bahia. Paraná, a state in the same ecoregion as Santa Catarina is likely to be invaded by all species. A second state in this region, Rio Grande do Sul, is vulnerable to A. accarense, the barnacle Megabalanus coccopoma, and the mussel Mytilus galloprovincialis. Climate change is changing species latitudinal distributions and most species will gain rather than lose area in near future (by 2050). As an ideal habitat for fouling organisms and invasive species, aquaculture farms can increase propagule pressure and thus the probability that species will expand their distributions, especially if they are close to ports. Therefore, an integrated approach of the risks of both aquaculture an…
format: application/pdf
format: text/html
creator: Daniel M. Lins
creator: Rosana M. Rocha
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Biological Oceanography
description: doi:10.7717/peerj.15456
publisher: PeerJ Inc.
rights: © 2023 Lins and Rocha
abstract: Non-indigenous species tend to colonize aquaculture installations, especially when they are near international ports. In addition to the local environmental hazard that colonizing non-indigenous species pose, they can also take advantage of local transport opportunities to spread elsewhere. In this study, we examined the risk of the spread of eight invasive fouling species that are found in mussel farms in southern Brazil. We used ensemble niche models based on worldwide occurrences of these species, and environmental variables (ocean temperature and salinity) to predict suitable areas for each species with three algorithms (Maxent, Random Forest, and Support Vector Machine). As a proxy for propagule pressure, we used the tonnage transported by container ships from Santa Catarina (the main mariculture region) that travel to other Brazilian ports. We found that ports in the tropical states of Pernambuco, Ceará, and Bahia received the largest tonnage, although far from Santa Catarina and in a different ecoregion. The ascidians Aplidium accarense and Didemnum perlucidum are known from Bahia, with a high risk of invasion in the other states. The bryozoan Watersipora subtorquata also has a high risk of establishment in Pernambuco, while the ascidian Botrylloides giganteus has a medium risk in Bahia. Paraná, a state in the same ecoregion as Santa Catarina is likely to be invaded by all species. A second state in this region, Rio Grande do Sul, is vulnerable to A. accarense, the barnacle Megabalanus coccopoma, and the mussel Mytilus galloprovincialis. Climate change is changing species latitudinal distributions and most species will gain rather than lose area in near future (by 2050). As an ideal habitat for fouling organisms and invasive species, aquaculture farms can increase propagule pressure and thus the probability that species will expand their distributions, especially if they are close to ports. Therefore, an integrated approach of the risks of both aquaculture an…
bibliographic citation: Lins et al. (2023) Marine aquaculture as a source of propagules of invasive fouling species. PeerJ 11:e15456 https://doi.org/10.7717/peerj.15456
date submitted: 2023-01-20
date accepted: 2023-05-03
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lins
  given name: Daniel M.
author list: Agent
  family name: Rocha
  given name: Rosana M.
doi: 10.7717/peerj.15456
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: © 2023 Lins and Rocha
attribution name: Lins and Rocha

Remimazolam versus propofol for procedural sedation: a meta-analysis of randomized controlled trials
type: item
type: AcademicArticle
description: Background To improve patient tolerability and satisfaction as well as minimize complications, procedural sedation has been widely used. Propofol is the most widely used agent for induction of anesthesia and sedation by anesthesiologists. With a different mechanism compared to propofol, remimazolam is a new short-acting GABA-A receptor agonist. It is an ester-based benzodiazepine. This meta-analysis aims to clarify the efficacy and safety of remimazolam versus propofol for procedure sedation. Methods Electronic databases were searched for randomized controlled trials (RCTs) comparing efficacy or safety of remimazolam versus propofol. Meta-analysis were conducted using RStudio with “metafor” package with random-effects model. Results A total of twelve RCTs were included in the meta-analysis. The pooled results demonstrated that patients with remimazolam for procedural sedation had lower risk of bradycardia (OR 0.28, 95% CI [0.14–0.57]), hypotension (OR 0.26, 95% CI [0.22–0.32]), and respiratory depression (OR 0.22, 95% CI [0.14–0.36]). There was no difference in the risk of developing postoperative nausea and vomiting (PONV) (OR 0.65, 95% CI [0.15–2.79]) and dizziness (OR 0.93, 95% CI [0.53–1.61]) between the remimazolam and propofol groups. Using remimazolam for procedural sedation is significantly associated with less injection pain compared to propofol (OR 0.06, 95% CI [0.03–0.13]). Regarding the sedation efficacy, there was no difference in sedation success rate or time to loss of consciousness, recover and discharge between the remimazolam and the propofol groups. Conclusions Based on our meta-analysis, patients receiving procedural sedation with remimazolam had lower risk of bradycardia, hypotension, respiratory depression and injection pain compared with propofol. On the other hand, there was no difference in sedation success rate, risk of PONV, dizziness, time to LOC, recovery and discharge between these two sedatives. PROSPERO registration number CRD42022362…
format: application/pdf
format: text/html
creator: Yu Chang
creator: Yun-Ting Huang
creator: Kuan-Yu Chi
creator: Yen-Ta Huang
subject: Anesthesiology and Pain Management
subject: Pharmacology
description: doi:10.7717/peerj.15495
publisher: PeerJ Inc.
rights: © 2023 Chang et al.
abstract: Background To improve patient tolerability and satisfaction as well as minimize complications, procedural sedation has been widely used. Propofol is the most widely used agent for induction of anesthesia and sedation by anesthesiologists. With a different mechanism compared to propofol, remimazolam is a new short-acting GABA-A receptor agonist. It is an ester-based benzodiazepine. This meta-analysis aims to clarify the efficacy and safety of remimazolam versus propofol for procedure sedation. Methods Electronic databases were searched for randomized controlled trials (RCTs) comparing efficacy or safety of remimazolam versus propofol. Meta-analysis were conducted using RStudio with “metafor” package with random-effects model. Results A total of twelve RCTs were included in the meta-analysis. The pooled results demonstrated that patients with remimazolam for procedural sedation had lower risk of bradycardia (OR 0.28, 95% CI [0.14–0.57]), hypotension (OR 0.26, 95% CI [0.22–0.32]), and respiratory depression (OR 0.22, 95% CI [0.14–0.36]). There was no difference in the risk of developing postoperative nausea and vomiting (PONV) (OR 0.65, 95% CI [0.15–2.79]) and dizziness (OR 0.93, 95% CI [0.53–1.61]) between the remimazolam and propofol groups. Using remimazolam for procedural sedation is significantly associated with less injection pain compared to propofol (OR 0.06, 95% CI [0.03–0.13]). Regarding the sedation efficacy, there was no difference in sedation success rate or time to loss of consciousness, recover and discharge between the remimazolam and the propofol groups. Conclusions Based on our meta-analysis, patients receiving procedural sedation with remimazolam had lower risk of bradycardia, hypotension, respiratory depression and injection pain compared with propofol. On the other hand, there was no difference in sedation success rate, risk of PONV, dizziness, time to LOC, recovery and discharge between these two sedatives. PROSPERO registration number CRD42022362…
bibliographic citation: Chang et al. (2023) Remimazolam versus propofol for procedural sedation: a meta-analysis of randomized controlled trials. PeerJ 11:e15495 https://doi.org/10.7717/peerj.15495
date submitted: 2023-03-20
date accepted: 2023-05-11
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Yu
author list: Agent
  family name: Huang
  given name: Yun-Ting
author list: Agent
  family name: Chi
  given name: Kuan-Yu
author list: Agent
  family name: Huang
  given name: Yen-Ta
doi: 10.7717/peerj.15495
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: ©2023 Chang et al.
attribution name: Chang et al.

Analysis of brain activation and wave frequencies during a sentence completion task: a paradigm used with EEG in aphasic participants
type: item
type: AcademicArticle
description: Aphasia is a language disorder that occurs after brain injury and directly affects an individual’s communication. The incidence of stroke increases with age, and one-third of people who have had a stroke develop aphasia. The severity of aphasia changes over time and some aspects of language may improve, while others remain compromised. Battery task training strategies are used in the rehabilitation of aphasics. The idea of this research is to use electroencephalography (EEG) as a non-invasive method, of electrophysiological monitoring, with a group of aphasic patients in rehabilitation process in a prevention and rehabilitation unit of the person with disabilities of the Unified Health System (SUS), of reference in the state of Bahia-Brazil. In this study, the goal is to analyze brain activation and wave frequencies of aphasic individuals during a sentence completion task, to possibly assist health professionals with the analysis of the aphasic subject’s rehabilitation and task redefinition. We adopted the functional magnetic resonance imaging (fMRI) paradigm, proposed by the American Society for Functional Neuroradiology as a reference paradigm. We applied the paradigm in the group of aphasics with preserved comprehension, right hemiparesis, and left hemisphere injured or affected by stroke. We analyzed four electrodes (F3/F4 and F7/F8) corresponding to the left/right frontal cortex. Preliminary results of this study indicate a more robust activation in the right hemisphere (average of aphasics), with a difference of approximately 14% higher in Theta and Alpha frequencies, with 8% higher in low Beta (BetaL) and with approximately 1% higher in high Beta frequency (BetaH), Gamma frequency was higher by approximately 3% in the left hemisphere of the brain. The difference in electrical activation may be revealing to us a migration of language to the non-language dominant hemisphere. We point to possible evidence suggesting that EEG may be a promising tool for monitorin…
format: application/pdf
format: text/html
creator: Claudia Lima
creator: Jeferson Andris Lopes
creator: Victor Souza
creator: Sarah Barros
creator: Ingrid Winkler
creator: Valter Senna
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15518
publisher: PeerJ Inc.
rights: © 2023 Lima et al.
abstract: Aphasia is a language disorder that occurs after brain injury and directly affects an individual’s communication. The incidence of stroke increases with age, and one-third of people who have had a stroke develop aphasia. The severity of aphasia changes over time and some aspects of language may improve, while others remain compromised. Battery task training strategies are used in the rehabilitation of aphasics. The idea of this research is to use electroencephalography (EEG) as a non-invasive method, of electrophysiological monitoring, with a group of aphasic patients in rehabilitation process in a prevention and rehabilitation unit of the person with disabilities of the Unified Health System (SUS), of reference in the state of Bahia-Brazil. In this study, the goal is to analyze brain activation and wave frequencies of aphasic individuals during a sentence completion task, to possibly assist health professionals with the analysis of the aphasic subject’s rehabilitation and task redefinition. We adopted the functional magnetic resonance imaging (fMRI) paradigm, proposed by the American Society for Functional Neuroradiology as a reference paradigm. We applied the paradigm in the group of aphasics with preserved comprehension, right hemiparesis, and left hemisphere injured or affected by stroke. We analyzed four electrodes (F3/F4 and F7/F8) corresponding to the left/right frontal cortex. Preliminary results of this study indicate a more robust activation in the right hemisphere (average of aphasics), with a difference of approximately 14% higher in Theta and Alpha frequencies, with 8% higher in low Beta (BetaL) and with approximately 1% higher in high Beta frequency (BetaH), Gamma frequency was higher by approximately 3% in the left hemisphere of the brain. The difference in electrical activation may be revealing to us a migration of language to the non-language dominant hemisphere. We point to possible evidence suggesting that EEG may be a promising tool for monitorin…
bibliographic citation: Lima et al. (2023) Analysis of brain activation and wave frequencies during a sentence completion task: a paradigm used with EEG in aphasic participants. PeerJ 11:e15518 https://doi.org/10.7717/peerj.15518
date submitted: 2022-12-14
date accepted: 2023-05-15
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lima
  given name: Claudia
author list: Agent
  family name: Lopes
  given name: Jeferson Andris
author list: Agent
  family name: Souza
  given name: Victor
author list: Agent
  family name: Barros
  given name: Sarah
author list: Agent
  family name: Winkler
  given name: Ingrid
author list: Agent
  family name: Senna
  given name: Valter
doi: 10.7717/peerj.15518
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: © 2023 Lima et al.
attribution name: Lima et al.

Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae)
type: item
type: AcademicArticle
description: Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
format: application/pdf
format: text/html
creator: Tiffany JS Simpson
creator: Claire M. Wellington
creator: Sherralee S. Lukehurst
creator: Roger Huerlimann
creator: Heather Veilleux
creator: Michael Snow
creator: Joana Dias
creator: Justin I. McDonald
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.15522
publisher: PeerJ Inc.
rights: © 2023 Simpson et al.
abstract: Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
bibliographic citation: Simpson et al. (2023) Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae). PeerJ 11:e15522 https://doi.org/10.7717/peerj.15522
date submitted: 2022-10-13
date accepted: 2023-05-17
issued: 2023-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simpson
  given name: Tiffany JS
author list: Agent
  family name: Wellington
  given name: Claire M.
author list: Agent
  family name: Lukehurst
  given name: Sherralee S.
author list: Agent
  family name: Huerlimann
  given name: Roger
author list: Agent
  family name: Veilleux
  given name: Heather
author list: Agent
  family name: Snow
  given name: Michael
author list: Agent
  family name: Dias
  given name: Joana
author list: Agent
  family name: McDonald
  given name: Justin I.
doi: 10.7717/peerj.15522
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-12
copyright: © 2023 Simpson et al.
attribution name: Simpson et al.

Follow-up focused on psychological intervention initiated after intensive care unit in adult patients and informal caregivers: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Psychological dysfunction is one of the considerable health-related outcomes among critically-ill patients and their informal caregivers. Follow-up of intensive care unit (ICU) survivors has been conducted in a variety of different ways, with different timing after discharge, targets of interest (physical, psychological, social) and measures used. Of diverse ICU follow-up, the effects of follow-ups which focused on psychological interventions are unknown. Our research question was whether follow-up with patients and their informal caregivers after ICU discharge improved mental health compared to usual care. We published a protocol for this systematic review and meta-analysis in https://www.protocols.io/ (https://dx.doi.org/10.17504/protocols.io.bvjwn4pe). We searched PubMed, Cochrane Library, EMBASE, CINAHL and PsycInfo from their inception to May 2022. We included randomized controlled trials for follow-ups after ICU discharge and focused on psychological intervention for critically ill adult patients and their informal caregivers. We synthesized primary outcomes, including depression, post-traumatic stress disorder (PTSD), and adverse events using the random-effects method. We used the Grading of Recommendations Assessment, Development and Evaluation approach to rate the certainty of evidence. From the 10,471 records, we identified 13 studies (n = 3, 366) focusing on patients and four (n = 538) focusing on informal caregivers. ICU follow-up for patients resulted in little to no difference in the prevalence of depression (RR 0.89, 95% CI [0.59–1.34]; low-certainty evidence) and PTSD (RR 0.84, 95% CI [0.55–1.30]; low-certainty evidence) among patients; however, it increased the prevalence of depression (RR 1.58 95% CI [1.01–2.46]; very low-certainty evidence), PTSD (RR 1.36, 95% CI [0.91–2.03]; very low-certainty evidence) among informal caregivers. The evidence for the effect of ICU follow-up on adverse events among patients was insufficient. Eligible studies for i…
format: application/pdf
format: text/html
creator: Shodai Yoshihiro
creator: Shunsuke Taito
creator: Kota Yamauchi
creator: Shunsuke Kina
creator: Takero Terayama
creator: Yusuke Tsutsumi
creator: Yuki Kataoka
creator: Takeshi Unoki
subject: Emergency and Critical Care
subject: Nursing
subject: Psychiatry and Psychology
subject: Mental Health
subject: Rehabilitation
description: doi:10.7717/peerj.15260
publisher: PeerJ Inc.
rights: © 2023 Yoshihiro et al.
abstract: Psychological dysfunction is one of the considerable health-related outcomes among critically-ill patients and their informal caregivers. Follow-up of intensive care unit (ICU) survivors has been conducted in a variety of different ways, with different timing after discharge, targets of interest (physical, psychological, social) and measures used. Of diverse ICU follow-up, the effects of follow-ups which focused on psychological interventions are unknown. Our research question was whether follow-up with patients and their informal caregivers after ICU discharge improved mental health compared to usual care. We published a protocol for this systematic review and meta-analysis in https://www.protocols.io/ (https://dx.doi.org/10.17504/protocols.io.bvjwn4pe). We searched PubMed, Cochrane Library, EMBASE, CINAHL and PsycInfo from their inception to May 2022. We included randomized controlled trials for follow-ups after ICU discharge and focused on psychological intervention for critically ill adult patients and their informal caregivers. We synthesized primary outcomes, including depression, post-traumatic stress disorder (PTSD), and adverse events using the random-effects method. We used the Grading of Recommendations Assessment, Development and Evaluation approach to rate the certainty of evidence. From the 10,471 records, we identified 13 studies (n = 3, 366) focusing on patients and four (n = 538) focusing on informal caregivers. ICU follow-up for patients resulted in little to no difference in the prevalence of depression (RR 0.89, 95% CI [0.59–1.34]; low-certainty evidence) and PTSD (RR 0.84, 95% CI [0.55–1.30]; low-certainty evidence) among patients; however, it increased the prevalence of depression (RR 1.58 95% CI [1.01–2.46]; very low-certainty evidence), PTSD (RR 1.36, 95% CI [0.91–2.03]; very low-certainty evidence) among informal caregivers. The evidence for the effect of ICU follow-up on adverse events among patients was insufficient. Eligible studies for i…
bibliographic citation: Yoshihiro et al. (2023) Follow-up focused on psychological intervention initiated after intensive care unit in adult patients and informal caregivers: a systematic review and meta-analysis. PeerJ 11:e15260 https://doi.org/10.7717/peerj.15260
date submitted: 2022-10-17
date accepted: 2023-03-28
issued: 2023-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yoshihiro
  given name: Shodai
author list: Agent
  family name: Taito
  given name: Shunsuke
author list: Agent
  family name: Yamauchi
  given name: Kota
author list: Agent
  family name: Kina
  given name: Shunsuke
author list: Agent
  family name: Terayama
  given name: Takero
author list: Agent
  family name: Tsutsumi
  given name: Yusuke
author list: Agent
  family name: Kataoka
  given name: Yuki
author list: Agent
  family name: Unoki
  given name: Takeshi
doi: 10.7717/peerj.15260
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-09
copyright: ©2023 Yoshihiro et al.
attribution name: Yoshihiro et al.

Mineral nutrient variability of potato (Solanum tuberosum L.) tubers with different colors grown in Niksar, Kazova and Artova locations of Tokat Province, Turkey
type: item
type: AcademicArticle
description: Potato is one of the most commonly consumed non-grain staple food crops in the world therefore, the mineral nutrient content of the potato is extremely important for human nutrition. The lack of mineral nutrients causes significant health problems, thus, many of these nutrients are often taken as supplements. This study was carried out to investigate the effects of potato flesh color and location on different mineral nutrient contents under Niksar, Kazova and Artova locations in Tokat Province, Turkey, during 2013 and 2014 potato growing seasons. The experimental design in each location was randomized blocks with three replications. In this study, a total of 67 clones (including varieties and advanced breeding selections) with nine white, 10 cream, 30 light yellow, and 18 dark yellow flesh colors were used. Potatoes with cream flesh colors had the highest K (23.81 g kg−1), P (0.31 g kg−1), Mg (1.20 g kg−1), Zn (27.26 mg kg−1), Cu (8.28 mg kg−1) and Mn (7.21 mg kg−1) contents, and the lowest Ca (45.6 mg kg−1) content. The mineral contents (except K and Cu) of potatoes grown in Artova were higher compared to the other two locations. The results clearly suggested that Artova is the most suitable location to produce potatoes with a high mineral composition, and Kazova is suitable to cultivate potatoes with high K and Cu contents. In addition, the knowledge of nutrient rich potato accessions is valuable for developing biofortified potato genotypes.
format: application/pdf
format: text/html
creator: Yasin Bedrettin Karan
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15262
publisher: PeerJ Inc.
rights: © 2023 Karan
abstract: Potato is one of the most commonly consumed non-grain staple food crops in the world therefore, the mineral nutrient content of the potato is extremely important for human nutrition. The lack of mineral nutrients causes significant health problems, thus, many of these nutrients are often taken as supplements. This study was carried out to investigate the effects of potato flesh color and location on different mineral nutrient contents under Niksar, Kazova and Artova locations in Tokat Province, Turkey, during 2013 and 2014 potato growing seasons. The experimental design in each location was randomized blocks with three replications. In this study, a total of 67 clones (including varieties and advanced breeding selections) with nine white, 10 cream, 30 light yellow, and 18 dark yellow flesh colors were used. Potatoes with cream flesh colors had the highest K (23.81 g kg−1), P (0.31 g kg−1), Mg (1.20 g kg−1), Zn (27.26 mg kg−1), Cu (8.28 mg kg−1) and Mn (7.21 mg kg−1) contents, and the lowest Ca (45.6 mg kg−1) content. The mineral contents (except K and Cu) of potatoes grown in Artova were higher compared to the other two locations. The results clearly suggested that Artova is the most suitable location to produce potatoes with a high mineral composition, and Kazova is suitable to cultivate potatoes with high K and Cu contents. In addition, the knowledge of nutrient rich potato accessions is valuable for developing biofortified potato genotypes.
bibliographic citation: Karan (2023) Mineral nutrient variability of potato (Solanum tuberosum L.) tubers with different colors grown in Niksar, Kazova and Artova locations of Tokat Province, Turkey. PeerJ 11:e15262 https://doi.org/10.7717/peerj.15262
date submitted: 2022-10-06
date accepted: 2023-03-28
issued: 2023-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karan
  given name: Yasin Bedrettin
doi: 10.7717/peerj.15262
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-09
copyright: ©2023 Karan
attribution name: Karan

Systemic effect of calcium silicate-based cements with different radiopacifiers-histopathological analysis in rats
type: item
type: AcademicArticle
description: Aim This in vivo study aimed to examine the systemic effects of contemporary calcium silicate cements (CSC) contain different radiopacifiers in rats. Materials & Methods Polyethylene tubes filled with BIOfactor MTA (BIO), Neo MTA Plus (NEO), MTA Repair HP (REP), Biodentine (DENT) and empty tubes (control group) were implanted into the subcutaneous tissues of 80 male Spraque Dawley rats for 7 and 30 days (n = 8). After 7 and 30 day, samples of liver and kidney tissues were submitted to histopathological analysis. Blood samples were collected to evaluate changes in hepatic and renal functions of rats. Wilcoxon and post hoc Dunn Bonferroni tests were used to compare between the 7th and 30th days in order to evaluate the histopathological data. Paired-sample t-test was used to compare laboratory values between the 7th and 30th days, ANOVA analysis and a post hoc Tukey test were used to compare values between groups (p < 0.05). Results On the 7th day, REP, BIO and NEO groups were statistically similar in kidney tissue and the degree of inflammation was found to be significantly higher in these groups compared to the control and DENT groups. On the 30th day, the degree of inflammation of the REP and NEO groups in the kidney tissue was found to be significantly higher than the control, BIO and DENT groups. Although the inflammation in the liver was moderate and mild on the 7th and 30th days, no statistically significant difference was observed between the groups. Vascular congestion was evaluated as mild and moderate in kidney and liver in all groups, and no statistically significant difference was observed between the groups. While there was no statistically significant difference between the groups in the 7th day AST, ALT and urea values, when the creatinine values were compared, the DENT and NEO groups were found to be statistically similar and significantly lower than the control group. On the 30th day, ALT values were statistically similar between the groups. The AST …
format: application/pdf
format: text/html
creator: Osman Ataş
creator: Kubra Bılge
creator: Semsettin Yıldız
creator: Serkan Dundar
creator: Ilknur Calik
creator: Asime Gezer Ataş
creator: Alihan Bozoglan
subject: Biochemistry
subject: Dentistry
subject: Histology
description: doi:10.7717/peerj.15376
publisher: PeerJ Inc.
rights: © 2023 Ataş et al.
abstract: Aim This in vivo study aimed to examine the systemic effects of contemporary calcium silicate cements (CSC) contain different radiopacifiers in rats. Materials & Methods Polyethylene tubes filled with BIOfactor MTA (BIO), Neo MTA Plus (NEO), MTA Repair HP (REP), Biodentine (DENT) and empty tubes (control group) were implanted into the subcutaneous tissues of 80 male Spraque Dawley rats for 7 and 30 days (n = 8). After 7 and 30 day, samples of liver and kidney tissues were submitted to histopathological analysis. Blood samples were collected to evaluate changes in hepatic and renal functions of rats. Wilcoxon and post hoc Dunn Bonferroni tests were used to compare between the 7th and 30th days in order to evaluate the histopathological data. Paired-sample t-test was used to compare laboratory values between the 7th and 30th days, ANOVA analysis and a post hoc Tukey test were used to compare values between groups (p < 0.05). Results On the 7th day, REP, BIO and NEO groups were statistically similar in kidney tissue and the degree of inflammation was found to be significantly higher in these groups compared to the control and DENT groups. On the 30th day, the degree of inflammation of the REP and NEO groups in the kidney tissue was found to be significantly higher than the control, BIO and DENT groups. Although the inflammation in the liver was moderate and mild on the 7th and 30th days, no statistically significant difference was observed between the groups. Vascular congestion was evaluated as mild and moderate in kidney and liver in all groups, and no statistically significant difference was observed between the groups. While there was no statistically significant difference between the groups in the 7th day AST, ALT and urea values, when the creatinine values were compared, the DENT and NEO groups were found to be statistically similar and significantly lower than the control group. On the 30th day, ALT values were statistically similar between the groups. The AST …
bibliographic citation: Ataş et al. (2023) Systemic effect of calcium silicate-based cements with different radiopacifiers-histopathological analysis in rats. PeerJ 11:e15376 https://doi.org/10.7717/peerj.15376
date submitted: 2022-12-07
date accepted: 2023-04-18
issued: 2023-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ataş
  given name: Osman
author list: Agent
  family name: Bılge
  given name: Kubra
author list: Agent
  family name: Yıldız
  given name: Semsettin
author list: Agent
  family name: Dundar
  given name: Serkan
author list: Agent
  family name: Calik
  given name: Ilknur
author list: Agent
  family name: Gezer Ataş
  given name: Asime
author list: Agent
  family name: Bozoglan
  given name: Alihan
doi: 10.7717/peerj.15376
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-09
copyright: ©2023 Ataş et al.
attribution name: Ataş et al.

Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome
type: item
type: AcademicArticle
description: The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.
format: application/pdf
format: text/html
creator: Emma K. Bueren
creator: Alaina R. Weinheimer
creator: Frank O. Aylward
creator: Bryan B. Hsu
creator: David C. Haak
creator: Lisa K. Belden
subject: Entomology
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.15383
publisher: PeerJ Inc.
rights: © 2023 Bueren et al.
abstract: The gut of the European honey bee (Apis mellifera) possesses a relatively simple bacterial community, but little is known about its community of prophages (temperate bacteriophages integrated into the bacterial genome). Although prophages may eventually begin replicating and kill their bacterial hosts, they can also sometimes be beneficial for their hosts by conferring protection from other phage infections or encoding genes in metabolic pathways and for toxins. In this study, we explored prophages in 17 species of core bacteria in the honey bee gut and two honey bee pathogens. Out of the 181 genomes examined, 431 putative prophage regions were predicted. Among core gut bacteria, the number of prophages per genome ranged from zero to seven and prophage composition (the compositional percentage of each bacterial genome attributable to prophages) ranged from 0 to 7%. Snodgrassella alvi and Gilliamella apicola had the highest median prophages per genome (3.0 ± 1.46; 3.0 ± 1.59), as well as the highest prophage composition (2.58% ± 1.4; 3.0% ± 1.59). The pathogen Paenibacillus larvae had a higher median number of prophages (8.0 ± 5.33) and prophage composition (6.40% ± 3.08) than the pathogen Melissococcus plutonius or any of the core bacteria. Prophage populations were highly specific to their bacterial host species, suggesting most prophages were acquired recently relative to the divergence of these bacterial groups. Furthermore, functional annotation of the predicted genes encoded within the prophage regions indicates that some prophages in the honey bee gut encode additional benefits to their bacterial hosts, such as genes in carbohydrate metabolism. Collectively, this survey suggests that prophages within the honey bee gut may contribute to the maintenance and stability of the honey bee gut microbiome and potentially modulate specific members of the bacterial community, particularly S. alvi and G. apicola.
bibliographic citation: Bueren et al. (2023) Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome. PeerJ 11:e15383 https://doi.org/10.7717/peerj.15383
date submitted: 2022-12-19
date accepted: 2023-04-18
issued: 2023-06-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bueren
  given name: Emma K.
author list: Agent
  family name: Weinheimer
  given name: Alaina R.
author list: Agent
  family name: Aylward
  given name: Frank O.
author list: Agent
  family name: Hsu
  given name: Bryan B.
author list: Agent
  family name: Haak
  given name: David C.
author list: Agent
  family name: Belden
  given name: Lisa K.
doi: 10.7717/peerj.15383
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-09
copyright: ©2023 Bueren et al.
attribution name: Bueren et al.

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