PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone
items: The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study
items: Minos-mediated transgenesis in the pantry moth Plodia interpunctella
items: The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration
items: Decoding the bare necessities of decapod crustacean nomenclature through the ages
items: Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species
items: Modified STOP-Bang questionnaire for detecting obstructive sleep apnea in individuals with a body mass index below 35 kg/m2
items: Effects of combined application of compound fertilizer and biochar on absorption and utilization of phosphorus by wheat
items: Impact of historical land use change on the brown bear habitat connectivity in the Polish Carpathians
items: Integrated bioinformatics screening and experimental validation: construction of a LUAD prediction model based on Treg-related genes

Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone
type: item
type: AcademicArticle
description: Background The Personality Assessment Inventory (PAI), a self-report personality test, is one of the frequently used measures to assess psychopathology in a wide variety of settings including in high stakes assessments, for example, in child custody disputes, employment settings and fitness for duty assessments. The PAI has never been normed on a Canadian population and the PAI users have simply assumed that the US norms also describe the Canadian population. Moreover, accumulated research demonstrates that the PAI’s 35 years outdated and obsolete norms no longer describe neither university students’ nor normal adult US populations. Method We administered the PAI to over 200 university students in a mid-size Canadian university. Results Our students scored on average in moderately elevated range (60T to 69T) on many of the PAI scales including anxiety (ANX), anxiety-related disorders (ARD), depression (DEP), schizophrenia (SCZ), and borderline features (BOR). Multivariate base rate analyses revealed that approximately 95% of our sample scored in elevated range on at least one out of the 22 PAI Scales. Furthermore, although some of the PAI reliabilities are adequate for research, the PAI reliabilities are too low for using the PAI in high stakes and forensic assessment, for example, in insurance benefits, child custody, employment, and fitness for duty assessments. Discussion We conclude that the PAI US norms are no longer appropriate for high-stakes assessments, ought to be withdrawn immediately, and new up-to-date norms ought to be established to prevent mislabelling and diagnostic misclassifications of and harm to examinees. Continued use of the PAI outdated norms in high stakes assessments carries ethical risks, is non-scientific, and likely amounts to malpractice.
format: application/pdf
format: text/html
creator: Bob Uttl
creator: Kiefer Sikma
creator: Mikayla Tat
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20340
publisher: PeerJ Inc.
rights: © 2025 Uttl et al.
abstract: Background The Personality Assessment Inventory (PAI), a self-report personality test, is one of the frequently used measures to assess psychopathology in a wide variety of settings including in high stakes assessments, for example, in child custody disputes, employment settings and fitness for duty assessments. The PAI has never been normed on a Canadian population and the PAI users have simply assumed that the US norms also describe the Canadian population. Moreover, accumulated research demonstrates that the PAI’s 35 years outdated and obsolete norms no longer describe neither university students’ nor normal adult US populations. Method We administered the PAI to over 200 university students in a mid-size Canadian university. Results Our students scored on average in moderately elevated range (60T to 69T) on many of the PAI scales including anxiety (ANX), anxiety-related disorders (ARD), depression (DEP), schizophrenia (SCZ), and borderline features (BOR). Multivariate base rate analyses revealed that approximately 95% of our sample scored in elevated range on at least one out of the 22 PAI Scales. Furthermore, although some of the PAI reliabilities are adequate for research, the PAI reliabilities are too low for using the PAI in high stakes and forensic assessment, for example, in insurance benefits, child custody, employment, and fitness for duty assessments. Discussion We conclude that the PAI US norms are no longer appropriate for high-stakes assessments, ought to be withdrawn immediately, and new up-to-date norms ought to be established to prevent mislabelling and diagnostic misclassifications of and harm to examinees. Continued use of the PAI outdated norms in high stakes assessments carries ethical risks, is non-scientific, and likely amounts to malpractice.
bibliographic citation: Uttl et al. (2025) Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone. PeerJ 13:e20340 https://doi.org/10.7717/peerj.20340
date submitted: 2025-06-04
date accepted: 2025-10-14
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uttl
  given name: Bob
author list: Agent
  family name: Sikma
  given name: Kiefer
author list: Agent
  family name: Tat
  given name: Mikayla
doi: 10.7717/peerj.20340
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: ©2025 Uttl et al.
attribution name: Uttl et al.

The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Maintenance hemodialysis (MHD) is the main renal replacement therapy for patients with end-stage renal disease, and erythropoietin (EPO) is the main therapy for renal anemia in patients receiving maintenance hemodialysis. However, the risks of brain hemorrhage and infarction in patients on hemodialysis with erythropoietin therapy remain unclear. Methods Patients who underwent regular hemodialysis at the Blood Purification Center of the Northern Theater General Hospital from January 1, 2018, to January 1, 2022, were retrospectively selected. A total of 588 MHD patients were enrolled on the basis of the inclusion and exclusion criteria. The primary endpoint of follow-up was brain hemorrhage and infarction, or January 1, 2024. The secondary endpoint was all-cause death. The erythropoietin resistance index (ERI) was calculated as follows: erythropoiesis-stimulating agent (ESA) (IU/week)/body weight (kg)/hemoglobin level (g/dL). Patients were divided into four groups according to ERI quartile, and a Cox proportional risk model was applied to observe the associations between the ERI and the risks of brain hemorrhage and infarction and all-cause mortality. Results During a median follow-up of 6 years, brain hemorrhage events occurred in 41 (6.9%) MHD patients, and brain infarction events occurred in 61 (10.3%) MHD patients. According to the Kaplan–Meier curve, the incidence of brain hemorrhage and infarction was greater in the high-ERI subgroup than in the low-ERI subgroup (p < 0.001). Multivariate Cox regression analysis revealed that a high ERI was a significant predictor of brain hemorrhage (HR: 3.85, 95% CI [1.34–11.07], p = 0.012) and brain infarction (HR = 2.657, 95% CI [1.17–6.02], p = 0.020). A higher ERI was associated with an increased risk of all-cause death in MHD patients (HR: 1.72, 95% CI [1.05–2.82], p = 0.033). Conclusions Higher ERI scores were associated with brain hemorrhage and infarction in MHD patients.
format: application/pdf
format: text/html
creator: Mingyu Liu
creator: Kaiming Ren
creator: Qian Wang
creator: Chen Zhao
creator: Zhuo Ren
creator: Jiuxu Bai
creator: Ning Cao
subject: Cardiology
subject: Hematology
subject: Internal Medicine
subject: Nephrology
subject: Neurology
description: doi:10.7717/peerj.20326
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Maintenance hemodialysis (MHD) is the main renal replacement therapy for patients with end-stage renal disease, and erythropoietin (EPO) is the main therapy for renal anemia in patients receiving maintenance hemodialysis. However, the risks of brain hemorrhage and infarction in patients on hemodialysis with erythropoietin therapy remain unclear. Methods Patients who underwent regular hemodialysis at the Blood Purification Center of the Northern Theater General Hospital from January 1, 2018, to January 1, 2022, were retrospectively selected. A total of 588 MHD patients were enrolled on the basis of the inclusion and exclusion criteria. The primary endpoint of follow-up was brain hemorrhage and infarction, or January 1, 2024. The secondary endpoint was all-cause death. The erythropoietin resistance index (ERI) was calculated as follows: erythropoiesis-stimulating agent (ESA) (IU/week)/body weight (kg)/hemoglobin level (g/dL). Patients were divided into four groups according to ERI quartile, and a Cox proportional risk model was applied to observe the associations between the ERI and the risks of brain hemorrhage and infarction and all-cause mortality. Results During a median follow-up of 6 years, brain hemorrhage events occurred in 41 (6.9%) MHD patients, and brain infarction events occurred in 61 (10.3%) MHD patients. According to the Kaplan–Meier curve, the incidence of brain hemorrhage and infarction was greater in the high-ERI subgroup than in the low-ERI subgroup (p < 0.001). Multivariate Cox regression analysis revealed that a high ERI was a significant predictor of brain hemorrhage (HR: 3.85, 95% CI [1.34–11.07], p = 0.012) and brain infarction (HR = 2.657, 95% CI [1.17–6.02], p = 0.020). A higher ERI was associated with an increased risk of all-cause death in MHD patients (HR: 1.72, 95% CI [1.05–2.82], p = 0.033). Conclusions Higher ERI scores were associated with brain hemorrhage and infarction in MHD patients.
bibliographic citation: Liu et al. (2025) The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study. PeerJ 13:e20326 https://doi.org/10.7717/peerj.20326
date submitted: 2025-03-31
date accepted: 2025-10-13
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Mingyu
author list: Agent
  family name: Ren
  given name: Kaiming
author list: Agent
  family name: Wang
  given name: Qian
author list: Agent
  family name: Zhao
  given name: Chen
author list: Agent
  family name: Ren
  given name: Zhuo
author list: Agent
  family name: Bai
  given name: Jiuxu
author list: Agent
  family name: Cao
  given name: Ning
doi: 10.7717/peerj.20326
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: ©2025 Liu et al.
attribution name: Liu et al.

Minos-mediated transgenesis in the pantry moth Plodia interpunctella
type: item
type: AcademicArticle
description: Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results—along with previous findings in the silkworm Bombyx mori—demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant.
format: application/pdf
format: text/html
creator: Donya N. Shodja
creator: Luca Livraghi
creator: Arnaud Martin
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.20249
publisher: PeerJ Inc.
rights: © 2025 Shodja et al.
abstract: Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results—along with previous findings in the silkworm Bombyx mori—demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant.
bibliographic citation: Shodja et al. (2025) Minos-mediated transgenesis in the pantry moth Plodia interpunctella. PeerJ 13:e20249 https://doi.org/10.7717/peerj.20249
date submitted: 2025-03-30
date accepted: 2025-09-25
issued: 2025-11-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shodja
  given name: Donya N.
author list: Agent
  family name: Livraghi
  given name: Luca
author list: Agent
  family name: Martin
  given name: Arnaud
doi: 10.7717/peerj.20249
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-12
copyright: © 2025 Shodja et al.
attribution name: Shodja et al.

The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration
type: item
type: AcademicArticle
description: Objective Cuproptosis, a newly discovered cell death mechanism, has been linked to the pathogenesis of multiple diseases. However, its role in diabetic kidney disease (DKD) remains unclear. Methods By analyzing datasets GPL17586 and GPL571 from the GEO database and applying machine learning, cuproptosis-related marker genes associated with DKD were identified. The expression levels of these genes were examined in Mouse Podocyte Cell Line (MPC5) podocytes cultured in vitro and treated with high glucose (30 mM) for 24, 48, and 72 h to explore their roles in the onset and progression of DKD. Results Key genes in the cuproptosis pathway, integrin β6 (ITGB6) and latent transforming growth factor beta-binding protein 1 (LTBP1), were significantly upregulated in DKD patients. Consistent with this, in high glucose-treated podocytes, the expression of ITGB6 and LTBP1 was significantly higher than in the control group at 24, 48, and 72 h. The area under the receiver operating characteristic (ROC) curve (AUC) for ITGB6 and LTBP1 in both the training set (GPL17586) and validation set (GPL571) exceeded 0.7, indicating good diagnostic efficacy for DKD. Furthermore, immune infiltration analysis further revealed that ITGB6 and LTBP1 were significantly positively correlated with activated B cells, central memory Cluster of Differentiation 4 (CD4) T cells, effector memory CD4 T cells, effector memory Cluster of Differentiation 8 (CD8) T cells, and immature B cells, while showing a significant negative correlation with neutrophils. Conclusion This study suggests that cuproptosis-related genes ITGB6 and LTBP1 may be associated with the progression of DKD through their potential role in immune cell infiltration, and could serve as potential novel targets for the prevention and diagnosis of DKD.
format: application/pdf
format: text/html
creator: Suying Hu
creator: Mengdi Tian
creator: Wenjia Hu
creator: Liang Yao
creator: Ying Tang
creator: Wei Shen
creator: Qing He
creator: Jing Xu
creator: Huan Yao
creator: Lei Ji
creator: Feifei Fan
creator: Shiqiang Liu
creator: Zhen Wang
subject: Bioinformatics
subject: Cell Biology
description: doi:10.7717/peerj.20346
publisher: PeerJ Inc.
rights: © 2025 Hu et al.
abstract: Objective Cuproptosis, a newly discovered cell death mechanism, has been linked to the pathogenesis of multiple diseases. However, its role in diabetic kidney disease (DKD) remains unclear. Methods By analyzing datasets GPL17586 and GPL571 from the GEO database and applying machine learning, cuproptosis-related marker genes associated with DKD were identified. The expression levels of these genes were examined in Mouse Podocyte Cell Line (MPC5) podocytes cultured in vitro and treated with high glucose (30 mM) for 24, 48, and 72 h to explore their roles in the onset and progression of DKD. Results Key genes in the cuproptosis pathway, integrin β6 (ITGB6) and latent transforming growth factor beta-binding protein 1 (LTBP1), were significantly upregulated in DKD patients. Consistent with this, in high glucose-treated podocytes, the expression of ITGB6 and LTBP1 was significantly higher than in the control group at 24, 48, and 72 h. The area under the receiver operating characteristic (ROC) curve (AUC) for ITGB6 and LTBP1 in both the training set (GPL17586) and validation set (GPL571) exceeded 0.7, indicating good diagnostic efficacy for DKD. Furthermore, immune infiltration analysis further revealed that ITGB6 and LTBP1 were significantly positively correlated with activated B cells, central memory Cluster of Differentiation 4 (CD4) T cells, effector memory CD4 T cells, effector memory Cluster of Differentiation 8 (CD8) T cells, and immature B cells, while showing a significant negative correlation with neutrophils. Conclusion This study suggests that cuproptosis-related genes ITGB6 and LTBP1 may be associated with the progression of DKD through their potential role in immune cell infiltration, and could serve as potential novel targets for the prevention and diagnosis of DKD.
bibliographic citation: Hu et al. (2025) The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration. PeerJ 13:e20346 https://doi.org/10.7717/peerj.20346
date submitted: 2025-06-17
date accepted: 2025-10-15
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Suying
author list: Agent
  family name: Tian
  given name: Mengdi
author list: Agent
  family name: Hu
  given name: Wenjia
author list: Agent
  family name: Yao
  given name: Liang
author list: Agent
  family name: Tang
  given name: Ying
author list: Agent
  family name: Shen
  given name: Wei
author list: Agent
  family name: He
  given name: Qing
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Yao
  given name: Huan
author list: Agent
  family name: Ji
  given name: Lei
author list: Agent
  family name: Fan
  given name: Feifei
author list: Agent
  family name: Liu
  given name: Shiqiang
author list: Agent
  family name: Wang
  given name: Zhen
doi: 10.7717/peerj.20346
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 Hu et al.
attribution name: Hu et al.

Decoding the bare necessities of decapod crustacean nomenclature through the ages
type: item
type: AcademicArticle
description: Though taxonomists have been classifying species since 1758, the methods and biases of their naming practices have recently come under scrutiny. Despite some compelling claims on e.g., historical imperialism in the published literature, the knowledge base for making such assertions is small, as nomenclatural trends have only been researched in a select few taxa. Here, we investigate naming practices in Decapoda, one of the most studied crustacean groups, thereby extending the knowledge base to the marine realm in contrast to a previously studied cohort of largely terrestrial taxa. To date almost 18,000 species of decapods are known, from which a total of 22,363 unique names are analysed, as neither nomenclatorial nor taxonomic status has any bearing on the naming process. Despite taxonomists being inspired by a multitude of cultural influences, historically the majority of names were derived from the morphology of the animals. This dominance declined in the Victorian era, with a concomitant rise in the use of both geographically inspired names and eponyms (species named after people). Post-1958, a near-even split is achieved between these three categories, while other etymological classifications stake a minority claim on the dataset. Although a historic and contemporary gender imbalance is present amongst eponyms honouring scientists, contrary to previous findings our results detect no actual bias in naming practices, instead indicating that female scientists have been honoured in proportion to their collective presence in the field. Though previous studies have flagged a significant proportion of eponyms named for colonialist figures, these were found in relatively small numbers among Decapoda.
format: application/pdf
format: text/html
creator: Sammy De Grave
creator: Elizabeth Cole
creator: Sancia E. T. van der Meij
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.20337
publisher: PeerJ Inc.
rights: © 2025 De Grave et al.
abstract: Though taxonomists have been classifying species since 1758, the methods and biases of their naming practices have recently come under scrutiny. Despite some compelling claims on e.g., historical imperialism in the published literature, the knowledge base for making such assertions is small, as nomenclatural trends have only been researched in a select few taxa. Here, we investigate naming practices in Decapoda, one of the most studied crustacean groups, thereby extending the knowledge base to the marine realm in contrast to a previously studied cohort of largely terrestrial taxa. To date almost 18,000 species of decapods are known, from which a total of 22,363 unique names are analysed, as neither nomenclatorial nor taxonomic status has any bearing on the naming process. Despite taxonomists being inspired by a multitude of cultural influences, historically the majority of names were derived from the morphology of the animals. This dominance declined in the Victorian era, with a concomitant rise in the use of both geographically inspired names and eponyms (species named after people). Post-1958, a near-even split is achieved between these three categories, while other etymological classifications stake a minority claim on the dataset. Although a historic and contemporary gender imbalance is present amongst eponyms honouring scientists, contrary to previous findings our results detect no actual bias in naming practices, instead indicating that female scientists have been honoured in proportion to their collective presence in the field. Though previous studies have flagged a significant proportion of eponyms named for colonialist figures, these were found in relatively small numbers among Decapoda.
bibliographic citation: De Grave et al. (2025) Decoding the bare necessities of decapod crustacean nomenclature through the ages. PeerJ 13:e20337 https://doi.org/10.7717/peerj.20337
date submitted: 2025-08-21
date accepted: 2025-10-13
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Grave
  given name: Sammy
author list: Agent
  family name: Cole
  given name: Elizabeth
author list: Agent
  family name: van der Meij
  given name: Sancia E. T.
doi: 10.7717/peerj.20337
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 De Grave et al.
attribution name: De Grave et al.

Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species
type: item
type: AcademicArticle
description: Species movements along elevational or latitudinal gradients occur primarily due to climatic variations and food resource availability. However, the role of seasonal climatic conditions in species with highly restricted distributions has been poorly addressed. In this study, we analyzed the geographic distribution and seasonal climatic niche during the dry and rainy seasons of the Short-crested Coquette hummingbird (SCCH; Lophornis brachylophus), a species with high conservation priority at the global scale. We generated ecological niche and species distribution models for both seasons and used niche similarity tests to represent and compare their climatic differences. We recorded the availability of flowering and fruiting plants that the SCCH feeds on within its distribution area during both seasons and performed a kernel density analysis to evaluate the main peaks in food availability. Our results revealed that the potential distribution of the SCCH is larger (642 pixels) in the dry season than in the rainy season (487 pixels). In the dry season, the distribution of this hummingbird includes sites at lower elevations (reaching 780 m above sea level [masl]). In contrast, in the rainy season, it extends to higher elevations (up to 1,450 masl). This seasonal shift between the two seasons coincides with the availability of flowers and fruits along the elevational gradient. The climatic niche similarity between the dry and rainy seasons shows moderate overlap (Schoener’s D = 0.50) and is higher than expected by chance. Our results suggest that the SCCH moderate changes in its climatic niche throughout the year, with plant phenology being a primary driver of changes in its elevational range between seasons.
format: application/pdf
format: text/html
creator: Pablo Sierra-Morales
creator: Octavio R. Rojas-Soto
creator: Luis A. Sánchez-González
creator: Carina Gutiérrez-Flores
creator: R. Carlos Almazán-Núñez
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20312
publisher: PeerJ Inc.
rights: © 2025 Sierra-Morales et al.
abstract: Species movements along elevational or latitudinal gradients occur primarily due to climatic variations and food resource availability. However, the role of seasonal climatic conditions in species with highly restricted distributions has been poorly addressed. In this study, we analyzed the geographic distribution and seasonal climatic niche during the dry and rainy seasons of the Short-crested Coquette hummingbird (SCCH; Lophornis brachylophus), a species with high conservation priority at the global scale. We generated ecological niche and species distribution models for both seasons and used niche similarity tests to represent and compare their climatic differences. We recorded the availability of flowering and fruiting plants that the SCCH feeds on within its distribution area during both seasons and performed a kernel density analysis to evaluate the main peaks in food availability. Our results revealed that the potential distribution of the SCCH is larger (642 pixels) in the dry season than in the rainy season (487 pixels). In the dry season, the distribution of this hummingbird includes sites at lower elevations (reaching 780 m above sea level [masl]). In contrast, in the rainy season, it extends to higher elevations (up to 1,450 masl). This seasonal shift between the two seasons coincides with the availability of flowers and fruits along the elevational gradient. The climatic niche similarity between the dry and rainy seasons shows moderate overlap (Schoener’s D = 0.50) and is higher than expected by chance. Our results suggest that the SCCH moderate changes in its climatic niche throughout the year, with plant phenology being a primary driver of changes in its elevational range between seasons.
bibliographic citation: Sierra-Morales et al. (2025) Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species. PeerJ 13:e20312 https://doi.org/10.7717/peerj.20312
date submitted: 2025-06-03
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sierra-Morales
  given name: Pablo
author list: Agent
  family name: Rojas-Soto
  given name: Octavio R.
author list: Agent
  family name: Sánchez-González
  given name: Luis A.
author list: Agent
  family name: Gutiérrez-Flores
  given name: Carina
author list: Agent
  family name: Almazán-Núñez
  given name: R. Carlos
doi: 10.7717/peerj.20312
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: © 2025 Sierra-Morales et al.
attribution name: Sierra-Morales et al.

Modified STOP-Bang questionnaire for detecting obstructive sleep apnea in individuals with a body mass index below 35 kg/m2
type: item
type: AcademicArticle
description: Background Obstructive sleep apnea (OSA) is a common clinical condition. Due to its high prevalence, the waiting list for polysomnography is often long. A screening tool is needed to identify individuals at high risk for OSA who should undergo polysomnography. The STOP-Bang questionnaire is a widely used screening tool; however, it may require modification for individuals with a body mass index (BMI) below 35 kg/m2. This study aimed to evaluate whether the STOP-Bang questionnaire should be modified for patients with a BMI under 35 kg/m2. Methods This retrospective analytical study included adult patients suspected of having OSA who underwent polysomnography. Exclusion criteria included pregnancy and a BMI over 35 kg/m2 or meeting criteria for bariatric surgery. Patients were categorized into OSA and non-OSA groups. Logistic regression analysis was used to assess the predictive value of STOP-Bang factors for OSA. Results A total of 188 patients were included, of whom 158 (84.04%) were diagnosed with OSA. Among the eight STOP-Bang criteria, only age was independently associated with OSA after adjustment for other variables (adjusted odds ratio: 1.04; 95% CI [1.02–1.08]). Optimal cut-off points for predicting OSA were identified as age ≥ 40 years (sensitivity: 84.18%), BMI ≥ 23 kg/m2 (sensitivity: 82.91%), and neck circumference ≥ 35 cm (sensitivity: 86.08%). A modified STOP-Bang score incorporating these cut-offs showed improved sensitivity at a score of 3: 93.0% for apnea-hypopnea index (AHI) ≥ 5 events/hr, 95.9% for AHI ≥ 15 events/hr, and 97.6% for AHI ≥ 30 events/hr. In comparison, the original STOP-Bang score of 3 had sensitivities of 50.0%, 53.6%, and 56.1% for AHI ≥ 5 events/hr, AHI ≥ 15 events/hr, and AHI > 30 events/hr, respectively. Conclusions The STOP-Bang questionnaire may require modification for individuals with a BMI below 35 kg/m2 who are suspected of having OSA. Revised cut-off values for age, neck circumference, and BMI—40 years, 35 cm, and 23 kg/m2…
format: application/pdf
format: text/html
creator: Napassorn Sinsopa
creator: Viriya Tripakornkusol
creator: Sittichai Khamsai
creator: Kittisak Sawanyawisuth
subject: Internal Medicine
subject: Respiratory Medicine
subject: Obesity
description: doi:10.7717/peerj.20310
publisher: PeerJ Inc.
rights: © 2025 Sinsopa et al.
abstract: Background Obstructive sleep apnea (OSA) is a common clinical condition. Due to its high prevalence, the waiting list for polysomnography is often long. A screening tool is needed to identify individuals at high risk for OSA who should undergo polysomnography. The STOP-Bang questionnaire is a widely used screening tool; however, it may require modification for individuals with a body mass index (BMI) below 35 kg/m2. This study aimed to evaluate whether the STOP-Bang questionnaire should be modified for patients with a BMI under 35 kg/m2. Methods This retrospective analytical study included adult patients suspected of having OSA who underwent polysomnography. Exclusion criteria included pregnancy and a BMI over 35 kg/m2 or meeting criteria for bariatric surgery. Patients were categorized into OSA and non-OSA groups. Logistic regression analysis was used to assess the predictive value of STOP-Bang factors for OSA. Results A total of 188 patients were included, of whom 158 (84.04%) were diagnosed with OSA. Among the eight STOP-Bang criteria, only age was independently associated with OSA after adjustment for other variables (adjusted odds ratio: 1.04; 95% CI [1.02–1.08]). Optimal cut-off points for predicting OSA were identified as age ≥ 40 years (sensitivity: 84.18%), BMI ≥ 23 kg/m2 (sensitivity: 82.91%), and neck circumference ≥ 35 cm (sensitivity: 86.08%). A modified STOP-Bang score incorporating these cut-offs showed improved sensitivity at a score of 3: 93.0% for apnea-hypopnea index (AHI) ≥ 5 events/hr, 95.9% for AHI ≥ 15 events/hr, and 97.6% for AHI ≥ 30 events/hr. In comparison, the original STOP-Bang score of 3 had sensitivities of 50.0%, 53.6%, and 56.1% for AHI ≥ 5 events/hr, AHI ≥ 15 events/hr, and AHI > 30 events/hr, respectively. Conclusions The STOP-Bang questionnaire may require modification for individuals with a BMI below 35 kg/m2 who are suspected of having OSA. Revised cut-off values for age, neck circumference, and BMI—40 years, 35 cm, and 23 kg/m2…
bibliographic citation: Sinsopa et al. (2025) Modified STOP-Bang questionnaire for detecting obstructive sleep apnea in individuals with a body mass index below 35 kg/m2. PeerJ 13:e20310 https://doi.org/10.7717/peerj.20310
date submitted: 2024-05-23
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sinsopa
  given name: Napassorn
author list: Agent
  family name: Tripakornkusol
  given name: Viriya
author list: Agent
  family name: Khamsai
  given name: Sittichai
author list: Agent
  family name: Sawanyawisuth
  given name: Kittisak
doi: 10.7717/peerj.20310
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Sinsopa et al.
attribution name: Sinsopa et al.

Effects of combined application of compound fertilizer and biochar on absorption and utilization of phosphorus by wheat
type: item
type: AcademicArticle
description: Unreasonable fertilization practices are still applied in agricultural production, resulting in reduced crop yields and wasting resources. Therefore, it is essential to optimize fertilization regimes to improve the nutrient absorption capacity of crops. However, the effects of combining nitrogen, phosphorus, and potassium (NPK) compound fertilizer with biochar on the uptake and utilization of phosphorus (P) by wheat and soil fertility remain poorly understood. Thus, we tested three biochar levels (0 quintal (q) ha−1 (B1), 75 q ha−1 (B2), and 150 q ha−1(B3)) and four compound fertilizer levels (0 q ha−1 (F1), 2.25 q ha –1(F2), 4.50 q ha−1 (F3), and 6.75 q ha−1 (F4)), and compared the effects of different experimental combinations across two years. The results showed that combined application could increase the wheat yield, soil P content, accumulated plant P, and P utilization efficiency. Among the different treatments, the wheat yields in both years were highest under B2F3, and the total soil P contents in the booting and flowering stages were also the highest. The soil available P contents in the jointing stage, booting stage, and flowering stage were highest under B3F3. The available P soil contents at maturity in both years were highest under B3F4. In addition, compared with B1F4, the accumulated plant P amounts in the booting and flowering stages were 17.6–77.3% and 17.0–87.3% higher, respectively, under B2F2, B2F3, B3F2, and B3F4 (P < 0.05). The accumulated plant P amounts in the maturity stage during the two years were highest under B2F3 (0.83 q ha−1) and B3F3 (0.42 q ha−1), respectively. Moreover, the partial factor productivity and agronomic use efficiency were significantly higher under B2F2, B2F3, B3F2, and B3F3 than B1F4. In summary, under the experimental conditions in this study, applying compound fertilizer at 4.50 q ha−1 combined with biochar at 75 q ha−1 is recommended as the optimal fertilization scheme.
format: application/pdf
format: text/html
creator: Yun Li
creator: Jiatong Wang
creator: Jiahui Lu
creator: Yanfei Feng
creator: Jingjing Li
creator: Zhenqing Guo
creator: Xiaohu Lin
creator: Yucui Han
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20308
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Unreasonable fertilization practices are still applied in agricultural production, resulting in reduced crop yields and wasting resources. Therefore, it is essential to optimize fertilization regimes to improve the nutrient absorption capacity of crops. However, the effects of combining nitrogen, phosphorus, and potassium (NPK) compound fertilizer with biochar on the uptake and utilization of phosphorus (P) by wheat and soil fertility remain poorly understood. Thus, we tested three biochar levels (0 quintal (q) ha−1 (B1), 75 q ha−1 (B2), and 150 q ha−1(B3)) and four compound fertilizer levels (0 q ha−1 (F1), 2.25 q ha –1(F2), 4.50 q ha−1 (F3), and 6.75 q ha−1 (F4)), and compared the effects of different experimental combinations across two years. The results showed that combined application could increase the wheat yield, soil P content, accumulated plant P, and P utilization efficiency. Among the different treatments, the wheat yields in both years were highest under B2F3, and the total soil P contents in the booting and flowering stages were also the highest. The soil available P contents in the jointing stage, booting stage, and flowering stage were highest under B3F3. The available P soil contents at maturity in both years were highest under B3F4. In addition, compared with B1F4, the accumulated plant P amounts in the booting and flowering stages were 17.6–77.3% and 17.0–87.3% higher, respectively, under B2F2, B2F3, B3F2, and B3F4 (P < 0.05). The accumulated plant P amounts in the maturity stage during the two years were highest under B2F3 (0.83 q ha−1) and B3F3 (0.42 q ha−1), respectively. Moreover, the partial factor productivity and agronomic use efficiency were significantly higher under B2F2, B2F3, B3F2, and B3F3 than B1F4. In summary, under the experimental conditions in this study, applying compound fertilizer at 4.50 q ha−1 combined with biochar at 75 q ha−1 is recommended as the optimal fertilization scheme.
bibliographic citation: Li et al. (2025) Effects of combined application of compound fertilizer and biochar on absorption and utilization of phosphorus by wheat. PeerJ 13:e20308 https://doi.org/10.7717/peerj.20308
date submitted: 2025-05-02
date accepted: 2025-10-08
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yun
author list: Agent
  family name: Wang
  given name: Jiatong
author list: Agent
  family name: Lu
  given name: Jiahui
author list: Agent
  family name: Feng
  given name: Yanfei
author list: Agent
  family name: Li
  given name: Jingjing
author list: Agent
  family name: Guo
  given name: Zhenqing
author list: Agent
  family name: Lin
  given name: Xiaohu
author list: Agent
  family name: Han
  given name: Yucui
doi: 10.7717/peerj.20308
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Li et al.
attribution name: Li et al.

Impact of historical land use change on the brown bear habitat connectivity in the Polish Carpathians
type: item
type: AcademicArticle
description: Background Europe has undergone dynamic land use changes in recent decades that have affected the extent, quality, and connectivity of large carnivore habitats. However, the current distribution of large carnivores also depends on historical land use processes. In this article, we analyse the impact of historical land use changes on the potential connectivity of brown bear habitats in the region linking the western and eastern parts of the Carpathians, one of Europe’s biodiversity hotspots. Methods The analyses were conducted based on elevation, slope, and distance-based, land use-related variables representing four time periods: 1860s, 1930s, 1970s, and 2013, using cost surface and least-cost path analyses. We used two different approaches to create cost surfaces: weighted, where the weights differentiated between variables according to their relative importance, reflecting their role in either bear space selection or avoidance, and unweighted, where all the variables were treated as equally important. Results The results of both approaches showed a gradual improvement in habitat connectivity for brown bears over time, driven by the increase in forest cover observed over the whole analysed period. However, the dynamics of these changes were much higher after the forced post-war resettlement in the 1940s. These tragic events resulted in the removal of settlements over large areas, substantially reducing human pressure and allowing brown bears to spread into new territories, expanding their habitats and creating new connectivity opportunities. We found that up to 40% of the current corridor was stable since mid-19th century. Our analysis shows that the current population decline in many rural areas of Europe may have positive implications for the habitats and population connectivity of large carnivores, but careful planning is needed to avoid negative interactions with local communities.
format: application/pdf
format: text/html
creator: Anna Szwagierczak
creator: El.zbieta Ziółkowska
creator: Joanna Wąs
creator: Michał Jakiel
creator: Dominik Kaim
subject: Coupled Natural and Human Systems
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.20295
publisher: PeerJ Inc.
rights: © 2025 Szwagierczak et al.
abstract: Background Europe has undergone dynamic land use changes in recent decades that have affected the extent, quality, and connectivity of large carnivore habitats. However, the current distribution of large carnivores also depends on historical land use processes. In this article, we analyse the impact of historical land use changes on the potential connectivity of brown bear habitats in the region linking the western and eastern parts of the Carpathians, one of Europe’s biodiversity hotspots. Methods The analyses were conducted based on elevation, slope, and distance-based, land use-related variables representing four time periods: 1860s, 1930s, 1970s, and 2013, using cost surface and least-cost path analyses. We used two different approaches to create cost surfaces: weighted, where the weights differentiated between variables according to their relative importance, reflecting their role in either bear space selection or avoidance, and unweighted, where all the variables were treated as equally important. Results The results of both approaches showed a gradual improvement in habitat connectivity for brown bears over time, driven by the increase in forest cover observed over the whole analysed period. However, the dynamics of these changes were much higher after the forced post-war resettlement in the 1940s. These tragic events resulted in the removal of settlements over large areas, substantially reducing human pressure and allowing brown bears to spread into new territories, expanding their habitats and creating new connectivity opportunities. We found that up to 40% of the current corridor was stable since mid-19th century. Our analysis shows that the current population decline in many rural areas of Europe may have positive implications for the habitats and population connectivity of large carnivores, but careful planning is needed to avoid negative interactions with local communities.
bibliographic citation: Szwagierczak et al. (2025) Impact of historical land use change on the brown bear habitat connectivity in the Polish Carpathians. PeerJ 13:e20295 https://doi.org/10.7717/peerj.20295
date submitted: 2025-05-13
date accepted: 2025-10-06
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szwagierczak
  given name: Anna
author list: Agent
  family name: Ziółkowska
  given name: El.zbieta
author list: Agent
  family name: Wąs
  given name: Joanna
author list: Agent
  family name: Jakiel
  given name: Michał
author list: Agent
  family name: Kaim
  given name: Dominik
doi: 10.7717/peerj.20295
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Szwagierczak et al.
attribution name: Szwagierczak et al.

Integrated bioinformatics screening and experimental validation: construction of a LUAD prediction model based on Treg-related genes
type: item
type: AcademicArticle
description: Background The prognosis of lung adenocarcinoma (LUAD) is poor, and clinical treatment mainly comprises a combination of traditional therapy and immunotherapy. However, the role and mechanism of tumor-infiltrating regulatory T cells (Tregs) in immunotherapy remain controversial. Therefore, we aimed to determine the role of Tregs in LUAD and to construct a relevant prognostic model for future clinical treatment. Methods A LUAD dataset was downloaded from the Gene Expression Omnibus (GEO) database, screened, integrated, and divided into test and validation datasets. CIBERSORT and weighted correlation network analysis (WGCNA) algorithms were combined to screen for Treg cell-related modules. Minimum absolute contraction and selection operator (LASSO) and univariate and multivariate Cox regression analyses were used to screen genes in the key modules and construct Treg-related prognostic models. Then, the expression differences of genes in the prognostic model were analyzed, and the results were verified by Western blotting. Result Among all cluster modules, the correlation between the brown module and Treg s (R2 = 0.43, P = 1e − 30) was the highest. After LASSO and univariate and multivariate Cox regression screening, six genes (ADARB2, B3GALT, FER, LTB4R2, N6AMT1, and SCN9A) were selected to construct the prognosis model, and the prognosis of low-risk patients was found to be better than that of high-risk patients. Finally, the SCN9A gene with the highest correlation with the model was selected and verified using Western blot analysis. The results showed that the expression of Treg surface markers in LUAD cells was increased, and the expression of SCN9A was decreased compared with that in normal lung epithelial cells. Conclusion We identified the role of Treg-related genes in LUAD, constructed and verified a related prognostic model, and explored a potential therapeutic target, SCN9A, to provide a new perspective for the clinical treatment of LUAD.
format: application/pdf
format: text/html
creator: Tian Zhao
creator: Yan Yao
creator: Yan Sun
creator: Qingliang Lv
creator: Changgang Sun
creator: Yining Cheng
creator: Chundi Gao
creator: Jing Zhuang
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20287
publisher: PeerJ Inc.
rights: © 2025 Zhao et al.
abstract: Background The prognosis of lung adenocarcinoma (LUAD) is poor, and clinical treatment mainly comprises a combination of traditional therapy and immunotherapy. However, the role and mechanism of tumor-infiltrating regulatory T cells (Tregs) in immunotherapy remain controversial. Therefore, we aimed to determine the role of Tregs in LUAD and to construct a relevant prognostic model for future clinical treatment. Methods A LUAD dataset was downloaded from the Gene Expression Omnibus (GEO) database, screened, integrated, and divided into test and validation datasets. CIBERSORT and weighted correlation network analysis (WGCNA) algorithms were combined to screen for Treg cell-related modules. Minimum absolute contraction and selection operator (LASSO) and univariate and multivariate Cox regression analyses were used to screen genes in the key modules and construct Treg-related prognostic models. Then, the expression differences of genes in the prognostic model were analyzed, and the results were verified by Western blotting. Result Among all cluster modules, the correlation between the brown module and Treg s (R2 = 0.43, P = 1e − 30) was the highest. After LASSO and univariate and multivariate Cox regression screening, six genes (ADARB2, B3GALT, FER, LTB4R2, N6AMT1, and SCN9A) were selected to construct the prognosis model, and the prognosis of low-risk patients was found to be better than that of high-risk patients. Finally, the SCN9A gene with the highest correlation with the model was selected and verified using Western blot analysis. The results showed that the expression of Treg surface markers in LUAD cells was increased, and the expression of SCN9A was decreased compared with that in normal lung epithelial cells. Conclusion We identified the role of Treg-related genes in LUAD, constructed and verified a related prognostic model, and explored a potential therapeutic target, SCN9A, to provide a new perspective for the clinical treatment of LUAD.
bibliographic citation: Zhao et al. (2025) Integrated bioinformatics screening and experimental validation: construction of a LUAD prediction model based on Treg-related genes. PeerJ 13:e20287 https://doi.org/10.7717/peerj.20287
date submitted: 2025-05-09
date accepted: 2025-10-03
issued: 2025-11-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhao
  given name: Tian
author list: Agent
  family name: Yao
  given name: Yan
author list: Agent
  family name: Sun
  given name: Yan
author list: Agent
  family name: Lv
  given name: Qingliang
author list: Agent
  family name: Sun
  given name: Changgang
author list: Agent
  family name: Cheng
  given name: Yining
author list: Agent
  family name: Gao
  given name: Chundi
author list: Agent
  family name: Zhuang
  given name: Jing
doi: 10.7717/peerj.20287
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-11
copyright: ©2025 Zhao et al.
attribution name: Zhao et al.

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