PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth
items: Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L.
items: Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus
items: Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia
items: COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression
items: The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures
items: Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis
items: Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index
items: Development of a welfare assessment tool for tourist camp elephants in Asia
items: Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part

The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth
type: item
type: AcademicArticle
description: Background The present in vitro study aimed to evaluate the fatigue behavior of teeth filled with a calcium silicate-based sealer (Bio-C Sealer, BC) or an epoxy resin-based sealer (AH Plus, AH), in bulk or associated with gutta-percha as main core material. Methods Seventy-two sound human maxillary anterior teeth were initially selected. Sixty of them, were randomly chosen, and had their root canals prepared using nickel-titanium reciprocating instruments, being again randomly assigned to five experimental groups (n = 12): C+ (control + prepared but not filled); BC-B (BC in bulk); BC-GP (BC+ gutta-percha); AP-B (AH in bulk); AP-GP (AH+ gutta-percha). An additional negative control group (C−) was considered (n = 12), consisting only on sound teeth, without preparation and filling. The specimens were submitted to a survival analysis after the cyclic fatigue test. Results Sound teeth (C−) presented the best fatigue performance (P < 0.05), being similar only to the AP-GP group (P > 0.05). Despite that, all experimental groups showed similar fatigue behavior (P > 0.05) to C+ (BC-B = BC-GP = AP-B = AP-GP = C+). Based on that, it can be seen that the use of gutta-percha, as a main core material, associated with the AH Plus sealer, reestablished the mechanical fatigue performance of endodontically treated teeth comparable to sound teeth, still consisting on the most promising approach to rehabilitate such scenario. Teeth filled in bulk, had discreetly higher risk of premature failures and inferior fatigue performance.
format: application/pdf
format: text/html
creator: Isabella Marian Lena
creator: Luiza Colpo Chiaratti
creator: Rafaela Oliveira Pilecco
creator: Renan Vaz Machry
creator: João Paulo Mendes Tribst
creator: Cornelis Johannes Kleverlaan
creator: Gabriel Kalil Rocha Pereira
creator: Renata Dornelles Morgental
subject: Dentistry
subject: Science and Medical Education
description: doi:10.7717/peerj.18221
publisher: PeerJ Inc.
rights: © 2024 Lena et al.
abstract: Background The present in vitro study aimed to evaluate the fatigue behavior of teeth filled with a calcium silicate-based sealer (Bio-C Sealer, BC) or an epoxy resin-based sealer (AH Plus, AH), in bulk or associated with gutta-percha as main core material. Methods Seventy-two sound human maxillary anterior teeth were initially selected. Sixty of them, were randomly chosen, and had their root canals prepared using nickel-titanium reciprocating instruments, being again randomly assigned to five experimental groups (n = 12): C+ (control + prepared but not filled); BC-B (BC in bulk); BC-GP (BC+ gutta-percha); AP-B (AH in bulk); AP-GP (AH+ gutta-percha). An additional negative control group (C−) was considered (n = 12), consisting only on sound teeth, without preparation and filling. The specimens were submitted to a survival analysis after the cyclic fatigue test. Results Sound teeth (C−) presented the best fatigue performance (P < 0.05), being similar only to the AP-GP group (P > 0.05). Despite that, all experimental groups showed similar fatigue behavior (P > 0.05) to C+ (BC-B = BC-GP = AP-B = AP-GP = C+). Based on that, it can be seen that the use of gutta-percha, as a main core material, associated with the AH Plus sealer, reestablished the mechanical fatigue performance of endodontically treated teeth comparable to sound teeth, still consisting on the most promising approach to rehabilitate such scenario. Teeth filled in bulk, had discreetly higher risk of premature failures and inferior fatigue performance.
bibliographic citation: Lena et al. (2024) The impact of the filling technique with two sealers in bulk or associated with gutta-percha on the fatigue behavior and failure patterns of endodontically treated teeth. PeerJ 12:e18221 https://doi.org/10.7717/peerj.18221
date submitted: 2024-06-20
date accepted: 2024-09-11
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lena
  given name: Isabella Marian
author list: Agent
  family name: Chiaratti
  given name: Luiza Colpo
author list: Agent
  family name: Pilecco
  given name: Rafaela Oliveira
author list: Agent
  family name: Machry
  given name: Renan Vaz
author list: Agent
  family name: Tribst
  given name: João Paulo Mendes
author list: Agent
  family name: Kleverlaan
  given name: Cornelis Johannes
author list: Agent
  family name: Pereira
  given name: Gabriel Kalil Rocha
author list: Agent
  family name: Morgental
  given name: Renata Dornelles
doi: 10.7717/peerj.18221
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Lena et al.
attribution name: Lena et al.

Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L.
type: item
type: AcademicArticle
description: Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (i.e., hydro-priming, halopriming by KNO3, and acid priming with HCl) in four ancient and neglected cultivars of Capsicum annuum L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO3 6% for 96 h > KNO3 4% for 48 h > hydropriming for 24 h. In particular, KNO3 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes.
format: application/pdf
format: text/html
creator: Angelo Granata
creator: Fiore Capozzi
creator: Anna Gaglione
creator: Riccardo Riccardi
creator: Patrizia Spigno
creator: Simonetta Giordano
creator: Maria Cristina Sorrentino
creator: Valeria Spagnuolo
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.18293
publisher: PeerJ Inc.
rights: © 2024 Granata et al.
abstract: Priming is basically a water-based technique inducing controlled seed rehydration to trigger the metabolic processes normally activated during the early phase of germination. It is regarded as an ecofriendly approach alternative to fertilizers in traditional agriculture, but also a method to synchronize off-field crops and resume stored seeds, improving vigor, and allowing for a rapid, uniform seedling emergence. In this work we tested several methods of seed priming (i.e., hydro-priming, halopriming by KNO3, and acid priming with HCl) in four ancient and neglected cultivars of Capsicum annuum L., a crop species belonging to Solanaceae family cultivated worldwide. We followed germination performance, seedling growth and selected morphological traits, antioxidant production in the leaves, and protein content of the seeds. Apart from acid priming, which inhibited root emergence, both hydropriming and halopriming decreased the mean germination time in all cultivars. The best treatments were KNO3 6% for 96 h > KNO3 4% for 48 h > hydropriming for 24 h. In particular, KNO3 6% for 96 h in all four cultivars significantly increased plant growth, simple vigor index, development germination index, leaf antioxidant concentration and protein content in the seeds, in comparison to control and other priming treatments, indicating the prompt activation of pre-germinative processes.
bibliographic citation: Granata et al. (2024) Seed priming enhances seed germination and plant growth in four neglected cultivars of Capsicum annuum L.. PeerJ 12:e18293 https://doi.org/10.7717/peerj.18293
date submitted: 2024-07-26
date accepted: 2024-09-21
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Granata
  given name: Angelo
author list: Agent
  family name: Capozzi
  given name: Fiore
author list: Agent
  family name: Gaglione
  given name: Anna
author list: Agent
  family name: Riccardi
  given name: Riccardo
author list: Agent
  family name: Spigno
  given name: Patrizia
author list: Agent
  family name: Giordano
  given name: Simonetta
author list: Agent
  family name: Sorrentino
  given name: Maria Cristina
author list: Agent
  family name: Spagnuolo
  given name: Valeria
doi: 10.7717/peerj.18293
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Granata et al.
attribution name: Granata et al.

Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus
type: item
type: AcademicArticle
description: Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family’s evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family.
format: application/pdf
format: text/html
creator: Xiaoqin Wang
creator: Dong Yan
creator: Ling Chen
subject: Bioinformatics
subject: Developmental Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18322
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Platycodon grandiflorus stands as one of the most extensively utilized traditional Chinese medicinal herbs, with triterpenoids and their derivatives serving as its primary medicinal components. Oxido squalene cyclase (OSC), serving as a crucial enzyme in the triterpenoid synthesis pathway, has the capability to enzymatically generate significant quantities of sterols and triterpenoid intermediates. While the OSC gene family has been identified in numerous species, bioinformatics research on this family remains scant. Presently, the specific members of this gene family in Platycodon grandiflorus have yet to be definitively determined. In this study, we successfully identified a total of 15 PgOSC genes within the genome of Platycodon grandiflorus by conducting homology comparisons. These genes were discovered to be unevenly distributed across the five chromosomes of the species, organized in the form of gene clusters. Subsequently, we conducted a thorough analysis of the OSC gene family’s evolutionary relationship by constructing a phylogenetic tree. Other characteristics of PgOSC family members, including gene structure, conserved motifs, protein three-dimensional structure, subcellular localization, and cis-acting elements were thoroughly characterized. Furthermore, We analyzed the expression of PgOSC gene in different tissues of Platycodon grandiflorus by qRT-PCR, and found that the expression of PgOSC genes in root was higher than that in stem and leaf. Upon comparing the effects of salt, heat, and drought treatments, we observed a significant induction of PgOSC gene expression in Platycodon grandiflorus specifically under salt stress conditions. In summary, this study comprehensively identified and analyzed the OSC gene family, aiming to provide basic biological information for exploring the members of PgOSC gene family.
bibliographic citation: Wang et al. (2024) Genome-wide identification and expression analysis of the OSC gene family in Platycodon grandiflorus. PeerJ 12:e18322 https://doi.org/10.7717/peerj.18322
date submitted: 2024-05-16
date accepted: 2024-09-24
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoqin
author list: Agent
  family name: Yan
  given name: Dong
author list: Agent
  family name: Chen
  given name: Ling
doi: 10.7717/peerj.18322
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: ©2024 Wang et al.
attribution name: Wang et al.

Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia
type: item
type: AcademicArticle
description: Background The interplay between chronic kidney disease (CKD) and thyroid dysfunction is becoming more evident in the biomedical community. However, the intricacies of their relationship warrant deeper investigation to understand the clinical implications fully. Objective This study aims to systematically evaluate the correlation between thyroid hormone levels, including thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4), and markers of renal disease severity. These markers include serum creatinine, urea, and parathyroid hormone (PTH) levels in individuals diagnosed with CK). Methods We conducted a cross-sectional observational study involving a cohort of 86 participants with CKD recruited from the renal clinic at King Fahad Hospital in Tabuk. Biochemical parameters, encompassing plasma electrolytes and thyroid hormone concentrations, were quantitatively assessed. These measurements were performed with the aid of a Roche Cobas E411 analyzer. The Pearson correlation coefficient was employed to delineate the strength and direction of the associations between the thyroid function markers and renal disease indicators. Results The statistical analysis highlighted a generally weak correlation between the concentrations of thyroid hormones and the indicators of renal disease severity, with Pearson correlation coefficients between −0.319 and 0.815. Critically, no significant correlation was found between creatinine and thyroid hormones (TSH, T3, T4), nor was any substantial correlation between urea and thyroid hormones. Conversely, a robust positive correlation was noted between the levels of parathyroid hormone and serum creatinine (r = 0.718, p < 0.001). Conclusion The data suggests that thyroid hormone levels have a minimal correlation with the severity of renal disease markers. In contrast, the pronounced correlation between PTH and creatinine underscores the importance of considering PTH as a significant factor in managing and therapeutic inte…
format: application/pdf
format: text/html
creator: Basmah Awwaadh
creator: Amal Hussain Mohammed
creator: Basmah F. Alharbi
creator: Abdulmohsen Alruwetei
creator: Tarique Sarwar
creator: Hajed Obaid Alharbi
creator: Fahad Alhumaydhi
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Hematology
subject: Nephrology
description: doi:10.7717/peerj.18338
publisher: PeerJ Inc.
rights: © 2024 Awwaadh et al.
abstract: Background The interplay between chronic kidney disease (CKD) and thyroid dysfunction is becoming more evident in the biomedical community. However, the intricacies of their relationship warrant deeper investigation to understand the clinical implications fully. Objective This study aims to systematically evaluate the correlation between thyroid hormone levels, including thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4), and markers of renal disease severity. These markers include serum creatinine, urea, and parathyroid hormone (PTH) levels in individuals diagnosed with CK). Methods We conducted a cross-sectional observational study involving a cohort of 86 participants with CKD recruited from the renal clinic at King Fahad Hospital in Tabuk. Biochemical parameters, encompassing plasma electrolytes and thyroid hormone concentrations, were quantitatively assessed. These measurements were performed with the aid of a Roche Cobas E411 analyzer. The Pearson correlation coefficient was employed to delineate the strength and direction of the associations between the thyroid function markers and renal disease indicators. Results The statistical analysis highlighted a generally weak correlation between the concentrations of thyroid hormones and the indicators of renal disease severity, with Pearson correlation coefficients between −0.319 and 0.815. Critically, no significant correlation was found between creatinine and thyroid hormones (TSH, T3, T4), nor was any substantial correlation between urea and thyroid hormones. Conversely, a robust positive correlation was noted between the levels of parathyroid hormone and serum creatinine (r = 0.718, p < 0.001). Conclusion The data suggests that thyroid hormone levels have a minimal correlation with the severity of renal disease markers. In contrast, the pronounced correlation between PTH and creatinine underscores the importance of considering PTH as a significant factor in managing and therapeutic inte…
bibliographic citation: Awwaadh et al. (2024) Association of thyroid hormones with the severity of chronic kidney disease: a cross-sectional observational study at Tabuk, Saudi Arabia. PeerJ 12:e18338 https://doi.org/10.7717/peerj.18338
date submitted: 2024-04-29
date accepted: 2024-09-26
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Awwaadh
  given name: Basmah
author list: Agent
  family name: Mohammed
  given name: Amal Hussain
author list: Agent
  family name: Alharbi
  given name: Basmah F.
author list: Agent
  family name: Alruwetei
  given name: Abdulmohsen
author list: Agent
  family name: Sarwar
  given name: Tarique
author list: Agent
  family name: Alharbi
  given name: Hajed Obaid
author list: Agent
  family name: Alhumaydhi
  given name: Fahad
doi: 10.7717/peerj.18338
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: ©2024 Awwaadh et al.
attribution name: Awwaadh et al.

COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression
type: item
type: AcademicArticle
description: Background Colorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression. Methods Using the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. The candidate biomarkers were also examined for constructing a prognostic model based on survival analysis. Results Among the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN…
format: application/pdf
format: text/html
creator: Ashok Palaniappan
creator: Sangeetha Muthamilselvan
creator: Arjun Sarathi
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.18347
publisher: PeerJ Inc.
rights: © 2024 Palaniappan et al.
abstract: Background Colorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression. Methods Using the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. The candidate biomarkers were also examined for constructing a prognostic model based on survival analysis. Results Among the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN…
bibliographic citation: Palaniappan et al. (2024) COADREADx: A comprehensive algorithmic dissection of colorectal cancer unravels salient biomarkers and actionable insights into its discrete progression. PeerJ 12:e18347 https://doi.org/10.7717/peerj.18347
date submitted: 2024-06-05
date accepted: 2024-09-27
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palaniappan
  given name: Ashok
author list: Agent
  family name: Muthamilselvan
  given name: Sangeetha
author list: Agent
  family name: Sarathi
  given name: Arjun
doi: 10.7717/peerj.18347
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: ©2024 Palaniappan et al.
attribution name: Palaniappan et al.

The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures
type: item
type: AcademicArticle
description: Background Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ) but not ${\mathrm{NO}}_{2}^{-}$ NO 2 − to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$ NO 3 − to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Furthermore, ${\mathrm{NO}}_{3}^{-}$ NO 3 − is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Methods Both strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$ NO 3 − , or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − / ${\mathrm{NO}}_{2}^{-}$ NO 2 − transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. Results The …
format: application/pdf
format: text/html
creator: Livie Lestin
creator: Richard Villemur
subject: Biochemistry
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.18361
publisher: PeerJ Inc.
rights: © 2024 Lestin and Villemur
abstract: Background Strain JAM1T and strain GP59 of the methylotrophic, bacterial species Methylophaga nitratireducenticrescens were isolated from a microbial community of the biofilm that developed in a fluidized-bed, methanol-fed, marine denitrification system. Despite of their common origin, both strains showed distinct physiological characters towards the dynamics of nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ) reduction. Strain JAM1T can reduce ${\mathrm{NO}}_{3}^{-}$ NO 3 − to nitrite ( ${\mathrm{NO}}_{2}^{-}$ NO 2 − ) but not ${\mathrm{NO}}_{2}^{-}$ NO 2 − to nitric oxide (NO) as it lacks a NO-forming ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase. Strain GP59 on the other hand can carry the complete reduction of ${\mathrm{NO}}_{3}^{-}$ NO 3 − to N2. Strain GP59 cultured under anoxic conditions shows a 24-48h lag phase before ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction occurs. In strain JAM1T cultures, ${\mathrm{NO}}_{3}^{-}$ NO 3 − reduction begins immediately with accumulation of ${\mathrm{NO}}_{2}^{-}$ NO 2 − . Furthermore, ${\mathrm{NO}}_{3}^{-}$ NO 3 − is reduced under oxic conditions in strain JAM1T cultures, which does not appear in strain GP59 cultures. These distinct characters suggest differences in the regulation pathways impacting the expression of denitrification genes, and ultimately growth. Methods Both strains were cultured under oxic conditions either with or without ${\mathrm{NO}}_{3}^{-}$ NO 3 − , or under anoxic conditions with ${\mathrm{NO}}_{3}^{-}$ NO 3 − . Transcript levels of selected denitrification genes (nar1 and nar2 encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − reductases, nirK encoding ${\mathrm{NO}}_{2}^{-}$ NO 2 − reductase, narK12f encoding ${\mathrm{NO}}_{3}^{-}$ NO 3 − / ${\mathrm{NO}}_{2}^{-}$ NO 2 − transporter) and regulatory genes (narXL and fnr) were determined by quantitative reverse transcription polymerase chain reaction. We also derived the transcriptomes of these cultures and determined their relative gene expression profiles. Results The …
bibliographic citation: Lestin et al. (2024) The bacterial strains JAM1T and GP59 of the species Methylophaga nitratireducenticrescens differ in their expression profiles of denitrification genes in oxic and anoxic cultures. PeerJ 12:e18361 https://doi.org/10.7717/peerj.18361
date submitted: 2024-06-11
date accepted: 2024-09-29
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lestin
  given name: Livie
author list: Agent
  family name: Villemur
  given name: Richard
doi: 10.7717/peerj.18361
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: ©2024 Lestin and Villemur
attribution name: Lestin and Villemur

Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis
type: item
type: AcademicArticle
description: Objective This study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis. Methods Single-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment. Results Two subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration. Conclusion The study revealed the heterogeneity of TE…
format: application/pdf
format: text/html
creator: Jiachun Sun
creator: Shujun Zhang
creator: Yafeng Liu
creator: Kaijie Liu
creator: Xinyu Gu
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.18362
publisher: PeerJ Inc.
rights: © 2024 Sun et al.
abstract: Objective This study aimed to explore the heterogeneity of tumor endothelial cells (TECs) in hepatocellular carcinoma (HCC) and their role in tumor progression, with the goal of identifying new therapeutic targets and strategies to improve patient prognosis. Methods Single-cell RNA sequencing data from nine primary liver cancer samples were analyzed, obtained from the Gene Expression Omnibus (GEO) database. Data preprocessing, normalization, dimensionality reduction, and batch effect correction were performed based on the Seurat package. HCC cell types were identified using uniform manifold approximation and projection (UMAP) and cluster analysis, and the different cell types were annotated using the CellMarker database. Pseudotime trajectory analysis was conducted with Monocle to explore the differentiation trajectory of TECs. MAPK signaling pathway activity and copy number variations (CNV) in TECs were analyzed in conjunction with data from The Cancer Genome Atlas (TCGA), the trans-well and wound healing assay was used for cell invasion and migration activity assessment. Results Two subgroups of TECs (TECs 1 and TECs 2) were identified, exhibiting distinct functional activities and signaling pathways. Specifically, TECs 1 may be involved in tumor cell proliferation and inflammatory responses, whereas TECs 2 is not only involved in cell proliferation pathways, but also enriched in pathways such as metabolic synthesis. Pseudotime analysis revealed dynamic changes in TECs subgroups during HCC progression, correlating specific gene expressions (such as PDGFRB, PGF, JUN, and NR4A1). Subsequently, the JUN gene was predicted by performing binding sites and was shown to act as a transcription factor that may regulate the expression of the PGF gene. CNV analysis highlighted key genes and pathways in TECs that might influence HCC progression, and the PGF as key regulatory factor mediated cell proliferation and migration. Conclusion The study revealed the heterogeneity of TE…
bibliographic citation: Sun et al. (2024) Exploring tumor endothelial cells heterogeneity in hepatocellular carcinoma: insights from single-cell sequencing and pseudotime analysis. PeerJ 12:e18362 https://doi.org/10.7717/peerj.18362
date submitted: 2024-07-18
date accepted: 2024-09-29
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Jiachun
author list: Agent
  family name: Zhang
  given name: Shujun
author list: Agent
  family name: Liu
  given name: Yafeng
author list: Agent
  family name: Liu
  given name: Kaijie
author list: Agent
  family name: Gu
  given name: Xinyu
doi: 10.7717/peerj.18362
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Sun et al.
attribution name: Sun et al.

Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index
type: item
type: AcademicArticle
description: Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000–2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran’s Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000–2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000–2020 period, with a relatively stable overall spatial distribution. Areas with high–high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low–low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could d…
format: application/pdf
format: text/html
creator: Congcang Tang
creator: Qiao Li
creator: Hongfei Tao
creator: Mahemujiang Aihemaiti
creator: Zhenxia Mu
creator: Youwei Jiang
subject: Environmental Contamination and Remediation
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.18368
publisher: PeerJ Inc.
rights: © 2024 Tang et al.
abstract: Changes in the ecological environment quality (EEQ) in the main inland Tarim River Basin in China substantially impact the regional development. Indeed, comprehensive ecological environment measures have been implemented in the Tarim River Basin since 2000. In this context, the main objective of the present study was to investigate the spatiotemporal evolution of the EEQ and monitor the effectiveness of ecological restoration measures in the Tarim River Basin over the 2000–2020 period using remote sensing data. First, a Remote Sensing Ecological Index (RSEI) was constructed based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Second, the spatial distributions and factors of the RSEI were analyzed by using Moran’s Index and Geodetector. The results indicated that the overall RSEI values for the Tarim River Basin increased from 0.22 in 2000 to 0.25 in 2020. Moreover, the values for areas with poor EEQ decreased from 50.7% to 44.73%, while those with moderate EEQ increased from 11.45% to 16.91%. Therefore, the results demonstrated a slight overall improvement in the EEQ of the study area over the 2000–2020 period. On the other hand, the EEQ in the Tarim River Basin exhibited a significant spatial autocorrelation in the 2000–2020 period, with a relatively stable overall spatial distribution. Areas with high–high aggregation were distributed in the high-elevation mountainous areas in the western, northern, and southern parts of the study area. In contrast, areas with low–low aggregation were observed in the central and eastern low-elevation desert areas. The EEQ in the Tarim River Basin was driven by the interactions of several factors, including the normalized difference vegetation index, land surface moisture, land surface temperature, normalized differential build-up and bare soil index, and elevation. In particular, heat was the main driving factor that severely impacted the EEQ in the study area. Indeed, increase in the heat values could d…
bibliographic citation: Tang et al. (2024) Evaluation and driving factors of ecological environment quality in the Tarim River basin based on remote sensing ecological index. PeerJ 12:e18368 https://doi.org/10.7717/peerj.18368
date submitted: 2024-05-09
date accepted: 2024-09-30
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tang
  given name: Congcang
author list: Agent
  family name: Li
  given name: Qiao
author list: Agent
  family name: Tao
  given name: Hongfei
author list: Agent
  family name: Aihemaiti
  given name: Mahemujiang
author list: Agent
  family name: Mu
  given name: Zhenxia
author list: Agent
  family name: Jiang
  given name: Youwei
doi: 10.7717/peerj.18368
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Tang et al.
attribution name: Tang et al.

Development of a welfare assessment tool for tourist camp elephants in Asia
type: item
type: AcademicArticle
description: Background Approximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps. Methods Using direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (e.g., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0–2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests. Results The initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (n = 5), Environment (n = 14), Health (n = 10), and Behavior and Mental State (n = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfac…
format: application/pdf
format: text/html
creator: Raman Ghimire
creator: Janine L. Brown
creator: Chatchote Thitaram
creator: Sharon S. Glaeser
creator: Kannika Na-Lampang
creator: Pawinee Kulnanan
creator: Pakkanut Bansiddhi
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.18370
publisher: PeerJ Inc.
rights: © 2024 Ghimire et al.
abstract: Background Approximately one-third of Asian elephants are managed under human care, participating in educational, cultural, religious, and tourist activities. Management conditions vary considerably among venues, raising questions about whether welfare needs are consistently being met, particularly for Asian tourist camp elephants. To evaluate the well-being of elephants engaged in tourist activities, an evidence-based tool is needed for routine assessments to identify potential welfare risks, aid in the development of better camp standards, and enable caretakers to address specific concerns. While many animal welfare tools exist, none have been designed to consider specific environments and management practices faced by elephants living and working in tourist camps. Methods Using direct observations and interviews, the Elephant Welfare Assessment Tool (EWAT) was developed for tourist camp elephants using the Five Domains Model as a framework. Measures were selected based on peer-reviewed literature, existing standards and guidelines, and opinions from animal welfare experts working with zoo and tourist camp elephants. The EWAT differs from existing tools by including criteria on work activities and restraint methods (e.g., chaining and ankus use), factors common in Asia but not often encountered by western zoo elephants. Measures were scored using a 0–2 Likert Scale. The tool was tested in Thailand and determined by calculating a content validity index (CVI) and conducting inter-rater and test-retest reliability tests. Results The initial tool included 18 animal-based and 21 resource-based measures across four domains: Nutrition (n = 5), Environment (n = 14), Health (n = 10), and Behavior and Mental State (n = 10). Index scores of content validity (CVI) (Item CVI (0.83), Scale CVI/Average (0.98), and Scale CVI/Universal (0.89)) were high. Measures scoring less than 0.83 were removed: the opportunity to mate, the mahout-elephant relationship, and mahout job satisfac…
bibliographic citation: Ghimire et al. (2024) Development of a welfare assessment tool for tourist camp elephants in Asia. PeerJ 12:e18370 https://doi.org/10.7717/peerj.18370
date submitted: 2024-07-09
date accepted: 2024-09-30
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghimire
  given name: Raman
author list: Agent
  family name: Brown
  given name: Janine L.
author list: Agent
  family name: Thitaram
  given name: Chatchote
author list: Agent
  family name: Glaeser
  given name: Sharon S.
author list: Agent
  family name: Na-Lampang
  given name: Kannika
author list: Agent
  family name: Kulnanan
  given name: Pawinee
author list: Agent
  family name: Bansiddhi
  given name: Pakkanut
doi: 10.7717/peerj.18370
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Ghimire et al.
attribution name: Ghimire et al.

Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part
type: item
type: AcademicArticle
description: Background Occupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a “service gap”. Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site. Methods This study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part. Results The results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences accor…
format: application/pdf
format: text/html
creator: Yasumasa Oka
creator: Takumi Jiroumaru
creator: Michio Wachi
creator: Noriyuki Kida
subject: Anesthesiology and Pain Management
subject: Health Policy
subject: Mental Health
subject: Rehabilitation
description: doi:10.7717/peerj.18389
publisher: PeerJ Inc.
rights: © 2024 Oka et al.
abstract: Background Occupational health, grounded in occupational medicine, aims to enhance the well-being and labor productivity of the working population. Within this realm, there has been growing concern over the increasing instances of labor loss due to diminished physical capacity and the rise in musculoskeletal disorders. Chronic pain is also associated with musculoskeletal disorders. Another pressing issue related to chronic musculoskeletal pain was needed assistance services are underutilized, is referred to as a “service gap”. Understanding trends based on age and affected regions of the body is indispensable for developing strategies to address chronic musculoskeletal pain in workers. This study aimed to elucidate age-specific trends in the prevalence and number of pain sites in chronic musculoskeletal pain as well as the patterns of treatment during chronic musculoskeletal pain, categorized by age and affected site. Methods This study was conducted in December 2022 in contract to Cross Marketing Inc. The survey began on December 12, 2022 and ended on December 15, 2022. An online survey was administered to 1,946 participants (973 women and 973 men), and responses were collected, ensuring a roughly equal distribution of samples among men and women across six age groups ranging from their 20 to 70 s. The survey inquired about the presence of chronic pain in each of the eight body parts and the adoption of five different treatments when experiencing pain. Statistical analysis was performed using the chi-square test, with the measurement data categorized by age group and body part. Results The results indicated a significantly higher prevalence of chronic pain at three or more sites among individuals in their 30 s: the prevalence of pain at each of the eight body sites varied with age. Approximately half of the participants did not engage in specific treatments during episodes of chronic pain. The presence or absence of treatment showed no significant differences accor…
bibliographic citation: Oka et al. (2024) Prevalence and treatment of chronic musculoskeletal pain focused on service gaps: a comparative analysis by age group and body part. PeerJ 12:e18389 https://doi.org/10.7717/peerj.18389
date submitted: 2024-02-13
date accepted: 2024-10-02
issued: 2024-10-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Oka
  given name: Yasumasa
author list: Agent
  family name: Jiroumaru
  given name: Takumi
author list: Agent
  family name: Wachi
  given name: Michio
author list: Agent
  family name: Kida
  given name: Noriyuki
doi: 10.7717/peerj.18389
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-10-28
copyright: © 2024 Oka et al.
attribution name: Oka et al.

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