PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new neornithischian dinosaur from the Upper Jurassic Tiaojishan Formation of northern China
items: An R package for survival-based gene set enrichment analysis
items: Integrated platform for structural and functional analysis of terpene synthases of Cannabis sativa
items: Vocal constraints on song amplitude in star finches Bathilda ruficauda
items: A Jack of All Trades—Tawaki/Fiordland penguins are able to utilise diverse marine habitats during winter migration
items: Expression of the IL-18-related gene PTX3 correlates with clinicopathological features and prognosis in glioma patients
items: Cryptic diversity on the genus Caenolestes (Caenolestidae: Paucituberculata) in the Ecuadorian Andes
items: Neuroprotective effects of essential oils in animal models of Alzheimer’s and Parkinson’s disease: a systematic review
items: Correlation between preoperative uric acid levels and lymph node metastases in patients with papillary thyroid cancer: a retrospective study
items: Survival benefit from adjuvant chemoradiotherapy in local advanced gastric cancer without accurate D2 confirmation: a real-world retrospective study (TJ-ARK01)

A new neornithischian dinosaur from the Upper Jurassic Tiaojishan Formation of northern China
type: item
type: AcademicArticle
description: The Middle and Late Jurassic Yanliao Biota is different from other contemporaneous fossil assemblages in that it lacks neornithischian dinosaurs. Here, we report a new, early-diverging neornithischian, Pulaosaurus qinglong gen. et sp. nov., from the Upper Jurassic Tiaojishan Formation of Qinglong, Hebei Province, of northern China. Diagnostic or noteworthy morphological characteristics of P. qinglong include: five premaxillary teeth; a small boss is present on the caudoventral corner of the dorsal ramus of the jugal; a nuchal crest is located along the parietal; the manus has five digits; a supra-acetabular crest is present on the ilium; the paired arytenoids are gracile and leaf-like in form; the obturator process along the ischium is located near the pubic peduncle; a notch-like shaped obturator opening is present within the pubis; a robust fibular condyle forms a dorsoventrally extending crest on the tibia; a subtriangular flange on the anterior surface of the astragalus extends dorsolaterally along three distal tarsals; three of the distal tarsals are unfused, including a small drop-shaped distal tarsal 3; distal tarsal 3 is pierced by a foramen. A phylogenetic analysis places P. qinglong as one of the earliest-diverging neornithischians yet described. Moreover, P. qinglong represents the second known dinosaur to preserve ossified laryngeal elements, thus suggesting that a bird-like vocalization evolved early in non-avian dinosaur evolution.
format: application/pdf
format: text/html
creator: Yunfeng Yang
creator: James L. King
creator: Xing Xu
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.19664
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: The Middle and Late Jurassic Yanliao Biota is different from other contemporaneous fossil assemblages in that it lacks neornithischian dinosaurs. Here, we report a new, early-diverging neornithischian, Pulaosaurus qinglong gen. et sp. nov., from the Upper Jurassic Tiaojishan Formation of Qinglong, Hebei Province, of northern China. Diagnostic or noteworthy morphological characteristics of P. qinglong include: five premaxillary teeth; a small boss is present on the caudoventral corner of the dorsal ramus of the jugal; a nuchal crest is located along the parietal; the manus has five digits; a supra-acetabular crest is present on the ilium; the paired arytenoids are gracile and leaf-like in form; the obturator process along the ischium is located near the pubic peduncle; a notch-like shaped obturator opening is present within the pubis; a robust fibular condyle forms a dorsoventrally extending crest on the tibia; a subtriangular flange on the anterior surface of the astragalus extends dorsolaterally along three distal tarsals; three of the distal tarsals are unfused, including a small drop-shaped distal tarsal 3; distal tarsal 3 is pierced by a foramen. A phylogenetic analysis places P. qinglong as one of the earliest-diverging neornithischians yet described. Moreover, P. qinglong represents the second known dinosaur to preserve ossified laryngeal elements, thus suggesting that a bird-like vocalization evolved early in non-avian dinosaur evolution.
bibliographic citation: Yang et al. (2025) A new neornithischian dinosaur from the Upper Jurassic Tiaojishan Formation of northern China. PeerJ 13:e19664 https://doi.org/10.7717/peerj.19664
date submitted: 2025-01-29
date accepted: 2025-06-05
issued: 2025-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yunfeng
author list: Agent
  family name: King
  given name: James L.
author list: Agent
  family name: Xu
  given name: Xing
doi: 10.7717/peerj.19664
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-11
copyright: ©2025 Yang et al.
attribution name: Yang et al.

An R package for survival-based gene set enrichment analysis
type: item
type: AcademicArticle
description: Functional enrichment analysis is usually used to assess the effects of experimental differences. However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. Therefore, we suggest the use of Survival-based Gene Set Enrichment Analysis (SGSEA) to help determine biological functions associated with a disease’s survival. Despite the availability of this method to researchers, there are no standard tools or software to perform this analysis. We developed an R package and Shiny app called SGSEA and presented a study of kidney renal clear cell carcinoma (KIRC) to demonstrate the approach. In Gene Set Enrichment Analysis (GSEA), the log-fold change in expression between treatments is used to rank genes, to determine if a biological function has a non-random distribution of altered gene expression. SGSEA is a variation of GSEA using the hazard ratio instead of a log fold change. Our study shows that pathways enriched with genes whose increased transcription is associated with mortality (NES > 0, adjusted p-value < 0.15) have previously been linked to KIRC survival, helping to demonstrate the value of this approach. This method allows rapid identification of disease variant pathways and provides supplementary information to standard GSEA, all within a single R package at https://github.com/ShellsheDeng/SGSEA or via the convenient app at https://biostats-shinyr.kumc.edu/SGSEA/.
format: application/pdf
format: text/html
creator: Xiaoxu Deng
creator: Jeffrey Thompson
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Statistics
description: doi:10.7717/peerj.19489
publisher: PeerJ Inc.
rights: © 2025 Deng and Thompson
abstract: Functional enrichment analysis is usually used to assess the effects of experimental differences. However, researchers sometimes want to understand the relationship between transcriptomic variation and health outcomes like survival. Therefore, we suggest the use of Survival-based Gene Set Enrichment Analysis (SGSEA) to help determine biological functions associated with a disease’s survival. Despite the availability of this method to researchers, there are no standard tools or software to perform this analysis. We developed an R package and Shiny app called SGSEA and presented a study of kidney renal clear cell carcinoma (KIRC) to demonstrate the approach. In Gene Set Enrichment Analysis (GSEA), the log-fold change in expression between treatments is used to rank genes, to determine if a biological function has a non-random distribution of altered gene expression. SGSEA is a variation of GSEA using the hazard ratio instead of a log fold change. Our study shows that pathways enriched with genes whose increased transcription is associated with mortality (NES > 0, adjusted p-value < 0.15) have previously been linked to KIRC survival, helping to demonstrate the value of this approach. This method allows rapid identification of disease variant pathways and provides supplementary information to standard GSEA, all within a single R package at https://github.com/ShellsheDeng/SGSEA or via the convenient app at https://biostats-shinyr.kumc.edu/SGSEA/.
bibliographic citation: Deng et al. (2025) An R package for survival-based gene set enrichment analysis. PeerJ 13:e19489 https://doi.org/10.7717/peerj.19489
date submitted: 2024-11-07
date accepted: 2025-04-28
issued: 2025-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Xiaoxu
author list: Agent
  family name: Thompson
  given name: Jeffrey
doi: 10.7717/peerj.19489
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-11
copyright: ©2025 Deng and Thompson
attribution name: Deng and Thompson

Integrated platform for structural and functional analysis of terpene synthases of Cannabis sativa
type: item
type: AcademicArticle
description: Terpenoids are the largest and most diverse family of natural products. Volatile terpenes from Cannabis sativa are crucial in flavours, fragrances, and pharmaceuticals due to their unique odours and biological activities, including antimalarial, antibacterial, and insecticidal properties. Their synthesis is catalysed by terpene synthase (TPS) enzymes, which perform cyclisation and rearrangement reactions of over 55,000 distinct terpene compounds. However, low catalytic efficiency of C. sativa TPSs limits their use in large-scale commercial production. The complex biochemistry of these reactions is not well understood due to limited enzyme structure information. To address this, we have developed an integrated platform for the systematic expression, purification, enzymatic characterisation, and crystallisation of TPS enzymes from C. sativa. This workflow combines kinetic, thermostability, and structural analyses with a data-mining-informed crystallisation screen that enabled the production of diffraction-quality crystals. As a demonstration of the platform’s utility, ten C. sativa TPS enzymes were functionally characterised, revealing turnover rates (kcat) ranging from 0.0011 to 0.0204 s−1 and diverse substrate specificities, with each enzyme producing a distinct product profile, highlighting the need for systematic characterisation of C. sativa terpene biosynthesis. Our findings provide a framework for the structural and functional study of C. sativa TPSs. The developed platform sets the stage for future metabolic engineering aimed at optimising terpene production for pharmaceutical, pest management, and synthetic biology applications.
format: application/pdf
format: text/html
creator: Danielle Wiles
creator: James Roest
creator: Bhuvana Shanbhag
creator: Julian Vivian
creator: Travis Beddoe
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.19723
publisher: PeerJ Inc.
rights: © 2025 Wiles et al.
abstract: Terpenoids are the largest and most diverse family of natural products. Volatile terpenes from Cannabis sativa are crucial in flavours, fragrances, and pharmaceuticals due to their unique odours and biological activities, including antimalarial, antibacterial, and insecticidal properties. Their synthesis is catalysed by terpene synthase (TPS) enzymes, which perform cyclisation and rearrangement reactions of over 55,000 distinct terpene compounds. However, low catalytic efficiency of C. sativa TPSs limits their use in large-scale commercial production. The complex biochemistry of these reactions is not well understood due to limited enzyme structure information. To address this, we have developed an integrated platform for the systematic expression, purification, enzymatic characterisation, and crystallisation of TPS enzymes from C. sativa. This workflow combines kinetic, thermostability, and structural analyses with a data-mining-informed crystallisation screen that enabled the production of diffraction-quality crystals. As a demonstration of the platform’s utility, ten C. sativa TPS enzymes were functionally characterised, revealing turnover rates (kcat) ranging from 0.0011 to 0.0204 s−1 and diverse substrate specificities, with each enzyme producing a distinct product profile, highlighting the need for systematic characterisation of C. sativa terpene biosynthesis. Our findings provide a framework for the structural and functional study of C. sativa TPSs. The developed platform sets the stage for future metabolic engineering aimed at optimising terpene production for pharmaceutical, pest management, and synthetic biology applications.
bibliographic citation: Wiles et al. (2025) Integrated platform for structural and functional analysis of terpene synthases of Cannabis sativa. PeerJ 13:e19723 https://doi.org/10.7717/peerj.19723
date submitted: 2025-03-07
date accepted: 2025-06-17
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wiles
  given name: Danielle
author list: Agent
  family name: Roest
  given name: James
author list: Agent
  family name: Shanbhag
  given name: Bhuvana
author list: Agent
  family name: Vivian
  given name: Julian
author list: Agent
  family name: Beddoe
  given name: Travis
doi: 10.7717/peerj.19723
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: © 2025 Wiles et al.
attribution name: Wiles et al.

Vocal constraints on song amplitude in star finches Bathilda ruficauda
type: item
type: AcademicArticle
description: Given the two main functions of birdsong, mate attraction and territory defence, song amplitude is crucial for communication because it determines the communication range and it can also carry information. To understand the evolution of signals, it is helpful to consider the constraints on signal production, as physical constraints set the limits for signal plasticity and how signals can respond to selection. Previous work on the constraints of song amplitude was restricted to species that use loud vocalisations for long-distance communication. However, the low song amplitudes of some non-territorial species may hint at unknown limitations considering that females may prefer loud song. The star finch (Bathilda ruficauda) is one such species. In this study, we recorded the songs of male star finches in the laboratory and investigated the relationship between vocal amplitude and other acoustic parameters of their song syllables. We found that vocal amplitude was linked to the phonetic structure of the syllables. More complex sounds (measured as higher syllable bandwidth and higher Wiener entropy) were produced at lower amplitudes than less complex sounds. To the best of our knowledge, this is the first report of a trade-off between song complexity and vocal amplitude. More complex song syllables possibly require a more intricate control of the syrinx and vocal tract, which might only be possible at lower amplitudes. We speculate that if female star finches prefer complex songs, this would cause males to sing quietly, as they cannot produce complex syllables with high amplitudes. We also provided a phonetogram (vocal range profile) for the star finch, indicating a positive correlation between amplitude and peak frequency. This finding corroborates earlier studies on species that use loud vocalisations for long-range communication, which, like the star finches in our study, were also unable to produce low frequencies at high amplitudes. This suggests that the frequency-…
format: application/pdf
format: text/html
creator: Hana Goto
creator: Masayo Soma
creator: Ayumi Mizuno
creator: Henrik Brumm
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.19705
publisher: PeerJ Inc.
rights: © 2025 Goto et al.
abstract: Given the two main functions of birdsong, mate attraction and territory defence, song amplitude is crucial for communication because it determines the communication range and it can also carry information. To understand the evolution of signals, it is helpful to consider the constraints on signal production, as physical constraints set the limits for signal plasticity and how signals can respond to selection. Previous work on the constraints of song amplitude was restricted to species that use loud vocalisations for long-distance communication. However, the low song amplitudes of some non-territorial species may hint at unknown limitations considering that females may prefer loud song. The star finch (Bathilda ruficauda) is one such species. In this study, we recorded the songs of male star finches in the laboratory and investigated the relationship between vocal amplitude and other acoustic parameters of their song syllables. We found that vocal amplitude was linked to the phonetic structure of the syllables. More complex sounds (measured as higher syllable bandwidth and higher Wiener entropy) were produced at lower amplitudes than less complex sounds. To the best of our knowledge, this is the first report of a trade-off between song complexity and vocal amplitude. More complex song syllables possibly require a more intricate control of the syrinx and vocal tract, which might only be possible at lower amplitudes. We speculate that if female star finches prefer complex songs, this would cause males to sing quietly, as they cannot produce complex syllables with high amplitudes. We also provided a phonetogram (vocal range profile) for the star finch, indicating a positive correlation between amplitude and peak frequency. This finding corroborates earlier studies on species that use loud vocalisations for long-range communication, which, like the star finches in our study, were also unable to produce low frequencies at high amplitudes. This suggests that the frequency-…
bibliographic citation: Goto et al. (2025) Vocal constraints on song amplitude in star finches Bathilda ruficauda. PeerJ 13:e19705 https://doi.org/10.7717/peerj.19705
date submitted: 2024-12-10
date accepted: 2025-06-15
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goto
  given name: Hana
author list: Agent
  family name: Soma
  given name: Masayo
author list: Agent
  family name: Mizuno
  given name: Ayumi
author list: Agent
  family name: Brumm
  given name: Henrik
doi: 10.7717/peerj.19705
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: © 2025 Goto et al.
attribution name: Goto et al.

A Jack of All Trades—Tawaki/Fiordland penguins are able to utilise diverse marine habitats during winter migration
type: item
type: AcademicArticle
description: Migration and non-breeding movements are common across animal groups and are often driven by seasonal changes in habitat conditions. This behaviour is prevalent in crested penguins (Eudyptes sp.), which have evolved in and still primarily inhabit the subantarctic regions of the Southern Hemisphere. These species migrate outside the reproductive phase due to the limited year-round productivity around the breeding sites. Tawaki/Fiordland penguins (Eudyptes pachyrhynchus) are unusual in that they breed in temperate, continental New Zealand, an environment that appears productive enough to support year-round residency, yet they undertake extensive migrations during the non-breeding period. To investigate the drivers and patterns behind this behaviour, we used satellite telemetry to track 14 adult tawaki from across their breeding range during the winter of 2019. We examined whether migration routes differed by breeding location, and used maximum entropy (Maxent) modelling to identify environmental predictors of habitat use during the non-breeding period. All penguins followed a similar south-westerly trajectory toward the subantarctic waters south of Tasmania, irrespective of origin. Birds reached maximum distances of up to 2,193 km from their colonies, traveling a median total distance of 6,086 km over 135 days. Maxent models showed that mixed layer depth (i.e., the mixing height at the ocean surface) around 80 m was the strongest predictor of habitat suitability, aligning with known foraging depths in this species. Tawaki were associated with oceanic habitats ranging from polar to subtropical regions—a broader environmental range than other crested penguins, which tend to remain within a single water mass. These findings highlight the flexibility of tawaki in their use of marine habitats. This behavioural plasticity may suggest resilience to environmental variability, offering insights into why tawaki appear to be maintaining stable population trends while other New Z…
format: application/pdf
format: text/html
creator: Thomas Mattern
creator: Klemens Pütz
creator: Pablo Garcia Borboroglu
creator: Ursula Ellenberg
creator: David M. Houston
creator: Bernhard Lüthi
creator: Philip J. Seddon
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.19695
publisher: PeerJ Inc.
rights: © 2025 Mattern et al.
abstract: Migration and non-breeding movements are common across animal groups and are often driven by seasonal changes in habitat conditions. This behaviour is prevalent in crested penguins (Eudyptes sp.), which have evolved in and still primarily inhabit the subantarctic regions of the Southern Hemisphere. These species migrate outside the reproductive phase due to the limited year-round productivity around the breeding sites. Tawaki/Fiordland penguins (Eudyptes pachyrhynchus) are unusual in that they breed in temperate, continental New Zealand, an environment that appears productive enough to support year-round residency, yet they undertake extensive migrations during the non-breeding period. To investigate the drivers and patterns behind this behaviour, we used satellite telemetry to track 14 adult tawaki from across their breeding range during the winter of 2019. We examined whether migration routes differed by breeding location, and used maximum entropy (Maxent) modelling to identify environmental predictors of habitat use during the non-breeding period. All penguins followed a similar south-westerly trajectory toward the subantarctic waters south of Tasmania, irrespective of origin. Birds reached maximum distances of up to 2,193 km from their colonies, traveling a median total distance of 6,086 km over 135 days. Maxent models showed that mixed layer depth (i.e., the mixing height at the ocean surface) around 80 m was the strongest predictor of habitat suitability, aligning with known foraging depths in this species. Tawaki were associated with oceanic habitats ranging from polar to subtropical regions—a broader environmental range than other crested penguins, which tend to remain within a single water mass. These findings highlight the flexibility of tawaki in their use of marine habitats. This behavioural plasticity may suggest resilience to environmental variability, offering insights into why tawaki appear to be maintaining stable population trends while other New Z…
bibliographic citation: Mattern et al. (2025) A Jack of All Trades—Tawaki/Fiordland penguins are able to utilise diverse marine habitats during winter migration. PeerJ 13:e19695 https://doi.org/10.7717/peerj.19695
date submitted: 2025-02-14
date accepted: 2025-06-11
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mattern
  given name: Thomas
author list: Agent
  family name: Pütz
  given name: Klemens
author list: Agent
  family name: Borboroglu
  given name: Pablo Garcia
author list: Agent
  family name: Ellenberg
  given name: Ursula
author list: Agent
  family name: Houston
  given name: David M.
author list: Agent
  family name: Lüthi
  given name: Bernhard
author list: Agent
  family name: Seddon
  given name: Philip J.
doi: 10.7717/peerj.19695
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: ©2025 Mattern et al.
attribution name: Mattern et al.

Expression of the IL-18-related gene PTX3 correlates with clinicopathological features and prognosis in glioma patients
type: item
type: AcademicArticle
description: Background Glioma, a highly aggressive brain tumor, presents significant challenges in prognosis and treatment. This study investigates the role of PTX3 expression in glioma and its correlation with patient outcomes, addressing a gap in current research regarding its molecular mechanisms. Materials and Methods RNA sequencing data and clinical information for glioma patients were obtained from The Cancer Genome Atlas (TCGA). A multigene prognostic signature based on IL-18 signaling-related genes (ISRGs) was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression method. The functional roles of PTX3 were analyzed through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Single-sample GSEA (ssGSEA) was used to assess the association between PTX3 expression and immune cell infiltration. The relationship between PTX3 expression and clinicopathological features was also examined. Prognostic relevance was evaluated using univariate and multivariate Cox regression models, and Kaplan–Meier survival analysis was performed. PTX3 protein expression was validated via immunohistochemistry in 56 glioma specimens. Results The LASSO Cox regression model identified a nine-gene prognostic signature, including BMP2, NCF1, HSPB1, PIGT, PTX3, CCNA2, CCNB2, CCN4, and DES. Functional enrichment analysis revealed that PTX3-associated differentially expressed genes were significantly enriched in pathways such as cytokine–cytokine receptor interaction and PI3K-Akt signaling, which are critical for immune response and cell proliferation in glioma. PTX3 expression showed a strong correlation with immune cell infiltration, particularly macrophages, neutrophils, T cells, and natural killer cells, suggesting a role in modulating the tumor microenvironment. Pan-cancer analysis indicated that PTX3 is markedly upregulated in various cancers, especially gliomas, highlighting its potential as a biomarker. PT…
format: application/pdf
format: text/html
creator: Delin Wang
creator: Cuimei Liu
creator: Bohao Sun
creator: Xiaodong Zhang
creator: Yejun Zhou
creator: Zhonglin Hu
creator: Duanzheng Cao
creator: Jing Zhang
creator: Jinfang Xu
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Pathology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.19675
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Glioma, a highly aggressive brain tumor, presents significant challenges in prognosis and treatment. This study investigates the role of PTX3 expression in glioma and its correlation with patient outcomes, addressing a gap in current research regarding its molecular mechanisms. Materials and Methods RNA sequencing data and clinical information for glioma patients were obtained from The Cancer Genome Atlas (TCGA). A multigene prognostic signature based on IL-18 signaling-related genes (ISRGs) was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression method. The functional roles of PTX3 were analyzed through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Single-sample GSEA (ssGSEA) was used to assess the association between PTX3 expression and immune cell infiltration. The relationship between PTX3 expression and clinicopathological features was also examined. Prognostic relevance was evaluated using univariate and multivariate Cox regression models, and Kaplan–Meier survival analysis was performed. PTX3 protein expression was validated via immunohistochemistry in 56 glioma specimens. Results The LASSO Cox regression model identified a nine-gene prognostic signature, including BMP2, NCF1, HSPB1, PIGT, PTX3, CCNA2, CCNB2, CCN4, and DES. Functional enrichment analysis revealed that PTX3-associated differentially expressed genes were significantly enriched in pathways such as cytokine–cytokine receptor interaction and PI3K-Akt signaling, which are critical for immune response and cell proliferation in glioma. PTX3 expression showed a strong correlation with immune cell infiltration, particularly macrophages, neutrophils, T cells, and natural killer cells, suggesting a role in modulating the tumor microenvironment. Pan-cancer analysis indicated that PTX3 is markedly upregulated in various cancers, especially gliomas, highlighting its potential as a biomarker. PT…
bibliographic citation: Wang et al. (2025) Expression of the IL-18-related gene PTX3 correlates with clinicopathological features and prognosis in glioma patients. PeerJ 13:e19675 https://doi.org/10.7717/peerj.19675
date submitted: 2025-02-19
date accepted: 2025-06-09
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Delin
author list: Agent
  family name: Liu
  given name: Cuimei
author list: Agent
  family name: Sun
  given name: Bohao
author list: Agent
  family name: Zhang
  given name: Xiaodong
author list: Agent
  family name: Zhou
  given name: Yejun
author list: Agent
  family name: Hu
  given name: Zhonglin
author list: Agent
  family name: Cao
  given name: Duanzheng
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Xu
  given name: Jinfang
doi: 10.7717/peerj.19675
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: ©2025 Wang et al.
attribution name: Wang et al.

Cryptic diversity on the genus Caenolestes (Caenolestidae: Paucituberculata) in the Ecuadorian Andes
type: item
type: AcademicArticle
description: The shrew-opposums of the genus Caenolestes (Thomas, 1895) belong to a group of Ameridelphian marsupial mammals in the order Paucituberculata, an order in which most of its representatives are extinct. This genus contains five formally described species: C. caniventer, C. convelatus, C. condorensis, C. fuliginosus, and C. sangay, all with type localities in Ecuador, plus at least three candidate species from Colombia now recognized as subspecies C. convelatus barbarensis, C. fuliginosus centralis and C. fuliginosus obscurus. Records of this genus are not abundant, both in biological collections and in sequence repositories (GenBank); thus, showing a discontinuous geographical distribution that could be a consequence of incomplete sampling. Systematic expeditions by the Instituto Nacional de Biodiversidad (INABIO) have increased the geographic sampling of this genus in Ecuador, which allowed us to reevaluate its genetic diversity. We obtained 43 sequences of cytb and 30 of RAG1 from 28 Ecuadorian localities in 12 Provinces, including novel topotypical material from C. caniventer, C. convelatus, and C. condorensis. We present a new hypothesis on the genetic diversity of Caenolestes using maximum likelihood inference for phylogenetic analysis, estimate p-genetic distances and divergence times for the genus. We found a species complex in the C. fuliginosus clade, with at least three candidate new species, having a threshold above 5% for the estimated genetic distance of the cytb among them. Also, we found two additional lineages hidden within C. caniventer. We expect that future work, with similar or larger sampling efforts in Colombia and Peru would reveal greater phylogenetic diversity and more complete evolutionary relationships.
format: application/pdf
format: text/html
creator: Julio C. Carrión-Olmedo
creator: Jorge Brito
subject: Biodiversity
subject: Ecosystem Science
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.19648
publisher: PeerJ Inc.
rights: © 2025 Carrión-Olmedo and Brito
abstract: The shrew-opposums of the genus Caenolestes (Thomas, 1895) belong to a group of Ameridelphian marsupial mammals in the order Paucituberculata, an order in which most of its representatives are extinct. This genus contains five formally described species: C. caniventer, C. convelatus, C. condorensis, C. fuliginosus, and C. sangay, all with type localities in Ecuador, plus at least three candidate species from Colombia now recognized as subspecies C. convelatus barbarensis, C. fuliginosus centralis and C. fuliginosus obscurus. Records of this genus are not abundant, both in biological collections and in sequence repositories (GenBank); thus, showing a discontinuous geographical distribution that could be a consequence of incomplete sampling. Systematic expeditions by the Instituto Nacional de Biodiversidad (INABIO) have increased the geographic sampling of this genus in Ecuador, which allowed us to reevaluate its genetic diversity. We obtained 43 sequences of cytb and 30 of RAG1 from 28 Ecuadorian localities in 12 Provinces, including novel topotypical material from C. caniventer, C. convelatus, and C. condorensis. We present a new hypothesis on the genetic diversity of Caenolestes using maximum likelihood inference for phylogenetic analysis, estimate p-genetic distances and divergence times for the genus. We found a species complex in the C. fuliginosus clade, with at least three candidate new species, having a threshold above 5% for the estimated genetic distance of the cytb among them. Also, we found two additional lineages hidden within C. caniventer. We expect that future work, with similar or larger sampling efforts in Colombia and Peru would reveal greater phylogenetic diversity and more complete evolutionary relationships.
bibliographic citation: Carrión-Olmedo et al. (2025) Cryptic diversity on the genus Caenolestes (Caenolestidae: Paucituberculata) in the Ecuadorian Andes. PeerJ 13:e19648 https://doi.org/10.7717/peerj.19648
date submitted: 2024-11-22
date accepted: 2025-06-02
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrión-Olmedo
  given name: Julio C.
author list: Agent
  family name: Brito
  given name: Jorge
doi: 10.7717/peerj.19648
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: ©2025 Carrión-Olmedo and Brito
attribution name: Carrión-Olmedo and Brito

Neuroprotective effects of essential oils in animal models of Alzheimer’s and Parkinson’s disease: a systematic review
type: item
type: AcademicArticle
description: Essential oils (EOs), derived from aromatic plants, have garnered significant attention for their potential neuroprotective properties in neurodegenerative diseases. This systematic review evaluates recent advancements in understanding the neuroprotective role of EOs against Alzheimer’s disease (AD) and Parkinson’s disease (PD). Following PRISMA guidelines, we conducted a comprehensive literature search across three major databases (PubMed, Virtual Health Library, and Web of Science) from inception to January 2024, resulting in thirteen high-quality in vivo studies for qualitative analysis. The review assessed various EOs, with hydrodistillation being the predominant extraction method (66.66% of studies). Studies primarily utilized Wistar rats (46.15%) and various mouse strains, employing diverse disease induction methods including β-amyloid administration (30.7% of AD models), rotenone (7.7% of PD models), and 6-hydroxydopamine (7.7% of PD models). Administration routes varied, with oral administration being most common (38.4%), with gavage and inhalation each accounting for 23.1% of studies. Key findings revealed that EOs exhibit multifaceted neuroprotective mechanisms. In AD models (69.3% of studies), EOs reduced oxidative stress markers, decreased pro-inflammatory cytokine levels, and increased neuroprotective protein expression. In PD models (30.7% of studies), EOs demonstrated significant dopaminergic neuroprotection, with improvements in behavioral outcomes. Behavioral assessments showed consistent enhancements in memory, learning, and motor functions across studies. The systematic analysis provides compelling evidence for EOs’ neuroprotective efficacy, particularly in early-stage intervention. However, limitations include the predominance of animal studies, variability in dosing, and administration methods. The most promising EOs identified were from Pinus halepensis, Citrus limon, and Acorus species, showing particular efficacy in reducing cognitive deficit…
format: application/pdf
format: text/html
creator: Adrielle do Espírito Santos Macedo
creator: Thayná Moraes Ferreira
creator: Lane Viana Krejcová
creator: Fernando Allan de Farias Rocha
creator: Joyce Kelly R. da Silva
creator: Laís Resque Russo Pedrosa
creator: Bruno Duarte Gomes
subject: Biochemistry
subject: Biotechnology
subject: Neuroscience
subject: Plant Science
description: doi:10.7717/peerj.19643
publisher: PeerJ Inc.
rights: © 2025 Macedo et al.
abstract: Essential oils (EOs), derived from aromatic plants, have garnered significant attention for their potential neuroprotective properties in neurodegenerative diseases. This systematic review evaluates recent advancements in understanding the neuroprotective role of EOs against Alzheimer’s disease (AD) and Parkinson’s disease (PD). Following PRISMA guidelines, we conducted a comprehensive literature search across three major databases (PubMed, Virtual Health Library, and Web of Science) from inception to January 2024, resulting in thirteen high-quality in vivo studies for qualitative analysis. The review assessed various EOs, with hydrodistillation being the predominant extraction method (66.66% of studies). Studies primarily utilized Wistar rats (46.15%) and various mouse strains, employing diverse disease induction methods including β-amyloid administration (30.7% of AD models), rotenone (7.7% of PD models), and 6-hydroxydopamine (7.7% of PD models). Administration routes varied, with oral administration being most common (38.4%), with gavage and inhalation each accounting for 23.1% of studies. Key findings revealed that EOs exhibit multifaceted neuroprotective mechanisms. In AD models (69.3% of studies), EOs reduced oxidative stress markers, decreased pro-inflammatory cytokine levels, and increased neuroprotective protein expression. In PD models (30.7% of studies), EOs demonstrated significant dopaminergic neuroprotection, with improvements in behavioral outcomes. Behavioral assessments showed consistent enhancements in memory, learning, and motor functions across studies. The systematic analysis provides compelling evidence for EOs’ neuroprotective efficacy, particularly in early-stage intervention. However, limitations include the predominance of animal studies, variability in dosing, and administration methods. The most promising EOs identified were from Pinus halepensis, Citrus limon, and Acorus species, showing particular efficacy in reducing cognitive deficit…
bibliographic citation: Macedo et al. (2025) Neuroprotective effects of essential oils in animal models of Alzheimer’s and Parkinson’s disease: a systematic review. PeerJ 13:e19643 https://doi.org/10.7717/peerj.19643
date submitted: 2024-11-13
date accepted: 2025-06-02
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Macedo
  given name: Adrielle do Espírito Santos
author list: Agent
  family name: Ferreira
  given name: Thayná Moraes
author list: Agent
  family name: Krejcová
  given name: Lane Viana
author list: Agent
  family name: Rocha
  given name: Fernando Allan de Farias
author list: Agent
  family name: da Silva
  given name: Joyce Kelly R.
author list: Agent
  family name: Pedrosa
  given name: Laís Resque Russo
author list: Agent
  family name: Gomes
  given name: Bruno Duarte
doi: 10.7717/peerj.19643
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: © 2025 Macedo et al.
attribution name: Macedo et al.

Correlation between preoperative uric acid levels and lymph node metastases in patients with papillary thyroid cancer: a retrospective study
type: item
type: AcademicArticle
description: Background In the past decade, numerous studies have highlighted a notable correlation between the prognosis of various cancers and uric acid (UA). Nevertheless, scientific literature regarding the association between central lymph node metastasis (CLNM) and UA remains lacking. This study sought to examine the association between UA and the likelihood of CLNM in individuals with papillary thyroid cancer (PTC) and to determine the UA threshold. Methods Three hundred and seventy individuals with confirmed PTC who underwent surgery at the First People’s Hospital of Kunshan from October 2018 to July 2024 were included in this study. Initially, UA levels were measured, and the incidence of CLNM in PTC patients was assessed through postoperative pathology. Propensity score-matched (PSM) analysis was used to match patients. Multivariate logistic regression and a two-piecewise linear regression model were utilized to analyze the relationship between UA and CLNM and identify the threshold effect of UA concentrations on CLNM. Results The correlation between UA and CLNM in PTC patients was found to be positive. Upon adjusting for various confounding factors, it was determined that, relative to the referential level, the odds ratio for CLNM was 4.01 at peak UA levels. After PSM analysis, the odds ratio for CLNM was 5.23 at the highest levels to the lowest levels. A non-linear relationship between UA and CLNM emerged following adjustment for potential confounding factors. The study identified 219.20 µmol/L as the UA threshold, serving as the optimal inflection point. The effect sizes and confidence intervals on both sides of the inflection point were −4.43 (−9.69–0.84) and 3.78 (1.70–5.85), respectively. Conclusion The study concludes that the association between UA and CLNM is non-linear. A positive relationship between UA and CLNM was observed when UA levels exceeded 219.20 µmol/L.
format: application/pdf
format: text/html
creator: ShaoKun Sun
creator: Qin Zhou
creator: Tao Hu
subject: Epidemiology
subject: Oncology
subject: Surgery and Surgical Specialties
subject: Metabolic Sciences
description: doi:10.7717/peerj.19410
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background In the past decade, numerous studies have highlighted a notable correlation between the prognosis of various cancers and uric acid (UA). Nevertheless, scientific literature regarding the association between central lymph node metastasis (CLNM) and UA remains lacking. This study sought to examine the association between UA and the likelihood of CLNM in individuals with papillary thyroid cancer (PTC) and to determine the UA threshold. Methods Three hundred and seventy individuals with confirmed PTC who underwent surgery at the First People’s Hospital of Kunshan from October 2018 to July 2024 were included in this study. Initially, UA levels were measured, and the incidence of CLNM in PTC patients was assessed through postoperative pathology. Propensity score-matched (PSM) analysis was used to match patients. Multivariate logistic regression and a two-piecewise linear regression model were utilized to analyze the relationship between UA and CLNM and identify the threshold effect of UA concentrations on CLNM. Results The correlation between UA and CLNM in PTC patients was found to be positive. Upon adjusting for various confounding factors, it was determined that, relative to the referential level, the odds ratio for CLNM was 4.01 at peak UA levels. After PSM analysis, the odds ratio for CLNM was 5.23 at the highest levels to the lowest levels. A non-linear relationship between UA and CLNM emerged following adjustment for potential confounding factors. The study identified 219.20 µmol/L as the UA threshold, serving as the optimal inflection point. The effect sizes and confidence intervals on both sides of the inflection point were −4.43 (−9.69–0.84) and 3.78 (1.70–5.85), respectively. Conclusion The study concludes that the association between UA and CLNM is non-linear. A positive relationship between UA and CLNM was observed when UA levels exceeded 219.20 µmol/L.
bibliographic citation: Sun et al. (2025) Correlation between preoperative uric acid levels and lymph node metastases in patients with papillary thyroid cancer: a retrospective study. PeerJ 13:e19410 https://doi.org/10.7717/peerj.19410
date submitted: 2025-01-06
date accepted: 2025-04-10
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: ShaoKun
author list: Agent
  family name: Zhou
  given name: Qin
author list: Agent
  family name: Hu
  given name: Tao
doi: 10.7717/peerj.19410
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: ©2025 Sun et al.
attribution name: Sun et al.

Survival benefit from adjuvant chemoradiotherapy in local advanced gastric cancer without accurate D2 confirmation: a real-world retrospective study (TJ-ARK01)
type: item
type: AcademicArticle
description: The role of adjuvant chemoradiotherapy (CRT) is controversial following D2 dissection in advanced gastric cancer. Also, the extent of “D2 surgery” varied geographically due to the diversity in surgical techniques of radical lymphadenectomy and pathological accuracy in detecting positive lymph nodes detection. The purpose was to explore the role of adjuvant chemoradiation for gastric cancer and focus on patient stratification strategy. We retrospectively collected information of patients underwent surgery in Tongji Medical Cancer Center from January 2013 to December 2017 (2,489 in total). Propensity score match was applied to the chemotherapy (CT) group enrollment with well-balanced clinicopathological distributions. In total, 162 and 166 eligible patients were recruited into CT and CRT groups, nearly 75% diagnosed with advanced stage. The median follow-up duration was 61.3 months (4.0 to 109.0 months), 201 recurrence events occurred and 194 deaths events occurred. The 5-year disease-free-survival (DFS) rates were 32.0% in CT group and 44.0% in CRT group (P = 0.031), while 5-year overall survival (OS) rates were 36.0% in CT group and 50.0% in CRT group (P = 0.043). In the subgroup analysis, all patients were regrouped as subgroup 1 (positive lymph node (LN) ratio 0–50%) and subgroup 2 (positive LN ratio 51%–100%). There was a prolongation in 5-year DFS rates in subgroup 1 (40.0% in CT group, 61.0% in CRT group, P = 0.012) and in 5-year OS rates (48% in CT group, 64.0% in CRT group, P = 0.047). Further, patients with negative HER-2 expression had longer 5-year DFS (38% in CT, 49% in CRT, P = 0.115) and 5-year OS (36% in CT, 43% in CRT, P = 0.047). While previous studies found that the survival benefits were gained from chemoradiotherapy (CRT) inpatients of intestinal-type gastric cancer with lymph node metastasis, our findings highlight a distinct subgroup—patients with a lymph node ratio (LNR) ≤ 0.5 and HER2-negative tumors—for whom adjuvant chemoradiation may offer …
format: application/pdf
format: text/html
creator: Xiao-Xiao Luo
creator: Ben Zhao
creator: Li Sun
creator: Yu-Hong Dai
creator: Hong Qiu
creator: Xiang-Lin Yuan
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.19363
publisher: PeerJ Inc.
rights: © 2025 Luo et al.
abstract: The role of adjuvant chemoradiotherapy (CRT) is controversial following D2 dissection in advanced gastric cancer. Also, the extent of “D2 surgery” varied geographically due to the diversity in surgical techniques of radical lymphadenectomy and pathological accuracy in detecting positive lymph nodes detection. The purpose was to explore the role of adjuvant chemoradiation for gastric cancer and focus on patient stratification strategy. We retrospectively collected information of patients underwent surgery in Tongji Medical Cancer Center from January 2013 to December 2017 (2,489 in total). Propensity score match was applied to the chemotherapy (CT) group enrollment with well-balanced clinicopathological distributions. In total, 162 and 166 eligible patients were recruited into CT and CRT groups, nearly 75% diagnosed with advanced stage. The median follow-up duration was 61.3 months (4.0 to 109.0 months), 201 recurrence events occurred and 194 deaths events occurred. The 5-year disease-free-survival (DFS) rates were 32.0% in CT group and 44.0% in CRT group (P = 0.031), while 5-year overall survival (OS) rates were 36.0% in CT group and 50.0% in CRT group (P = 0.043). In the subgroup analysis, all patients were regrouped as subgroup 1 (positive lymph node (LN) ratio 0–50%) and subgroup 2 (positive LN ratio 51%–100%). There was a prolongation in 5-year DFS rates in subgroup 1 (40.0% in CT group, 61.0% in CRT group, P = 0.012) and in 5-year OS rates (48% in CT group, 64.0% in CRT group, P = 0.047). Further, patients with negative HER-2 expression had longer 5-year DFS (38% in CT, 49% in CRT, P = 0.115) and 5-year OS (36% in CT, 43% in CRT, P = 0.047). While previous studies found that the survival benefits were gained from chemoradiotherapy (CRT) inpatients of intestinal-type gastric cancer with lymph node metastasis, our findings highlight a distinct subgroup—patients with a lymph node ratio (LNR) ≤ 0.5 and HER2-negative tumors—for whom adjuvant chemoradiation may offer …
bibliographic citation: Luo et al. (2025) Survival benefit from adjuvant chemoradiotherapy in local advanced gastric cancer without accurate D2 confirmation: a real-world retrospective study (TJ-ARK01). PeerJ 13:e19363 https://doi.org/10.7717/peerj.19363
date submitted: 2024-09-20
date accepted: 2025-04-03
issued: 2025-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Xiao-Xiao
author list: Agent
  family name: Zhao
  given name: Ben
author list: Agent
  family name: Sun
  given name: Li
author list: Agent
  family name: Dai
  given name: Yu-Hong
author list: Agent
  family name: Qiu
  given name: Hong
author list: Agent
  family name: Yuan
  given name: Xiang-Lin
doi: 10.7717/peerj.19363
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-07-10
copyright: ©2025 Luo et al.
attribution name: Luo et al.

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