PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tibetan red deer (Cervus canadensis wallichi) diet composition patterns and associations during lean seasons in Tibet, China
items: Comparative efficacy and safety of 180 W XPS vs. 120 W HPS GreenLight laser therapy for benign prostatic hyperplasia: a systematic review and meta-analysis
items: Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria)
items: Early-diverging plesiosaurs from the Pliensbachian (Lower Jurassic) of northwestern Germany
items: Diffuse idiopathic skeletal hyperostosis was the specific risk factors of methicillin-susceptible Staphylococcus aureus spine infection: a retrospective study in a single center
items: Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma
items: LRR1 involved in the abscisic acid signaling pathway to regulate the early growth and development of Arabidopsis thaliana
items: A structural equation model for the patient safety competency of clinical nurses
items: Multi-environment QTL mapping identifies major genetic loci influencing soybean main stem node architecture
items: Effect of GR24 on the growth and development of licorice under low phosphorus stress

Tibetan red deer (Cervus canadensis wallichi) diet composition patterns and associations during lean seasons in Tibet, China
type: item
type: AcademicArticle
description: Tibetan red deer (Cervus canadensis wallichi) in the high-altitude environment of the Qinghai-Tibet Plateau could face seasonal challenges from food shortages and nutritional deficiencies but the nutritional requirements are complex. Analyzing diet composition pattern(s) is the first step to disentangle this complexity. From a systematic perspective, we hypothesize that: (A) diet composition pattern or patterns exist within the population and (B) a portion of the diet beyond characterized diet combinations will consist of random combinations. In this study, we investigated diet composition patterns of a Tibetan red deer population distributed in the Sangri Red Deer Reserve, Tibet Autonomous Region, during the harsh lean season. In March 2021 and 2022, we searched for Tibetan red deer in the reserve and collected freshly defecated samples. Diet composition at the individual level was determined using micro-histological analysis, followed by k-means clustering and co-occurrence network analysis to reveal population level diet composition patterns. Diet composition of Tibetan red deer included 14 and 19 plant species (or genera) in 2021 and 2022, respectively. K-means clustering indicated two distinct diet patterns within the population across both sampling periods. In 2021, diet composition of both clusters was dominated by Salix spp. (58.49% and 33.67%). In 2022, R. macrophylla had the highest ranking and occupied 34.83% of diet composition in the first cluster while Salix spp. (39.39%) was the most consumed food in the second cluster. Results of co-occurrence networks showed positively associated food combinations of less dominant food items, with a staple food occurring in all food item pairs in both years. However, randomness accounted for 95.83% and 93% of all food item pairs in 2021 and 2022, respectively, which implies a stable dietary complex system. The 2022 co-occurrence network displayed complex associations, while the 2021 network exhibited limited and sim…
format: application/pdf
format: text/html
creator: Xiaoping Liang
creator: Kaili Wei
creator: Qinfang Li
creator: Aaron Gooley
creator: Minghai Zhang
creator: Jingjing Yu
creator: Zhongbin Wang
creator: Changxiao Yin
creator: Weiqi Zhang
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.18614
publisher: PeerJ Inc.
rights: © 2024 Liang et al.
abstract: Tibetan red deer (Cervus canadensis wallichi) in the high-altitude environment of the Qinghai-Tibet Plateau could face seasonal challenges from food shortages and nutritional deficiencies but the nutritional requirements are complex. Analyzing diet composition pattern(s) is the first step to disentangle this complexity. From a systematic perspective, we hypothesize that: (A) diet composition pattern or patterns exist within the population and (B) a portion of the diet beyond characterized diet combinations will consist of random combinations. In this study, we investigated diet composition patterns of a Tibetan red deer population distributed in the Sangri Red Deer Reserve, Tibet Autonomous Region, during the harsh lean season. In March 2021 and 2022, we searched for Tibetan red deer in the reserve and collected freshly defecated samples. Diet composition at the individual level was determined using micro-histological analysis, followed by k-means clustering and co-occurrence network analysis to reveal population level diet composition patterns. Diet composition of Tibetan red deer included 14 and 19 plant species (or genera) in 2021 and 2022, respectively. K-means clustering indicated two distinct diet patterns within the population across both sampling periods. In 2021, diet composition of both clusters was dominated by Salix spp. (58.49% and 33.67%). In 2022, R. macrophylla had the highest ranking and occupied 34.83% of diet composition in the first cluster while Salix spp. (39.39%) was the most consumed food in the second cluster. Results of co-occurrence networks showed positively associated food combinations of less dominant food items, with a staple food occurring in all food item pairs in both years. However, randomness accounted for 95.83% and 93% of all food item pairs in 2021 and 2022, respectively, which implies a stable dietary complex system. The 2022 co-occurrence network displayed complex associations, while the 2021 network exhibited limited and sim…
bibliographic citation: Liang et al. (2024) Tibetan red deer (Cervus canadensis wallichi) diet composition patterns and associations during lean seasons in Tibet, China. PeerJ 12:e18614 https://doi.org/10.7717/peerj.18614
date submitted: 2024-07-18
date accepted: 2024-11-08
issued: 2024-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Liang
  given name: Xiaoping
author list: Agent
  family name: Wei
  given name: Kaili
author list: Agent
  family name: Li
  given name: Qinfang
author list: Agent
  family name: Gooley
  given name: Aaron
author list: Agent
  family name: Zhang
  given name: Minghai
author list: Agent
  family name: Yu
  given name: Jingjing
author list: Agent
  family name: Wang
  given name: Zhongbin
author list: Agent
  family name: Yin
  given name: Changxiao
author list: Agent
  family name: Zhang
  given name: Weiqi
doi: 10.7717/peerj.18614
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-27
copyright: ©2024 Liang et al.
attribution name: Liang et al.

Comparative efficacy and safety of 180 W XPS vs. 120 W HPS GreenLight laser therapy for benign prostatic hyperplasia: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Objectives To compare the surgical and functional outcomes of the 120 W HPS and 180 W XPS GreenLight laser vaporization systems in the treatment of benign prostatic hyperplasia (BPH). Methods In January 2024, a comprehensive search across PubMed, Cochrane Library, and EMBASE was conducted following PRISMA guidelines, registered under PROSPERO (CRD42024531176). Studies comparing 120 W and 180 W GreenLight lasers in BPH treatment were assessed for clinical outcomes. Results Eight studies were included. The 180 W XPS system improved operation time (MD: 12.70, 95% CI [5.29–20.11], p = 0.0008), lasing duration (MD: 10.09, 95% CI [0.85–19.33], p = 0.03), and catheterization duration (MD: 0.43, 95% CI [0.12–0.74], p = 0.007). No significant differences in energy consumption, energy density, or length of hospital stay were found. Functional outcomes such as International Prostate Symptom Score and maximum urinary flow rate showed no significant differences, except in quality of life (MD: 0.43, 95% CI [0.06–0.80], p = 0.02) and prostate-specific antigen levels (MD: −0.77, 95% CI [−1.28 to −0.25], p = 0.003). The 180 W system exhibited a lower rate of overall (OR: 1.52, 95% CI [1.14–2.04], p = 0.005) and minor complications (OR: 1.84, 95% CI [1.27–2.66], p = 0.001), with no significant differences in major complications or other adverse events. Conclusions The 180 W XPS system demonstrates enhanced efficiency and reduced complication rates, offering a favorable option for BPH treatment, particularly for larger prostates. Future studies should focus on randomized trials to confirm these findings and assess long-term outcomes.
format: application/pdf
format: text/html
creator: Min Wang
creator: Yu Xi
creator: Zan Qiu
creator: Nanxiang Huang
creator: Li Zhang
creator: Jinlong Liu
subject: Drugs and Devices
subject: Public Health
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.18615
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Objectives To compare the surgical and functional outcomes of the 120 W HPS and 180 W XPS GreenLight laser vaporization systems in the treatment of benign prostatic hyperplasia (BPH). Methods In January 2024, a comprehensive search across PubMed, Cochrane Library, and EMBASE was conducted following PRISMA guidelines, registered under PROSPERO (CRD42024531176). Studies comparing 120 W and 180 W GreenLight lasers in BPH treatment were assessed for clinical outcomes. Results Eight studies were included. The 180 W XPS system improved operation time (MD: 12.70, 95% CI [5.29–20.11], p = 0.0008), lasing duration (MD: 10.09, 95% CI [0.85–19.33], p = 0.03), and catheterization duration (MD: 0.43, 95% CI [0.12–0.74], p = 0.007). No significant differences in energy consumption, energy density, or length of hospital stay were found. Functional outcomes such as International Prostate Symptom Score and maximum urinary flow rate showed no significant differences, except in quality of life (MD: 0.43, 95% CI [0.06–0.80], p = 0.02) and prostate-specific antigen levels (MD: −0.77, 95% CI [−1.28 to −0.25], p = 0.003). The 180 W system exhibited a lower rate of overall (OR: 1.52, 95% CI [1.14–2.04], p = 0.005) and minor complications (OR: 1.84, 95% CI [1.27–2.66], p = 0.001), with no significant differences in major complications or other adverse events. Conclusions The 180 W XPS system demonstrates enhanced efficiency and reduced complication rates, offering a favorable option for BPH treatment, particularly for larger prostates. Future studies should focus on randomized trials to confirm these findings and assess long-term outcomes.
bibliographic citation: Wang et al. (2024) Comparative efficacy and safety of 180 W XPS vs. 120 W HPS GreenLight laser therapy for benign prostatic hyperplasia: a systematic review and meta-analysis. PeerJ 12:e18615 https://doi.org/10.7717/peerj.18615
date submitted: 2024-06-17
date accepted: 2024-11-08
issued: 2024-11-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Xi
  given name: Yu
author list: Agent
  family name: Qiu
  given name: Zan
author list: Agent
  family name: Huang
  given name: Nanxiang
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Liu
  given name: Jinlong
doi: 10.7717/peerj.18615
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-27
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria)
type: item
type: AcademicArticle
description: Background Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality. Methods We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2. Results D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.
format: application/pdf
format: text/html
creator: Ian Hewson
creator: Marilyn Brandt
creator: Kayla Budd
creator: Mya Breitbart
creator: Christopher DeRito
creator: Samuel Gittens Jr
creator: Michael W. Henson
creator: Alwin Hylkema
creator: Moriah Sevier
creator: Matthew Souza
creator: Brayan Vilanova-Cuevas
creator: Sarah Von Hoene
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Virology
subject: Biological Oceanography
description: doi:10.7717/peerj.18321
publisher: PeerJ Inc.
rights: © 2024 Hewson et al.
abstract: Background Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality. Methods We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2. Results D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.
bibliographic citation: Hewson et al. (2024) Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria). PeerJ 12:e18321 https://doi.org/10.7717/peerj.18321
date submitted: 2024-06-17
date accepted: 2024-09-24
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hewson
  given name: Ian
author list: Agent
  family name: Brandt
  given name: Marilyn
author list: Agent
  family name: Budd
  given name: Kayla
author list: Agent
  family name: Breitbart
  given name: Mya
author list: Agent
  family name: DeRito
  given name: Christopher
author list: Agent
  family name: Gittens Jr
  given name: Samuel
author list: Agent
  family name: Henson
  given name: Michael W.
author list: Agent
  family name: Hylkema
  given name: Alwin
author list: Agent
  family name: Sevier
  given name: Moriah
author list: Agent
  family name: Souza
  given name: Matthew
author list: Agent
  family name: Vilanova-Cuevas
  given name: Brayan
author list: Agent
  family name: Von Hoene
  given name: Sarah
doi: 10.7717/peerj.18321
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: ©2024 Hewson et al.
attribution name: Hewson et al.

Early-diverging plesiosaurs from the Pliensbachian (Lower Jurassic) of northwestern Germany
type: item
type: AcademicArticle
description: The knowledge of Pliensbachian (Early Jurassic, ∼192.9–184.2 Ma) plesiosaurs is notoriously insufficient. Although there have been specimens described from different parts of the world, only three of them have been established as diagnosable taxa. Here, we describe two previously unreported lower Pliensbachian plesiosaur occurrences that originate from two sites located in North Rhine-Westphalia, Germany. One of the new occurrences is represented by three cervical and three indeterminable vertebrae from Werther, the other includes two associated pectoral or anterior dorsal vertebrae from Bielefeld. Although highly incomplete, the Werther individual, which derived from the Uptonia jamesoni Zone, is found to represent the only reliably identified early Pliensbachian pliosaurid known to date. Its material is geographically and stratigraphically proximate to the late Pliensbachian pliosaurid Arminisaurus schuberti, found in a clay-pit located in the Bielefeld district of Jöllenbeck. However, even though the Werther plesiosaur and A. schuberti show a broadly similar morphology of the preserved cervical section, a precise identification of the Werther taxon is currently impossible.
format: application/pdf
format: text/html
creator: Sven Sachs
creator: Jahn J. Hornung
creator: Daniel Madzia
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.18408
publisher: PeerJ Inc.
rights: © 2024 Sachs et al.
abstract: The knowledge of Pliensbachian (Early Jurassic, ∼192.9–184.2 Ma) plesiosaurs is notoriously insufficient. Although there have been specimens described from different parts of the world, only three of them have been established as diagnosable taxa. Here, we describe two previously unreported lower Pliensbachian plesiosaur occurrences that originate from two sites located in North Rhine-Westphalia, Germany. One of the new occurrences is represented by three cervical and three indeterminable vertebrae from Werther, the other includes two associated pectoral or anterior dorsal vertebrae from Bielefeld. Although highly incomplete, the Werther individual, which derived from the Uptonia jamesoni Zone, is found to represent the only reliably identified early Pliensbachian pliosaurid known to date. Its material is geographically and stratigraphically proximate to the late Pliensbachian pliosaurid Arminisaurus schuberti, found in a clay-pit located in the Bielefeld district of Jöllenbeck. However, even though the Werther plesiosaur and A. schuberti show a broadly similar morphology of the preserved cervical section, a precise identification of the Werther taxon is currently impossible.
bibliographic citation: Sachs et al. (2024) Early-diverging plesiosaurs from the Pliensbachian (Lower Jurassic) of northwestern Germany. PeerJ 12:e18408 https://doi.org/10.7717/peerj.18408
date submitted: 2024-05-17
date accepted: 2024-10-06
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sachs
  given name: Sven
author list: Agent
  family name: Hornung
  given name: Jahn J.
author list: Agent
  family name: Madzia
  given name: Daniel
doi: 10.7717/peerj.18408
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: ©2024 Sachs et al.
attribution name: Sachs et al.

Diffuse idiopathic skeletal hyperostosis was the specific risk factors of methicillin-susceptible Staphylococcus aureus spine infection: a retrospective study in a single center
type: item
type: AcademicArticle
description: Aim To investigate how risk factors and reduced spinal mobility contribute to spinal infections arising from methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia, known for increased mortality and diagnostic difficulties, especially in patients with septic shock or coma. Methods This retrospective study divided MSSA bacteremia patients into three groups: spinal infections (Group A, n = 14), non-spinal/implant infections (Group B, n = 24), and implant-related infections (Group C, n = 21). Analyses focused on demographics, medical history, laboratory inflammatory markers at antibiotic initiation, and spinal pathologies detected by CT. All results of the statistical analyses were significant at P < 0.05. We employed multinomial univariable logistic regression and contingency table analysis to assess risk factors across three groups. Subsequently, binomial multivariable logistic regression was used to compare Group A against Groups B and C, successfully identifying significant predictors of spinal infection. Results A lower incidence of diabetes (p = 0.029), higher C-reactive protein (CRP) levels at onset (p = 0.014), and the presence of diffuse idiopathic skeletal hyperostosis (diffuse idiopathic skeletal hyperostosis (DISH); p = 0.022) were significantly associated with spinal infections in Group A. Furthermore, binomial analysis revealed DISH (Odds Ratio (OR) = 41.750; 95% Confidence Interval (CI) [1.86–939.0]; p = 0.019), absence of diabetes (OR = 1.20, CI [1.01–1.43], p = 0.038), elevated CRP (OR = 23.34, CI [1.13–483.4], p = 0.042), and a lower day 3/day 1 white blood cell (WBC) ratio (OR = 0.964, CI [0.93–1.00], p = 0.047) as risk factors when compared with other groups. Conclusion Spinal infection patients with MSSA bacteremia are less likely to have diabetes and more likely to have higher initial CRP levels and DISH. Notably, DISH might be emerging as a distinctive risk factor for spinal infection, underscoring its potential as a marker for clinical …
format: application/pdf
format: text/html
creator: Kaori Endo
subject: Microbiology
subject: Infectious Diseases
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Rheumatology
description: doi:10.7717/peerj.18432
publisher: PeerJ Inc.
rights: © 2024 Endo
abstract: Aim To investigate how risk factors and reduced spinal mobility contribute to spinal infections arising from methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia, known for increased mortality and diagnostic difficulties, especially in patients with septic shock or coma. Methods This retrospective study divided MSSA bacteremia patients into three groups: spinal infections (Group A, n = 14), non-spinal/implant infections (Group B, n = 24), and implant-related infections (Group C, n = 21). Analyses focused on demographics, medical history, laboratory inflammatory markers at antibiotic initiation, and spinal pathologies detected by CT. All results of the statistical analyses were significant at P < 0.05. We employed multinomial univariable logistic regression and contingency table analysis to assess risk factors across three groups. Subsequently, binomial multivariable logistic regression was used to compare Group A against Groups B and C, successfully identifying significant predictors of spinal infection. Results A lower incidence of diabetes (p = 0.029), higher C-reactive protein (CRP) levels at onset (p = 0.014), and the presence of diffuse idiopathic skeletal hyperostosis (diffuse idiopathic skeletal hyperostosis (DISH); p = 0.022) were significantly associated with spinal infections in Group A. Furthermore, binomial analysis revealed DISH (Odds Ratio (OR) = 41.750; 95% Confidence Interval (CI) [1.86–939.0]; p = 0.019), absence of diabetes (OR = 1.20, CI [1.01–1.43], p = 0.038), elevated CRP (OR = 23.34, CI [1.13–483.4], p = 0.042), and a lower day 3/day 1 white blood cell (WBC) ratio (OR = 0.964, CI [0.93–1.00], p = 0.047) as risk factors when compared with other groups. Conclusion Spinal infection patients with MSSA bacteremia are less likely to have diabetes and more likely to have higher initial CRP levels and DISH. Notably, DISH might be emerging as a distinctive risk factor for spinal infection, underscoring its potential as a marker for clinical …
bibliographic citation: Endo (2024) Diffuse idiopathic skeletal hyperostosis was the specific risk factors of methicillin-susceptible Staphylococcus aureus spine infection: a retrospective study in a single center. PeerJ 12:e18432 https://doi.org/10.7717/peerj.18432
date submitted: 2022-09-26
date accepted: 2024-10-09
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Endo
  given name: Kaori
doi: 10.7717/peerj.18432
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: ©2024 Endo
attribution name: Endo

Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma
type: item
type: AcademicArticle
description: Canine cutaneous histiocytoma (CCH) is a tumor that originates from dermal Langerhans cells and affects particularly young dogs. The common spontaneous regression of CCH makes it an interesting model in comparative oncology research. Previous studies have indicated that anti-tumor immune responses may be involved, but details remain speculative to date. Here, we asked which specific immuno-oncological dynamics underlie spontaneous regression of CCH on mRNA and protein levels. QuantSeq 3′ mRNA sequencing with functional over-representation analysis and an nCounter RNA hybridization assay were employed on 21 formalin-fixed, paraffin-embedded CCH samples representing three different tumor stages (dataset information: GSE261387—Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma—OmicsDI). Nine additional samples were subjected to matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Surprisingly, only minor stage-specific differences were found. When we investigated expression of B7 family ligands and CD28 family receptors holding co-stimulatory and -inhibitory functions, respectively, we found a higher abundance of CD80, CD86, CTLA4 and CD28, which may trigger a balanced activation of lymphocyte-mediated immune responses. CD80 and CD86 expressing cells were further quantified by in situ hybridization and compared with data from three cases of canine histiocytic sarcoma (HS), a malignant tumor variant originating from antigen-presenting interstitial dendritic cells. A stage-specific increase of CD80 expressing cells was recorded in CCH from the tumor bottom to the top, while CD86 was continuously and homogenously expressed at high levels. Overall expression of CD80 in CCH was similar to that in HS (73.3 ± 37.4% vs 62.1 ± 46.4%), while significantly more CD86 expressing tumor cells were found in CCH (94.7 ± 10.3%) when compared to HS (57.6 ± 11.0%). Our da…
format: application/pdf
format: text/html
creator: Alina K. Loriani Fard
creator: Alexander Haake
creator: Vladimir Jovanovic
creator: Sandro Andreotti
creator: Michael Hummel
creator: Benjamin-Florian Hempel
creator: Achim D. Gruber
subject: Molecular Biology
subject: Veterinary Medicine
subject: Immunology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.18444
publisher: PeerJ Inc.
rights: © 2024 Loriani Fard et al.
abstract: Canine cutaneous histiocytoma (CCH) is a tumor that originates from dermal Langerhans cells and affects particularly young dogs. The common spontaneous regression of CCH makes it an interesting model in comparative oncology research. Previous studies have indicated that anti-tumor immune responses may be involved, but details remain speculative to date. Here, we asked which specific immuno-oncological dynamics underlie spontaneous regression of CCH on mRNA and protein levels. QuantSeq 3′ mRNA sequencing with functional over-representation analysis and an nCounter RNA hybridization assay were employed on 21 formalin-fixed, paraffin-embedded CCH samples representing three different tumor stages (dataset information: GSE261387—Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma—OmicsDI). Nine additional samples were subjected to matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Surprisingly, only minor stage-specific differences were found. When we investigated expression of B7 family ligands and CD28 family receptors holding co-stimulatory and -inhibitory functions, respectively, we found a higher abundance of CD80, CD86, CTLA4 and CD28, which may trigger a balanced activation of lymphocyte-mediated immune responses. CD80 and CD86 expressing cells were further quantified by in situ hybridization and compared with data from three cases of canine histiocytic sarcoma (HS), a malignant tumor variant originating from antigen-presenting interstitial dendritic cells. A stage-specific increase of CD80 expressing cells was recorded in CCH from the tumor bottom to the top, while CD86 was continuously and homogenously expressed at high levels. Overall expression of CD80 in CCH was similar to that in HS (73.3 ± 37.4% vs 62.1 ± 46.4%), while significantly more CD86 expressing tumor cells were found in CCH (94.7 ± 10.3%) when compared to HS (57.6 ± 11.0%). Our da…
bibliographic citation: Loriani Fard et al. (2024) Immuno-oncologic profiling by stage-dependent transcriptome and proteome analyses of spontaneously regressing canine cutaneous histiocytoma. PeerJ 12:e18444 https://doi.org/10.7717/peerj.18444
date submitted: 2024-05-20
date accepted: 2024-10-11
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loriani Fard
  given name: Alina K.
author list: Agent
  family name: Haake
  given name: Alexander
author list: Agent
  family name: Jovanovic
  given name: Vladimir
author list: Agent
  family name: Andreotti
  given name: Sandro
author list: Agent
  family name: Hummel
  given name: Michael
author list: Agent
  family name: Hempel
  given name: Benjamin-Florian
author list: Agent
  family name: Gruber
  given name: Achim D.
doi: 10.7717/peerj.18444
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: © 2024 Loriani Fard et al.
attribution name: Loriani Fard et al.

LRR1 involved in the abscisic acid signaling pathway to regulate the early growth and development of Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Living organisms possess the remarkable capacity to swiftly adapt to fluctuations in their environment. In the context of cell signal transduction, a significant challenge lies in ensuring the effective perception of external signals and the execution of appropriate responses. To investigate this phenomenon, a recent study utilized Arabidopsis thaliana as a model plant and induced stress by administering abscisic acid (ABA), a plant hormone, to elucidate the involvement of leucine-rich repeat receptor-like kinase1 (LRR1) in ABA signaling pathways. Methods Homozygous T-DNA insertion alleles for LRR1 and KIN7 were isolated. Quantitative real-time PCR (qRT-PCR) was performed to confirm the expression of the LRR1 gene. Subcellular localization and beta-glucuronidase (GUS) tissue labeling techniques were utilized to determine the expression pattern of the LRR1 gene in cells and tissues. Yeast two-hybrid complementation, bimolecular fluorescence complementation assay, and GST pull-down assays were conducted to validate the interaction of LRR1 proteins. Results Phenotypic analyses revealed that lrr1 and kin7 mutants are less sensitive to the inhibitory effects of ABA on germination and cotyledon greening that is seen in WT. Mutants LRR1 and kinase 7 (KIN7) exhibited resistance to ABA and displayed normal growth patterns under control conditions. The double mutant lrr1kin7 showed reduced responsiveness to ABA. Conversely, overexpression lines LRR1ox2 and LRR1ox10 demonstrated heightened sensitivity to ABA, resulting in severe growth reduction. qRT-PCR assay indicated that exogenous application of ABA led to significant down-regulation of ABI3, ABI4, and ABI5 transcription factors in LRR1 material compared to wild-type WT material. An investigation was conducted to determine the expression pattern and transcriptional level of LRR1 in Arabidopsis. The results revealed ubiquitous expression of LRR1 across all developmental stages and tissue tested. Subcellular local…
format: application/pdf
format: text/html
creator: Xiaoyang Xie
creator: Lei Wei
creator: Hongyuan Han
creator: Bingnian Jing
creator: Yuqing Liu
creator: Yong Zhou
creator: Ningjie Li
creator: Xiao Li
creator: Wei Wang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.18460
publisher: PeerJ Inc.
rights: © 2024 Xie et al.
abstract: Background Living organisms possess the remarkable capacity to swiftly adapt to fluctuations in their environment. In the context of cell signal transduction, a significant challenge lies in ensuring the effective perception of external signals and the execution of appropriate responses. To investigate this phenomenon, a recent study utilized Arabidopsis thaliana as a model plant and induced stress by administering abscisic acid (ABA), a plant hormone, to elucidate the involvement of leucine-rich repeat receptor-like kinase1 (LRR1) in ABA signaling pathways. Methods Homozygous T-DNA insertion alleles for LRR1 and KIN7 were isolated. Quantitative real-time PCR (qRT-PCR) was performed to confirm the expression of the LRR1 gene. Subcellular localization and beta-glucuronidase (GUS) tissue labeling techniques were utilized to determine the expression pattern of the LRR1 gene in cells and tissues. Yeast two-hybrid complementation, bimolecular fluorescence complementation assay, and GST pull-down assays were conducted to validate the interaction of LRR1 proteins. Results Phenotypic analyses revealed that lrr1 and kin7 mutants are less sensitive to the inhibitory effects of ABA on germination and cotyledon greening that is seen in WT. Mutants LRR1 and kinase 7 (KIN7) exhibited resistance to ABA and displayed normal growth patterns under control conditions. The double mutant lrr1kin7 showed reduced responsiveness to ABA. Conversely, overexpression lines LRR1ox2 and LRR1ox10 demonstrated heightened sensitivity to ABA, resulting in severe growth reduction. qRT-PCR assay indicated that exogenous application of ABA led to significant down-regulation of ABI3, ABI4, and ABI5 transcription factors in LRR1 material compared to wild-type WT material. An investigation was conducted to determine the expression pattern and transcriptional level of LRR1 in Arabidopsis. The results revealed ubiquitous expression of LRR1 across all developmental stages and tissue tested. Subcellular local…
bibliographic citation: Xie et al. (2024) LRR1 involved in the abscisic acid signaling pathway to regulate the early growth and development of Arabidopsis thaliana. PeerJ 12:e18460 https://doi.org/10.7717/peerj.18460
date submitted: 2024-02-23
date accepted: 2024-10-14
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Xiaoyang
author list: Agent
  family name: Wei
  given name: Lei
author list: Agent
  family name: Han
  given name: Hongyuan
author list: Agent
  family name: Jing
  given name: Bingnian
author list: Agent
  family name: Liu
  given name: Yuqing
author list: Agent
  family name: Zhou
  given name: Yong
author list: Agent
  family name: Li
  given name: Ningjie
author list: Agent
  family name: Li
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Wei
doi: 10.7717/peerj.18460
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: ©2024 Xie et al.
attribution name: Xie et al.

A structural equation model for the patient safety competency of clinical nurses
type: item
type: AcademicArticle
description: Background Nurses are crucial for enhancing patient safety due to their continuous presence at patients’ bedsides and close interactions with families and other healthcare providers. This study aims to examine the relationships among safety education, perception of patient safety culture, safety control, and patient safety competence in clinical nurses, while also exploring the mediating effect of perceptions on patient safety culture and safety control. Methods The study involved 165 nurses, including 10 males (6.1%) and 155 females (93.9%). Structural equation modeling (SEM) was used to test the hypothesized model, and data were analyzed using SPSS and AMOS programs. Results Significant positive correlations were among the frequency of attending safety education, the perception of patient safety culture, safety control, and patient safety competency. The number of safety education briefings attended did not directly influence patient safety competence; however, safety education for nurses indirectly influenced patient safety competence via the perception of patient safety culture and safety control. These findings suggest that enhancing safety education for nurses can improve patient safety competence by shaping their perceptions of patient safety culture and safety control.
format: application/pdf
format: text/html
creator: Jung-hyun Choi
creator: KyoungEun Kim
subject: Nursing
subject: Healthcare Services
description: doi:10.7717/peerj.18462
publisher: PeerJ Inc.
rights: © 2024 Choi and Kim
abstract: Background Nurses are crucial for enhancing patient safety due to their continuous presence at patients’ bedsides and close interactions with families and other healthcare providers. This study aims to examine the relationships among safety education, perception of patient safety culture, safety control, and patient safety competence in clinical nurses, while also exploring the mediating effect of perceptions on patient safety culture and safety control. Methods The study involved 165 nurses, including 10 males (6.1%) and 155 females (93.9%). Structural equation modeling (SEM) was used to test the hypothesized model, and data were analyzed using SPSS and AMOS programs. Results Significant positive correlations were among the frequency of attending safety education, the perception of patient safety culture, safety control, and patient safety competency. The number of safety education briefings attended did not directly influence patient safety competence; however, safety education for nurses indirectly influenced patient safety competence via the perception of patient safety culture and safety control. These findings suggest that enhancing safety education for nurses can improve patient safety competence by shaping their perceptions of patient safety culture and safety control.
bibliographic citation: Choi et al. (2024) A structural equation model for the patient safety competency of clinical nurses. PeerJ 12:e18462 https://doi.org/10.7717/peerj.18462
date submitted: 2024-04-30
date accepted: 2024-10-14
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Jung-hyun
author list: Agent
  family name: Kim
  given name: KyoungEun
doi: 10.7717/peerj.18462
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: © 2024 Choi and Kim
attribution name: Choi and Kim

Multi-environment QTL mapping identifies major genetic loci influencing soybean main stem node architecture
type: item
type: AcademicArticle
description: Soybean plant architecture has a significant impact on yield potential, but the genetic underpinnings of key architectural traits remain elusive. The primary objective of this study was to explore the genetic foundations underlying main stem node number (MSN) in soybeans. Recombinant inbred lines (RILs) contained a 234 individual derived from crosses between two cultivars Zhonghuang35 (ZH35) and Jindou21 (JD21) was evaluated for seed hardness across 3 years (2013, 2014, and 2015 in Gansu). Markedly, the parent varieties, shown significant differences in MSN. Also, the RIL population exhibited a wide range of genetic variation in MSN. A high-density genetic map composed of 8,078 specific-locus amplified fragment (SLAF) markers, spanning 3,480.98 centimorgans (cM) with an average inter-marker distance of 0.59 cM were used to construct linkage map. Using ICIM analysis identified a total of 23 Quantitative Trait Loci (QTLs) across the 20 chromosome, of which five QTLs were detected in multiple years in Chr.6. Notably, we identified a stable major QTL, qMSN-6-4, explaining up to 24.81% of phenotypic variation. This QTL govern seven candidate genes with potential roles in regulating MSN development in soybean, including Glyma.06G027500 with a domain of unknown function, Glyma.06G027600 involved in proton transport, Glyma.06G027700 linked to proteolysis, Glyma.06G027900 related to transcriptional regulation, and Glyma.06G028000 and Glyma.06G028050 associated with membrane functions. The RT-PCR analysis confirmed that these genes were expressed differently between the parental lines this supports the idea that they may play a role in determining MSN. Glyma.06G027500 and Glyma.06G027600 showing higher expression in JD21 leaves and nodes, while Glyma.06G027700 and Glyma.06G028000 exhibited increased expression in ZH35 stems, highlighting their distinct roles in transcription regulation, membrane activities, and protein degradation that contribute to MSN formation in soybean. …
format: application/pdf
format: text/html
creator: Honglei Ren
creator: Xue Qu
creator: Huilong Hong
creator: Lingling Sun
creator: Sobhi F. Lamlom
creator: Zhangxiong Liu
creator: Wencheng Lu
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.18539
publisher: PeerJ Inc.
rights: © 2024 Ren et al.
abstract: Soybean plant architecture has a significant impact on yield potential, but the genetic underpinnings of key architectural traits remain elusive. The primary objective of this study was to explore the genetic foundations underlying main stem node number (MSN) in soybeans. Recombinant inbred lines (RILs) contained a 234 individual derived from crosses between two cultivars Zhonghuang35 (ZH35) and Jindou21 (JD21) was evaluated for seed hardness across 3 years (2013, 2014, and 2015 in Gansu). Markedly, the parent varieties, shown significant differences in MSN. Also, the RIL population exhibited a wide range of genetic variation in MSN. A high-density genetic map composed of 8,078 specific-locus amplified fragment (SLAF) markers, spanning 3,480.98 centimorgans (cM) with an average inter-marker distance of 0.59 cM were used to construct linkage map. Using ICIM analysis identified a total of 23 Quantitative Trait Loci (QTLs) across the 20 chromosome, of which five QTLs were detected in multiple years in Chr.6. Notably, we identified a stable major QTL, qMSN-6-4, explaining up to 24.81% of phenotypic variation. This QTL govern seven candidate genes with potential roles in regulating MSN development in soybean, including Glyma.06G027500 with a domain of unknown function, Glyma.06G027600 involved in proton transport, Glyma.06G027700 linked to proteolysis, Glyma.06G027900 related to transcriptional regulation, and Glyma.06G028000 and Glyma.06G028050 associated with membrane functions. The RT-PCR analysis confirmed that these genes were expressed differently between the parental lines this supports the idea that they may play a role in determining MSN. Glyma.06G027500 and Glyma.06G027600 showing higher expression in JD21 leaves and nodes, while Glyma.06G027700 and Glyma.06G028000 exhibited increased expression in ZH35 stems, highlighting their distinct roles in transcription regulation, membrane activities, and protein degradation that contribute to MSN formation in soybean. …
bibliographic citation: Ren et al. (2024) Multi-environment QTL mapping identifies major genetic loci influencing soybean main stem node architecture. PeerJ 12:e18539 https://doi.org/10.7717/peerj.18539
date submitted: 2024-10-10
date accepted: 2024-10-27
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Honglei
author list: Agent
  family name: Qu
  given name: Xue
author list: Agent
  family name: Hong
  given name: Huilong
author list: Agent
  family name: Sun
  given name: Lingling
author list: Agent
  family name: Lamlom
  given name: Sobhi F.
author list: Agent
  family name: Liu
  given name: Zhangxiong
author list: Agent
  family name: Lu
  given name: Wencheng
doi: 10.7717/peerj.18539
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: © 2024 Ren et al.
attribution name: Ren et al.

Effect of GR24 on the growth and development of licorice under low phosphorus stress
type: item
type: AcademicArticle
description: Background Glycyrrhiza, a perennial herbaceous medicinal plant, is extensively utilized in the pharmaceutical industry. The growth of Glycyrrhiza is frequently constrained by soil phosphorus availability, as a significant portion of arable land in China suffers from phosphorus deficiency. Method This study utilized Ural Glycyrrhiza uralensis Fisch as the subject and examined the application of GR24, a synthetic strigolactone, under three phosphorus conditions: none (P1), low (P2), and high (P3). The research aimed to ascertain the optimal concentration of GR24 for promoting licorice growth and development, thereby providing a theoretical foundation for its agricultural management. Results The optimal GR24 concentration for P3 and P2 conditions was identified as G3 (10 µM), which enhanced growth metrics, chlorophyll a and b levels, while also boosting antioxidant enzyme activities in licorice. Specifically under P3, significant increases in liquiritigenin and glycyrrhizic acid levels were observed. Under P2, increases were noted in isoliquiritigenin, liquiritigenin, and liquiritin levels. Transcriptome analysis revealed differential gene, with 137 and 270 genes up-regulated and 77 and 294 genes down-regulated in the P3 and P2 treatments, respectively. GO functional enrichment identified 132 and 436 differentially expressed genes for P3 and P2 respectively, while KEGG pathways were predominantly enriched in plant-pathogen interactions and phenylpropanoid biosynthesis. Application of GR24 in P1 conditions did not significantly affect growth indices but did enhance glycyrrhetic acid, isoliquiritin, and liquiritin accumulation. Transcriptome profiling in this treatment identified 465 up-regulated and 1,109 down-regulated genes. GO annotation involved 1,108 differentially expressed genes, and KEGG analysis was primarily enriched in the plant-pathogen interaction pathway. Furthermore, transcription factor analysis revealed alterations in the C2H2, NAC, and MYB families, wh…
format: application/pdf
format: text/html
creator: Yuting Jing
creator: Man Li
creator: Yong Wu
creator: Chengming Zhang
creator: Chengshu Qiu
creator: Hengming Zhao
creator: Li Zhuang
creator: Hongling Liu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18546
publisher: PeerJ Inc.
rights: © 2024 Jing et al.
abstract: Background Glycyrrhiza, a perennial herbaceous medicinal plant, is extensively utilized in the pharmaceutical industry. The growth of Glycyrrhiza is frequently constrained by soil phosphorus availability, as a significant portion of arable land in China suffers from phosphorus deficiency. Method This study utilized Ural Glycyrrhiza uralensis Fisch as the subject and examined the application of GR24, a synthetic strigolactone, under three phosphorus conditions: none (P1), low (P2), and high (P3). The research aimed to ascertain the optimal concentration of GR24 for promoting licorice growth and development, thereby providing a theoretical foundation for its agricultural management. Results The optimal GR24 concentration for P3 and P2 conditions was identified as G3 (10 µM), which enhanced growth metrics, chlorophyll a and b levels, while also boosting antioxidant enzyme activities in licorice. Specifically under P3, significant increases in liquiritigenin and glycyrrhizic acid levels were observed. Under P2, increases were noted in isoliquiritigenin, liquiritigenin, and liquiritin levels. Transcriptome analysis revealed differential gene, with 137 and 270 genes up-regulated and 77 and 294 genes down-regulated in the P3 and P2 treatments, respectively. GO functional enrichment identified 132 and 436 differentially expressed genes for P3 and P2 respectively, while KEGG pathways were predominantly enriched in plant-pathogen interactions and phenylpropanoid biosynthesis. Application of GR24 in P1 conditions did not significantly affect growth indices but did enhance glycyrrhetic acid, isoliquiritin, and liquiritin accumulation. Transcriptome profiling in this treatment identified 465 up-regulated and 1,109 down-regulated genes. GO annotation involved 1,108 differentially expressed genes, and KEGG analysis was primarily enriched in the plant-pathogen interaction pathway. Furthermore, transcription factor analysis revealed alterations in the C2H2, NAC, and MYB families, wh…
bibliographic citation: Jing et al. (2024) Effect of GR24 on the growth and development of licorice under low phosphorus stress. PeerJ 12:e18546 https://doi.org/10.7717/peerj.18546
date submitted: 2024-05-28
date accepted: 2024-10-28
issued: 2024-11-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jing
  given name: Yuting
author list: Agent
  family name: Li
  given name: Man
author list: Agent
  family name: Wu
  given name: Yong
author list: Agent
  family name: Zhang
  given name: Chengming
author list: Agent
  family name: Qiu
  given name: Chengshu
author list: Agent
  family name: Zhao
  given name: Hengming
author list: Agent
  family name: Zhuang
  given name: Li
author list: Agent
  family name: Liu
  given name: Hongling
doi: 10.7717/peerj.18546
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-26
copyright: ©2024 Jing et al.
attribution name: Jing et al.

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