PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploring probiotic awareness, perceptions, and practices in the Saudi population: a cross-sectional study
items: Bond strength between layering ceramic and zirconia core: influence of various surface conditioning of zirconia
items: Effect of major ozone autohemotherapy in fibromyalgia syndrome: a retrospective study
items: Development of a predictive model for severe hyperlipidemic acute pancreatitis based on LASSO regression: a retrospective study
items: Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms
items: Morpho-physiological traits and yield quality for cassava genotypes planted under drought during canopy establishment
items: Retrospective study on the clinical outcomes and characteristics of acute myeloid leukemia: different outcomes in the same risk group
items: Paw-spective shift: how our mood alters the way we read dog emotions
items: Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis
items: The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more

Exploring probiotic awareness, perceptions, and practices in the Saudi population: a cross-sectional study
type: item
type: AcademicArticle
description: Background Probiotics are composed of trillions of microorganisms, mainly located in the gastrointestinal tract (GIT), which play vital roles in digestion, immunity, and overall well-being. They help maintain gut health and prevent various gastrointestinal disorders. Despite the widespread use of probiotics in developed countries, such as North America and Western Europe, little is known about their use in Saudi Arabia. This study aimed to assess the knowledge, attitudes, and factors influencing probiotic awareness among the Saudi public to support healthier dietary choices. Materials A cross-sectional study using a structured questionnaire titled “Public Knowledge and Perception of Probiotics” was conducted among Saudi residents aged 18 years and older from July to October 2024. With a type I error rate of 5% (α = 0.05) and 80% power, the required sample size was 269; ultimately, 286 individuals participated in the study. Data were analyzed using the Statistical Package for the Social Sciences version 27 (IBM). Results The majority of the 286 participants were female (79%) and over 30 years old (54.9%). Awareness of probiotics was moderate (mean score: 5.2; 65%), with yogurt being the most recognized source (95%). Participants generally had positive perceptions (mean score: 3.74 ± 0.60), although barriers such as limited knowledge (56.2%) and high cost (3.28 ± 1.09) were reported. Probiotic use was noted in 54.5% of the respondents, with 71.2% preferring natural sources. Usage was significantly associated with demographic factors, including age ( $\chi^2$χ2 = 15.251, P < 0.001), education level ( $\chi^2$χ2 = 18.787, P < 0.001), marital status ( $\chi^2$χ2 = 9.825, P = 0.002), and monthly income ( $\chi^2$χ2 = 8.548, P = 0.014). Conclusion While awareness and positive perceptions of probiotics are growing among the Saudi population, challenges such as knowledge gaps, affordability, and limited advertising persist. To promote probiotic use and improve public health …
format: application/pdf
format: text/html
creator: Basmah F. Alharbi
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.20490
publisher: PeerJ Inc.
rights: © 2025 Alharbi
abstract: Background Probiotics are composed of trillions of microorganisms, mainly located in the gastrointestinal tract (GIT), which play vital roles in digestion, immunity, and overall well-being. They help maintain gut health and prevent various gastrointestinal disorders. Despite the widespread use of probiotics in developed countries, such as North America and Western Europe, little is known about their use in Saudi Arabia. This study aimed to assess the knowledge, attitudes, and factors influencing probiotic awareness among the Saudi public to support healthier dietary choices. Materials A cross-sectional study using a structured questionnaire titled “Public Knowledge and Perception of Probiotics” was conducted among Saudi residents aged 18 years and older from July to October 2024. With a type I error rate of 5% (α = 0.05) and 80% power, the required sample size was 269; ultimately, 286 individuals participated in the study. Data were analyzed using the Statistical Package for the Social Sciences version 27 (IBM). Results The majority of the 286 participants were female (79%) and over 30 years old (54.9%). Awareness of probiotics was moderate (mean score: 5.2; 65%), with yogurt being the most recognized source (95%). Participants generally had positive perceptions (mean score: 3.74 ± 0.60), although barriers such as limited knowledge (56.2%) and high cost (3.28 ± 1.09) were reported. Probiotic use was noted in 54.5% of the respondents, with 71.2% preferring natural sources. Usage was significantly associated with demographic factors, including age ( $\chi^2$χ2 = 15.251, P < 0.001), education level ( $\chi^2$χ2 = 18.787, P < 0.001), marital status ( $\chi^2$χ2 = 9.825, P = 0.002), and monthly income ( $\chi^2$χ2 = 8.548, P = 0.014). Conclusion While awareness and positive perceptions of probiotics are growing among the Saudi population, challenges such as knowledge gaps, affordability, and limited advertising persist. To promote probiotic use and improve public health …
bibliographic citation: Alharbi (2025) Exploring probiotic awareness, perceptions, and practices in the Saudi population: a cross-sectional study. PeerJ 13:e20490 https://doi.org/10.7717/peerj.20490
date submitted: 2025-02-05
date accepted: 2025-11-07
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alharbi
  given name: Basmah F.
doi: 10.7717/peerj.20490
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: © 2025 Alharbi
attribution name: Alharbi

Bond strength between layering ceramic and zirconia core: influence of various surface conditioning of zirconia
type: item
type: AcademicArticle
description: Objective It is recommended to apply various surface modification techniques to improve the mechanical and chemical interaction between zirconia core and veneering ceramic. Therefore, the objective of this in-vitro study was to evaluate and compare the effects of various surface treatments over the zirconia core on the shear bond strength (SBS) between layering ceramic and zirconia core. Methods A total of 90 zirconium oxide (Cercon, Degudent GmbH, Hanau-Wolfgang, Germany) specimens were prepared with standardized dimensions (10 mm × 10 mm × 5 mm). The specimens were randomly divided into six groups of 15 specimens each (Control group-no surface treatment; Sandblasting with 25 µm Al2O3; Sandblasting with 50 µm Al2O3; Sandblasting with 110 µm Al2O3; Etching with hydrofluoric acid (9.5%); Surface treatment using Zirface (nano layer etching technology for enhanced bonding strength of zirconia). All specimens were veneered with fluorapatite glass-ceramic (5 mm × 5 mm × 5 mm) using a custom silicone mold, sintered in a calibrated porcelain furnace, and verified with a digital caliper. Following veneering, the samples were embedded in self-curing acrylic resin within polyvinyl chloride molds and immersed in distilled water at 37 °C for 24 hours to simulate intraoral conditions. Using universal testing machine, specimens were tested for SBS. Analysis of variance (ANOVA) and Tukey’s-test were used for statistical analysis (P ≤ 0.05). Surface topography of the surfaces treated and after debonding were examined using scanning electron microscope (SEM) and failure mode of different groups was also noted. Results The application of Zirface to the zirconia core had the highest mean SBS value (26.56 ± 1.25 MPa), followed by the hydrofluoric acid only group (23.42 ± 0.94 MPa). The control group with no surface treatment showed the least SBS values. While the groups with surface treatments of 25 and 50 aluminum oxide (Al2O3) sandblasting showed SBS values of 17.16 ± 0.48 and 18.06 …
format: application/pdf
format: text/html
creator: Abdulaziz A. AlHelal
creator: Syed Rashid Habib
creator: Saleh Alyousef
creator: Nawaf Alhamzah
creator: Meshal Alqahtani
creator: Abdulaziz Alqahtani
subject: Biophysics
subject: Anatomy and Physiology
subject: Dentistry
subject: Evidence Based Medicine
subject: Pathology
description: doi:10.7717/peerj.20480
publisher: PeerJ Inc.
rights: © 2025 AlHelal et al.
abstract: Objective It is recommended to apply various surface modification techniques to improve the mechanical and chemical interaction between zirconia core and veneering ceramic. Therefore, the objective of this in-vitro study was to evaluate and compare the effects of various surface treatments over the zirconia core on the shear bond strength (SBS) between layering ceramic and zirconia core. Methods A total of 90 zirconium oxide (Cercon, Degudent GmbH, Hanau-Wolfgang, Germany) specimens were prepared with standardized dimensions (10 mm × 10 mm × 5 mm). The specimens were randomly divided into six groups of 15 specimens each (Control group-no surface treatment; Sandblasting with 25 µm Al2O3; Sandblasting with 50 µm Al2O3; Sandblasting with 110 µm Al2O3; Etching with hydrofluoric acid (9.5%); Surface treatment using Zirface (nano layer etching technology for enhanced bonding strength of zirconia). All specimens were veneered with fluorapatite glass-ceramic (5 mm × 5 mm × 5 mm) using a custom silicone mold, sintered in a calibrated porcelain furnace, and verified with a digital caliper. Following veneering, the samples were embedded in self-curing acrylic resin within polyvinyl chloride molds and immersed in distilled water at 37 °C for 24 hours to simulate intraoral conditions. Using universal testing machine, specimens were tested for SBS. Analysis of variance (ANOVA) and Tukey’s-test were used for statistical analysis (P ≤ 0.05). Surface topography of the surfaces treated and after debonding were examined using scanning electron microscope (SEM) and failure mode of different groups was also noted. Results The application of Zirface to the zirconia core had the highest mean SBS value (26.56 ± 1.25 MPa), followed by the hydrofluoric acid only group (23.42 ± 0.94 MPa). The control group with no surface treatment showed the least SBS values. While the groups with surface treatments of 25 and 50 aluminum oxide (Al2O3) sandblasting showed SBS values of 17.16 ± 0.48 and 18.06 …
bibliographic citation: AlHelal et al. (2025) Bond strength between layering ceramic and zirconia core: influence of various surface conditioning of zirconia. PeerJ 13:e20480 https://doi.org/10.7717/peerj.20480
date submitted: 2025-07-09
date accepted: 2025-11-05
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AlHelal
  given name: Abdulaziz A.
author list: Agent
  family name: Habib
  given name: Syed Rashid
author list: Agent
  family name: Alyousef
  given name: Saleh
author list: Agent
  family name: Alhamzah
  given name: Nawaf
author list: Agent
  family name: Alqahtani
  given name: Meshal
author list: Agent
  family name: Alqahtani
  given name: Abdulaziz
doi: 10.7717/peerj.20480
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 AlHelal et al.
attribution name: AlHelal et al.

Effect of major ozone autohemotherapy in fibromyalgia syndrome: a retrospective study
type: item
type: AcademicArticle
description: Background Fibromyalgia Syndrome (FMS) is a multifaceted chronic disease characterized by widespread musculoskeletal pain, fatigue, sleep disturbances, cognitive dysfunction, and increased sensitivity to stimuli, commonly referred to as central sensitization. Ozone therapy is currently used in the treatment of many chronic diseases by creating controlled oxidative stress. This study aimed to evaluate the effects of major autohemotherapy (MAH) on pain, quality of life, functional status, and sleep quality in patients with FMS. Methods A total of 72 patients who underwent 10 sessions of MAH between April 1, 2023 and September 1, 2023 were included in this retrospective study. A total of 10 sessions of major ozone therapy were applied to the patients, two sessions per week. In the first session, a total of 1,000 mcg of MAH (100 ml at 10 mcg/ml) was administered. In the following sessions, the concentration was gradually increased by 5 mg/ml at each session reaching up to 30 mcg/ml with a maximum cumulative dose of 3,000 mcg. Pre-and post-treatment pain status of the patients was evaluated with the Visual Analog Scale (VAS), functional status with the Fibromyalgia Impact Questionnaire (FIQ), quality of life with the Short Form-36 (SF-36), and sleep status with the Pittsburgh Sleep Quality Index (PSQI). Results The mean age of 68 female and 4 male patients included in the study was determined as 54.17 ± 11.17. VAS was determined as 7.76 ± 2.01 before treatment and 4.77 ± 2.20 after treatment. FIQ score was determined as 69.08 ± 16.01 before treatment and 56.18 ± 22.46 after treatment, Pittsburg Sleep Quality Index score was determine as 10.27 ± 3.37 before treatment and 9.61 ± 2.81 after treatment. Statistically significant differences were found in VAS, FIQ, SF-36, and PSQI values before and after treatment (p < 0.001). Conclusion According to the study results, MAH has been found to provide significantly positive effects in reducing pain intensity, improving functional…
format: application/pdf
format: text/html
creator: Oktay Faysal Tertemiz
creator: Erkan Ozduran
creator: Sinan Gursoy
creator: Volkan Hanci
creator: Kenan Kaygusuz
creator: Ilhan Celil Ozbek
creator: Mustafa Kurçaloğlu
creator: Ülkü Sabuncu
subject: Anesthesiology and Pain Management
subject: Internal Medicine
subject: Rheumatology
subject: Mental Health
subject: Rehabilitation
description: doi:10.7717/peerj.20475
publisher: PeerJ Inc.
rights: © 2025 Tertemiz et al.
abstract: Background Fibromyalgia Syndrome (FMS) is a multifaceted chronic disease characterized by widespread musculoskeletal pain, fatigue, sleep disturbances, cognitive dysfunction, and increased sensitivity to stimuli, commonly referred to as central sensitization. Ozone therapy is currently used in the treatment of many chronic diseases by creating controlled oxidative stress. This study aimed to evaluate the effects of major autohemotherapy (MAH) on pain, quality of life, functional status, and sleep quality in patients with FMS. Methods A total of 72 patients who underwent 10 sessions of MAH between April 1, 2023 and September 1, 2023 were included in this retrospective study. A total of 10 sessions of major ozone therapy were applied to the patients, two sessions per week. In the first session, a total of 1,000 mcg of MAH (100 ml at 10 mcg/ml) was administered. In the following sessions, the concentration was gradually increased by 5 mg/ml at each session reaching up to 30 mcg/ml with a maximum cumulative dose of 3,000 mcg. Pre-and post-treatment pain status of the patients was evaluated with the Visual Analog Scale (VAS), functional status with the Fibromyalgia Impact Questionnaire (FIQ), quality of life with the Short Form-36 (SF-36), and sleep status with the Pittsburgh Sleep Quality Index (PSQI). Results The mean age of 68 female and 4 male patients included in the study was determined as 54.17 ± 11.17. VAS was determined as 7.76 ± 2.01 before treatment and 4.77 ± 2.20 after treatment. FIQ score was determined as 69.08 ± 16.01 before treatment and 56.18 ± 22.46 after treatment, Pittsburg Sleep Quality Index score was determine as 10.27 ± 3.37 before treatment and 9.61 ± 2.81 after treatment. Statistically significant differences were found in VAS, FIQ, SF-36, and PSQI values before and after treatment (p < 0.001). Conclusion According to the study results, MAH has been found to provide significantly positive effects in reducing pain intensity, improving functional…
bibliographic citation: Tertemiz et al. (2025) Effect of major ozone autohemotherapy in fibromyalgia syndrome: a retrospective study. PeerJ 13:e20475 https://doi.org/10.7717/peerj.20475
date submitted: 2025-07-08
date accepted: 2025-11-04
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tertemiz
  given name: Oktay Faysal
author list: Agent
  family name: Ozduran
  given name: Erkan
author list: Agent
  family name: Gursoy
  given name: Sinan
author list: Agent
  family name: Hanci
  given name: Volkan
author list: Agent
  family name: Kaygusuz
  given name: Kenan
author list: Agent
  family name: Ozbek
  given name: Ilhan Celil
author list: Agent
  family name: Kurçaloğlu
  given name: Mustafa
author list: Agent
  family name: Sabuncu
  given name: Ülkü
doi: 10.7717/peerj.20475
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: © 2025 Tertemiz et al.
attribution name: Tertemiz et al.

Development of a predictive model for severe hyperlipidemic acute pancreatitis based on LASSO regression: a retrospective study
type: item
type: AcademicArticle
description: Background In recent years, the incidence of hyperlipidemic acute pancreatitis (HLAP) has been increasing. Identifying the risk factors associated with severe HLAP and developing a predictive model are crucial for early detection and intervention, thereby alleviating the disease burden. This study aimed to investigate the risk factors associated with severe HLAP and develop a predictive model. Methods Data on HLAP treated in Taixing People’s Hospital Affiliated to Yangzhou University from January 1, 2020, to June 30, 2023, were retrospectively collected and divided into a mild group (N = 296) and a moderate severe/severe group (N = 60). Univariate analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression were used to select variables, and the selected variables were incorporated into logistic regression to analyze the risk factors of severe disease. A logistic regression model was constructed. The receiver operating characteristic (ROC) curve and the area under the curve (AUC) were used to evaluate model differentiation, and the Hosmer–Lemeshow goodness-of-fit test and calibration curve were used to evaluate model consistency. Results The univariate analysis showed statistically significant differences in 50 variables between the mild and moderately severe/severe groups. LASSO regression identified the following variables: D-dimer, blood calcium, cholesterol, standard bicarbonate (SB), total carbon dioxide, and C-reactive protein–albumin ratio (CAR). The constructed logistic regression model included D-dimer, blood calcium, and cholesterol, with an AUC of 0.8341 (95% CI [0.7724–0.8958]). The model’s calibration was assessed using the Hosmer–Lemeshow goodness-of-fit test (χ2 = 6.8383, P = 0.5542), and the calibration curve demonstrated that the model’s predictions closely aligned with observed outcomes. Conclusion The risk factors of severe HLAP include D-dimer elevation, calcium depletion and cholesterol elevation. The predictive model establis…
format: application/pdf
format: text/html
creator: Qingyu Zhang
creator: Runping Han
creator: Zhenxing Li
creator: Kunfeng Yan
creator: Xiaorong Dai
creator: Gongchao Yu
subject: Gastroenterology and Hepatology
subject: Internal Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20471
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background In recent years, the incidence of hyperlipidemic acute pancreatitis (HLAP) has been increasing. Identifying the risk factors associated with severe HLAP and developing a predictive model are crucial for early detection and intervention, thereby alleviating the disease burden. This study aimed to investigate the risk factors associated with severe HLAP and develop a predictive model. Methods Data on HLAP treated in Taixing People’s Hospital Affiliated to Yangzhou University from January 1, 2020, to June 30, 2023, were retrospectively collected and divided into a mild group (N = 296) and a moderate severe/severe group (N = 60). Univariate analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression were used to select variables, and the selected variables were incorporated into logistic regression to analyze the risk factors of severe disease. A logistic regression model was constructed. The receiver operating characteristic (ROC) curve and the area under the curve (AUC) were used to evaluate model differentiation, and the Hosmer–Lemeshow goodness-of-fit test and calibration curve were used to evaluate model consistency. Results The univariate analysis showed statistically significant differences in 50 variables between the mild and moderately severe/severe groups. LASSO regression identified the following variables: D-dimer, blood calcium, cholesterol, standard bicarbonate (SB), total carbon dioxide, and C-reactive protein–albumin ratio (CAR). The constructed logistic regression model included D-dimer, blood calcium, and cholesterol, with an AUC of 0.8341 (95% CI [0.7724–0.8958]). The model’s calibration was assessed using the Hosmer–Lemeshow goodness-of-fit test (χ2 = 6.8383, P = 0.5542), and the calibration curve demonstrated that the model’s predictions closely aligned with observed outcomes. Conclusion The risk factors of severe HLAP include D-dimer elevation, calcium depletion and cholesterol elevation. The predictive model establis…
bibliographic citation: Zhang et al. (2025) Development of a predictive model for severe hyperlipidemic acute pancreatitis based on LASSO regression: a retrospective study. PeerJ 13:e20471 https://doi.org/10.7717/peerj.20471
date submitted: 2025-05-13
date accepted: 2025-11-03
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Qingyu
author list: Agent
  family name: Han
  given name: Runping
author list: Agent
  family name: Li
  given name: Zhenxing
author list: Agent
  family name: Yan
  given name: Kunfeng
author list: Agent
  family name: Dai
  given name: Xiaorong
author list: Agent
  family name: Yu
  given name: Gongchao
doi: 10.7717/peerj.20471
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms
type: item
type: AcademicArticle
description: Long-read amplicon sequencing has enabled us to return to full-length DNA barcodes, which benefit from the higher taxonomic resolution in metabarcoding-based biodiversity studies. However, chimeric sequences (artificial constructs formed when incomplete amplicons fuse during polymerase chain reaction (PCR)) remain challenging, potentially skewing diversity estimates and ecological inferences. Here, we benchmark three de novo chimera detection algorithms, uchime_denovo, removeBimeraDenovo, and chimeras_denovo, on simulated and empirical eukaryotic full-ITS (rRNA ITS1-5.8S-ITS2) datasets to evaluate their precision, sensitivity, and effects on the final OTUs composition/community structure. Upon simulated data, uchime_denovo achieved the highest precision even with default settings, whereas other algorithms displayed high false-positive chimera rates without setting adjustments. Similarly, the tests upon empirical data showed that uchime_denovo had lower false positive rates, whereas about half of the sequences in the putative chimeric batch were false positives when using chimeras_denovo and removeBimeraDenovo. We found that most of the false-negative chimeras contained multiple 5.8S regions, indicating PacBio library preparation artifacts rather than PCR artifacts. However, OTU-level comparisons indicated that overall richness and community-ordination patterns remain largely consistent across different chimera-filtering approaches with or without accounting for false positives and negatives.
format: application/pdf
format: text/html
creator: Ali Hakimzadeh
creator: Vladimir Mikryukov
creator: Martin Metsoja
creator: Leho Tedersoo
creator: Sten Anslan
subject: Biodiversity
subject: Bioinformatics
subject: Computational Biology
subject: Ecology
description: doi:10.7717/peerj.20456
publisher: PeerJ Inc.
rights: © 2025 Hakimzadeh et al.
abstract: Long-read amplicon sequencing has enabled us to return to full-length DNA barcodes, which benefit from the higher taxonomic resolution in metabarcoding-based biodiversity studies. However, chimeric sequences (artificial constructs formed when incomplete amplicons fuse during polymerase chain reaction (PCR)) remain challenging, potentially skewing diversity estimates and ecological inferences. Here, we benchmark three de novo chimera detection algorithms, uchime_denovo, removeBimeraDenovo, and chimeras_denovo, on simulated and empirical eukaryotic full-ITS (rRNA ITS1-5.8S-ITS2) datasets to evaluate their precision, sensitivity, and effects on the final OTUs composition/community structure. Upon simulated data, uchime_denovo achieved the highest precision even with default settings, whereas other algorithms displayed high false-positive chimera rates without setting adjustments. Similarly, the tests upon empirical data showed that uchime_denovo had lower false positive rates, whereas about half of the sequences in the putative chimeric batch were false positives when using chimeras_denovo and removeBimeraDenovo. We found that most of the false-negative chimeras contained multiple 5.8S regions, indicating PacBio library preparation artifacts rather than PCR artifacts. However, OTU-level comparisons indicated that overall richness and community-ordination patterns remain largely consistent across different chimera-filtering approaches with or without accounting for false positives and negatives.
bibliographic citation: Hakimzadeh et al. (2025) Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms. PeerJ 13:e20456 https://doi.org/10.7717/peerj.20456
date submitted: 2025-07-09
date accepted: 2025-10-31
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hakimzadeh
  given name: Ali
author list: Agent
  family name: Mikryukov
  given name: Vladimir
author list: Agent
  family name: Metsoja
  given name: Martin
author list: Agent
  family name: Tedersoo
  given name: Leho
author list: Agent
  family name: Anslan
  given name: Sten
doi: 10.7717/peerj.20456
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Hakimzadeh et al.
attribution name: Hakimzadeh et al.

Morpho-physiological traits and yield quality for cassava genotypes planted under drought during canopy establishment
type: item
type: AcademicArticle
description: Growth analysis provides better insight into the adaptability of cassava genotypes grown under drought conditions during canopy establishment and full irrigation. This study is intended to determine the growth rate and starch yield of different cassava genotypes grown under irrigation and drought treatments during canopy establishment. The experiment was conducted in two growing seasons at Khon Kaen University, Thailand, from August 2021 to August 2022 (2021/2022) and from August 2022 to August 2023 (2022/2023) using six cassava genotypes. A 2 × 6 split-plot design with four replications was used. The main plots were full irrigation and drought conditions during canopy establishment (90 to 150 days after planting (DAP)), and the cassava genotypes were assigned as subplots. The results showed that drought treatment applied during 90 to 150 DAP reduced relative water content (RWC) in cassava leaves for both growing seasons, storage root growth rate (SRGR) in the 2021/2022 growing season, and stem growth rate (SGR) and crop growth rate (CGR) in the 2022/2023 growing season. Re-watering after a drought supported cassava’s growth rate, resulting in desirable yield and biomass at final harvest. The Rayong 72 and CMR38-125-77 produced significantly higher storage root dry weight, harvest index (HI), and starch yield than the other tested genotypes. Growing under drought treatment, the best performance in storage root dry weight with statistical significance for both years was recorded for CMR38-125-77 (11.2 and 11.4 t ha−1 for the 2021/2022 and 2022/2023 growing seasons, respectively), and this was associated with a high crop growth rate (CGR, 12.3 g m−2 day−1 for the 2021/2022 growing season) and relative growth rate (RGR, 1.11 × 10−2 g g−1 day−1 for the 2022/2023 growing season) during 180 to 360 DAP. These favorable cassava genotypes should be utilized for future plant breeding programs and cultivation to achieve the desired productivity in the growing areas with drough…
format: application/pdf
format: text/html
creator: Passamon Ittipong
creator: Poramate Banterng
creator: Nimitr Vorasoot
creator: Sanun Jogloy
creator: Piyada Theerakulpisut
creator: Kochaphan Vongcharoen
creator: Supranee Santanoo
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.20440
publisher: PeerJ Inc.
rights: © 2025 Ittipong et al.
abstract: Growth analysis provides better insight into the adaptability of cassava genotypes grown under drought conditions during canopy establishment and full irrigation. This study is intended to determine the growth rate and starch yield of different cassava genotypes grown under irrigation and drought treatments during canopy establishment. The experiment was conducted in two growing seasons at Khon Kaen University, Thailand, from August 2021 to August 2022 (2021/2022) and from August 2022 to August 2023 (2022/2023) using six cassava genotypes. A 2 × 6 split-plot design with four replications was used. The main plots were full irrigation and drought conditions during canopy establishment (90 to 150 days after planting (DAP)), and the cassava genotypes were assigned as subplots. The results showed that drought treatment applied during 90 to 150 DAP reduced relative water content (RWC) in cassava leaves for both growing seasons, storage root growth rate (SRGR) in the 2021/2022 growing season, and stem growth rate (SGR) and crop growth rate (CGR) in the 2022/2023 growing season. Re-watering after a drought supported cassava’s growth rate, resulting in desirable yield and biomass at final harvest. The Rayong 72 and CMR38-125-77 produced significantly higher storage root dry weight, harvest index (HI), and starch yield than the other tested genotypes. Growing under drought treatment, the best performance in storage root dry weight with statistical significance for both years was recorded for CMR38-125-77 (11.2 and 11.4 t ha−1 for the 2021/2022 and 2022/2023 growing seasons, respectively), and this was associated with a high crop growth rate (CGR, 12.3 g m−2 day−1 for the 2021/2022 growing season) and relative growth rate (RGR, 1.11 × 10−2 g g−1 day−1 for the 2022/2023 growing season) during 180 to 360 DAP. These favorable cassava genotypes should be utilized for future plant breeding programs and cultivation to achieve the desired productivity in the growing areas with drough…
bibliographic citation: Ittipong et al. (2025) Morpho-physiological traits and yield quality for cassava genotypes planted under drought during canopy establishment. PeerJ 13:e20440 https://doi.org/10.7717/peerj.20440
date submitted: 2025-04-19
date accepted: 2025-10-31
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ittipong
  given name: Passamon
author list: Agent
  family name: Banterng
  given name: Poramate
author list: Agent
  family name: Vorasoot
  given name: Nimitr
author list: Agent
  family name: Jogloy
  given name: Sanun
author list: Agent
  family name: Theerakulpisut
  given name: Piyada
author list: Agent
  family name: Vongcharoen
  given name: Kochaphan
author list: Agent
  family name: Santanoo
  given name: Supranee
doi: 10.7717/peerj.20440
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Ittipong et al.
attribution name: Ittipong et al.

Retrospective study on the clinical outcomes and characteristics of acute myeloid leukemia: different outcomes in the same risk group
type: item
type: AcademicArticle
description: Background Acute myeloid leukemia (AML) remains a prognostically heterogeneous malignancy despite advances in molecular risk stratification. While the 2022 European Leukemia Network (ELN) guidelines refine risk classification, their accuracy in predicting survival outcomes across genetic requires validation. Methods We conducted a retrospective analysis of 154 newly diagnosed AML patients at Daping Hospital, integrating next-generation sequencing (NGS)-based genetic profiling, 2022 ELN risk classification, and clinical outcomes. Results The most frequent mutations were FLT3 (26.6%), DNMT3A (21.4%), NPM1 (18.2%), CEBPA (17.5%), and TET2 (15.6%). Median overall survival (OS) and progression-free survival (PFS) were 22.9 months and 14.1 months, respectively. Hematopoietic stem cell transplantation (HSCT), female sex, age < 60 years, and normal karyotype emerged as favorable prognostic factors. No significant differences were observed between allogeneic (allo-HSCT) and autologous HSCT (ASCT). Idarubicin, cytarabine, etoposide (IA ± E) chemotherapy yielded superior survival, while azacitidine+venetoclax (AZA+VEN) regimens underperformed. Conversely, TP53 and KIT mutations correlated with inferior survival, while NPM1, CEBPA mutations predicted longer survival. Notably, significant survival heterogeneity existed within 2022 ELN risk groups, particularly among patients with FLT3, CEBPA, or TET2 mutations. Conclusions The ELN risk classification demonstrate limitations in prognostication, particularly for patients with FLT3, CEBPA, or TET2 mutations. Our findings highlight the necessity for refined risk models incorporating additional molecular markers (KIT) and mutation interactions to enhance personalized prognostication. Gene coexistence is also a factor that needs to be considered when determining patient prognosis. Trial registration The study was registered on the Chinese clinical trial registry (ChiCTR) platform (No. ChiCTR2500096484).
format: application/pdf
format: text/html
creator: Fanqiao Meng
creator: Maoyuan Xiang
creator: Huan Xie
creator: Yu Liu
creator: Yan Qi
creator: Dongfeng Zeng
subject: Genetics
subject: Hematology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.20436
publisher: PeerJ Inc.
rights: © 2025 Meng et al.
abstract: Background Acute myeloid leukemia (AML) remains a prognostically heterogeneous malignancy despite advances in molecular risk stratification. While the 2022 European Leukemia Network (ELN) guidelines refine risk classification, their accuracy in predicting survival outcomes across genetic requires validation. Methods We conducted a retrospective analysis of 154 newly diagnosed AML patients at Daping Hospital, integrating next-generation sequencing (NGS)-based genetic profiling, 2022 ELN risk classification, and clinical outcomes. Results The most frequent mutations were FLT3 (26.6%), DNMT3A (21.4%), NPM1 (18.2%), CEBPA (17.5%), and TET2 (15.6%). Median overall survival (OS) and progression-free survival (PFS) were 22.9 months and 14.1 months, respectively. Hematopoietic stem cell transplantation (HSCT), female sex, age < 60 years, and normal karyotype emerged as favorable prognostic factors. No significant differences were observed between allogeneic (allo-HSCT) and autologous HSCT (ASCT). Idarubicin, cytarabine, etoposide (IA ± E) chemotherapy yielded superior survival, while azacitidine+venetoclax (AZA+VEN) regimens underperformed. Conversely, TP53 and KIT mutations correlated with inferior survival, while NPM1, CEBPA mutations predicted longer survival. Notably, significant survival heterogeneity existed within 2022 ELN risk groups, particularly among patients with FLT3, CEBPA, or TET2 mutations. Conclusions The ELN risk classification demonstrate limitations in prognostication, particularly for patients with FLT3, CEBPA, or TET2 mutations. Our findings highlight the necessity for refined risk models incorporating additional molecular markers (KIT) and mutation interactions to enhance personalized prognostication. Gene coexistence is also a factor that needs to be considered when determining patient prognosis. Trial registration The study was registered on the Chinese clinical trial registry (ChiCTR) platform (No. ChiCTR2500096484).
bibliographic citation: Meng et al. (2025) Retrospective study on the clinical outcomes and characteristics of acute myeloid leukemia: different outcomes in the same risk group. PeerJ 13:e20436 https://doi.org/10.7717/peerj.20436
date submitted: 2025-04-28
date accepted: 2025-10-30
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fanqiao
author list: Agent
  family name: Xiang
  given name: Maoyuan
author list: Agent
  family name: Xie
  given name: Huan
author list: Agent
  family name: Liu
  given name: Yu
author list: Agent
  family name: Qi
  given name: Yan
author list: Agent
  family name: Zeng
  given name: Dongfeng
doi: 10.7717/peerj.20436
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Meng et al.
attribution name: Meng et al.

Paw-spective shift: how our mood alters the way we read dog emotions
type: item
type: AcademicArticle
description: This study explored the influence of people’s mood on their perception of dog emotions in order to expand our understanding of how mood biases may shape emotional interpretation. Across two experiments, participants were primed into positive, neutral, or negative moods using validated visual stimuli before they evaluated video clips of dogs displaying positive, neutral, or negative emotional states. Participants were asked to rate valence and arousal of the dogs in the videos. Experiment 1 utilized visual primes unrelated to animals, while Experiment 2 employed dog-specific primes. Although mood priming significantly influenced participants’ self-reported emotions in Experiment 1, it did not affect their interpretation of the dogs’ emotional states. Dog-specific primes influenced participants’ interpretation of dog emotions in Experiment 2; however, the effect was a contrasting one, in that participants in the positively induced group rated dogs as sadder and those in the negative group rated dogs as happier. These findings challenge previous assumptions about mood-congruence effects in cross-species emotional perception, suggesting a more complex interplay of factors than anticipated. The study underscores the need for further research to disentangle the mechanisms governing how humans perceive and respond to animals’ emotional cues, with implications for improving animal welfare and human-animal interactions.
format: application/pdf
format: text/html
creator: Holly G. Molinaro
creator: Clive D.L. Wynne
subject: Animal Behavior
subject: Veterinary Medicine
subject: Zoology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.20411
publisher: PeerJ Inc.
rights: © 2025 Molinaro and Wynne
abstract: This study explored the influence of people’s mood on their perception of dog emotions in order to expand our understanding of how mood biases may shape emotional interpretation. Across two experiments, participants were primed into positive, neutral, or negative moods using validated visual stimuli before they evaluated video clips of dogs displaying positive, neutral, or negative emotional states. Participants were asked to rate valence and arousal of the dogs in the videos. Experiment 1 utilized visual primes unrelated to animals, while Experiment 2 employed dog-specific primes. Although mood priming significantly influenced participants’ self-reported emotions in Experiment 1, it did not affect their interpretation of the dogs’ emotional states. Dog-specific primes influenced participants’ interpretation of dog emotions in Experiment 2; however, the effect was a contrasting one, in that participants in the positively induced group rated dogs as sadder and those in the negative group rated dogs as happier. These findings challenge previous assumptions about mood-congruence effects in cross-species emotional perception, suggesting a more complex interplay of factors than anticipated. The study underscores the need for further research to disentangle the mechanisms governing how humans perceive and respond to animals’ emotional cues, with implications for improving animal welfare and human-animal interactions.
bibliographic citation: Molinaro et al. (2025) Paw-spective shift: how our mood alters the way we read dog emotions. PeerJ 13:e20411 https://doi.org/10.7717/peerj.20411
date submitted: 2025-03-19
date accepted: 2025-10-28
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Molinaro
  given name: Holly G.
author list: Agent
  family name: Wynne
  given name: Clive D.L.
doi: 10.7717/peerj.20411
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Molinaro and Wynne
attribution name: Molinaro and Wynne

Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis
type: item
type: AcademicArticle
description: Background Ulcerative colitis (UC) is a gastrointestinal condition characterized by chronic intestinal inflammation and damage to the mucosal barrier, with regulated cell death (RCD) playing a pivotal role in its pathogenesis. Among the various forms of RCD, mitochondrial permeability transition-driven necrosis (MPTDN) has not been thoroughly investigated in relation to UC in the current literature. Objective The objective of this study was to identify genes associated with MPTDN that are relevant to UC and to explore their potential implications in the disease process. Methods Data were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify differentially expressed MPTD-related genes (MPTDEGs). Machine learning techniques, including Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF), were employed to isolate key hub genes. The diagnostic potential of these genes was evaluated through receiver operating characteristic (ROC) curve analysis, and their expression was validated using an external dataset. Additionally, immunoinfiltration analysis was conducted to investigate the relationship between differentially expressed immune cells and the identified diagnostic genes. The correlation between gene expression and response to anti-TNF therapy was also assessed. Finally, the differential expression of these genes was confirmed in a mouse model of UC induced by 2.5% dextran sulfate sodium (DSS). Results A total of six MPTDEGs were identified. The genes CASP1 and CASP4, which were identified through machine learning algorithms, exhibited strong diagnostic performance, with area under the curve (AUC) values exceeding 0.7, indicating the effectiveness of the model. Immunoinfiltration analysis demonstrated a significant correlation between the expression of CASP1 and…
format: application/pdf
format: text/html
creator: Manqin Sun
creator: Fengjun Ni
creator: Yong Yao
creator: Huayuan Yang
subject: Bioinformatics
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.20345
publisher: PeerJ Inc.
rights: © 2025 Sun et al.
abstract: Background Ulcerative colitis (UC) is a gastrointestinal condition characterized by chronic intestinal inflammation and damage to the mucosal barrier, with regulated cell death (RCD) playing a pivotal role in its pathogenesis. Among the various forms of RCD, mitochondrial permeability transition-driven necrosis (MPTDN) has not been thoroughly investigated in relation to UC in the current literature. Objective The objective of this study was to identify genes associated with MPTDN that are relevant to UC and to explore their potential implications in the disease process. Methods Data were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify differentially expressed MPTD-related genes (MPTDEGs). Machine learning techniques, including Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF), were employed to isolate key hub genes. The diagnostic potential of these genes was evaluated through receiver operating characteristic (ROC) curve analysis, and their expression was validated using an external dataset. Additionally, immunoinfiltration analysis was conducted to investigate the relationship between differentially expressed immune cells and the identified diagnostic genes. The correlation between gene expression and response to anti-TNF therapy was also assessed. Finally, the differential expression of these genes was confirmed in a mouse model of UC induced by 2.5% dextran sulfate sodium (DSS). Results A total of six MPTDEGs were identified. The genes CASP1 and CASP4, which were identified through machine learning algorithms, exhibited strong diagnostic performance, with area under the curve (AUC) values exceeding 0.7, indicating the effectiveness of the model. Immunoinfiltration analysis demonstrated a significant correlation between the expression of CASP1 and…
bibliographic citation: Sun et al. (2025) Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis. PeerJ 13:e20345 https://doi.org/10.7717/peerj.20345
date submitted: 2024-12-06
date accepted: 2025-10-15
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Sun
  given name: Manqin
author list: Agent
  family name: Ni
  given name: Fengjun
author list: Agent
  family name: Yao
  given name: Yong
author list: Agent
  family name: Yang
  given name: Huayuan
doi: 10.7717/peerj.20345
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: © 2025 Sun et al.
attribution name: Sun et al.

The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more
type: item
type: AcademicArticle
description: Metatranscriptomics–the sequencing of community RNA–has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.
format: application/pdf
format: text/html
creator: Danilo Di Leo
creator: Emelie Nilsson
creator: Arianna Krinos
creator: Jarone Pinhassi
creator: Daniel Lundin
subject: Bioinformatics
subject: Computational Biology
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.20328
publisher: PeerJ Inc.
rights: © 2025 Di Leo et al.
abstract: Metatranscriptomics–the sequencing of community RNA–has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.
bibliographic citation: Di Leo et al. (2025) The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more. PeerJ 13:e20328 https://doi.org/10.7717/peerj.20328
date submitted: 2025-04-30
date accepted: 2025-10-13
issued: 2025-12-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Di Leo
  given name: Danilo
author list: Agent
  family name: Nilsson
  given name: Emelie
author list: Agent
  family name: Krinos
  given name: Arianna
author list: Agent
  family name: Pinhassi
  given name: Jarone
author list: Agent
  family name: Lundin
  given name: Daniel
doi: 10.7717/peerj.20328
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-12-05
copyright: ©2025 Di Leo et al.
attribution name: Di Leo et al.

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