PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Evaluating the Turkish validity and reliability of the Brief Illness Perception Questionnaire in periodontal diseases
items: Protective effect of astaxanthin nanoemulsion on mammalian inner ear hair cells
items: Ferrostatin-1 post-treatment attenuates acute kidney injury in mice by inhibiting ferritin production and regulating iron uptake-related proteins
items: Evolution of fertilization ability in obligatorily outcrossing populations of Caenorhabditis elegans
items: Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods
items: EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification
items: Dieting alleviates hyperuricemia and organ injuries in uricase-deficient rats via down-regulating cell cycle pathway
items: Predictors of one-year mortality following hip fracture surgery in elderly
items: Retrospective study: risk assessment model for osteoporosis—a detailed exploration involving 4,552 Shanghai dwellers
items: Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes

Evaluating the Turkish validity and reliability of the Brief Illness Perception Questionnaire in periodontal diseases
type: item
type: AcademicArticle
description: Background The Brief Illness Perception Questionnaire (Brief IPQ) is a widely used multifactorial scale that assesses the individuals’ perceptions of illness. Although there are studies investigating the psychometric properties of the Brief IPQ in many languages, the Turkish version of Brief IPQ on periodontal diseases has not been revealed so far. This study aimed to evaluate the Turkish validity and reliability of the Brief IPQ and contribute to the literature. It is also aimed to evaluate the patients’ illness perception with periodontal disease and to reveal the possible effects of the disease on the patients’ daily life. Methods This cross-sectional study was conducted with 209 patients with periodontal diseases (137 gingivitis and 72 periodontitis cases). Sociodemographic characteristics and clinical periodontal measurements of all patients were recorded. The Turkish versions of the Brief IPQ and the HAD Scale were applied to the patients via face-to-face. The construct validity was determined using confirmatory factor analysis. Test–retest reliability and internal consistency were performed using ICC test and Cronbach’s alpha, respectively. The concurrent validity was determined by using Spearman’s correlation coefficient. Results The confirmatory factor analysis showed that the scale has one factor. The Spearman’s correlation coefficient results were found 0.843 and 0.854 for concurrent validity. Cronbach’s alpha value of the scale was 0.944 in the internal consistency analysis. ICC value was found to be 0.987 for test-retest reliability. Floor/ceiling effects were considered not to be present. Conclusions It was found that the Turkish version of The Brief Illness Perception Questionnaire is valid and reliable. Brief IPQ may be used to determine the illness perception in patients with periodontal diseases.
format: application/pdf
format: text/html
creator: Canan Önder
creator: Batuhan Bakirarar
subject: Dentistry
subject: Infectious Diseases
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.16065
publisher: PeerJ Inc.
rights: © 2023 Önder and Bakirarar
abstract: Background The Brief Illness Perception Questionnaire (Brief IPQ) is a widely used multifactorial scale that assesses the individuals’ perceptions of illness. Although there are studies investigating the psychometric properties of the Brief IPQ in many languages, the Turkish version of Brief IPQ on periodontal diseases has not been revealed so far. This study aimed to evaluate the Turkish validity and reliability of the Brief IPQ and contribute to the literature. It is also aimed to evaluate the patients’ illness perception with periodontal disease and to reveal the possible effects of the disease on the patients’ daily life. Methods This cross-sectional study was conducted with 209 patients with periodontal diseases (137 gingivitis and 72 periodontitis cases). Sociodemographic characteristics and clinical periodontal measurements of all patients were recorded. The Turkish versions of the Brief IPQ and the HAD Scale were applied to the patients via face-to-face. The construct validity was determined using confirmatory factor analysis. Test–retest reliability and internal consistency were performed using ICC test and Cronbach’s alpha, respectively. The concurrent validity was determined by using Spearman’s correlation coefficient. Results The confirmatory factor analysis showed that the scale has one factor. The Spearman’s correlation coefficient results were found 0.843 and 0.854 for concurrent validity. Cronbach’s alpha value of the scale was 0.944 in the internal consistency analysis. ICC value was found to be 0.987 for test-retest reliability. Floor/ceiling effects were considered not to be present. Conclusions It was found that the Turkish version of The Brief Illness Perception Questionnaire is valid and reliable. Brief IPQ may be used to determine the illness perception in patients with periodontal diseases.
bibliographic citation: Önder et al. (2023) Evaluating the Turkish validity and reliability of the Brief Illness Perception Questionnaire in periodontal diseases. PeerJ 11:e16065 https://doi.org/10.7717/peerj.16065
date submitted: 2023-06-02
date accepted: 2023-08-18
issued: 2023-09-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Önder
  given name: Canan
author list: Agent
  family name: Bakirarar
  given name: Batuhan
doi: 10.7717/peerj.16065
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-11
copyright: © 2023 Önder and Bakirarar
attribution name: Önder and Bakirarar

Protective effect of astaxanthin nanoemulsion on mammalian inner ear hair cells
type: item
type: AcademicArticle
description: Background Aminoglycoside antibiotics are used for treating certain acute infections. However, these drugs cause ototoxicity by inducing inner ear hair cell death. Aims/Objectives We investigated the protective effect of a nanoemulsion of the carotenoid astaxanthin on mammalian inner ear hair cells against neomycin-induced ototoxicity. Material and Methods Dose-response relationship, quantification of hair cell loss, and reactive oxygen species production were assayed in response to neomycin with and without astaxanthin in cultured utricles of CBA/N mice. In addition, auditory brain response (ABR) and hair cell loss after exposure to the nanoformulation and loud noise were examined in vivo in guinea pigs. Results Astaxanthin suppressed neomycin-induced reduction of hair cells by reducing the production of hydroxy radicals. Furthermore, hair cell loss in the second rotation of the cochlea was significantly lower in the astaxanthin group than in the noise-only group. Conclusions and Significance The blood-labyrinth barrier limits the successful delivery of drugs for inner ear complications. However, in the nanoemulsion form, astaxanthin can penetrate the round window (fenestra ovale) membrane, enabling topical administration. Thus, astaxanthin nanoemulsion could be useful in treating ototoxicity in individuals with inner ear complications.
format: application/pdf
format: text/html
creator: Yuki Kobayashi
creator: Kazuma Sugahara
creator: Yosuke Takemoto
creator: Junko Tsuda
creator: Yoshinobu Hirose
creator: Makoto Hashimoto
creator: Hiroshi Yamashita
subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Otorhinolaryngology
description: doi:10.7717/peerj.15562
publisher: PeerJ Inc.
rights: © 2023 Kobayashi et al.
abstract: Background Aminoglycoside antibiotics are used for treating certain acute infections. However, these drugs cause ototoxicity by inducing inner ear hair cell death. Aims/Objectives We investigated the protective effect of a nanoemulsion of the carotenoid astaxanthin on mammalian inner ear hair cells against neomycin-induced ototoxicity. Material and Methods Dose-response relationship, quantification of hair cell loss, and reactive oxygen species production were assayed in response to neomycin with and without astaxanthin in cultured utricles of CBA/N mice. In addition, auditory brain response (ABR) and hair cell loss after exposure to the nanoformulation and loud noise were examined in vivo in guinea pigs. Results Astaxanthin suppressed neomycin-induced reduction of hair cells by reducing the production of hydroxy radicals. Furthermore, hair cell loss in the second rotation of the cochlea was significantly lower in the astaxanthin group than in the noise-only group. Conclusions and Significance The blood-labyrinth barrier limits the successful delivery of drugs for inner ear complications. However, in the nanoemulsion form, astaxanthin can penetrate the round window (fenestra ovale) membrane, enabling topical administration. Thus, astaxanthin nanoemulsion could be useful in treating ototoxicity in individuals with inner ear complications.
bibliographic citation: Kobayashi et al. (2023) Protective effect of astaxanthin nanoemulsion on mammalian inner ear hair cells. PeerJ 11:e15562 https://doi.org/10.7717/peerj.15562
date submitted: 2020-11-26
date accepted: 2023-05-24
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kobayashi
  given name: Yuki
author list: Agent
  family name: Sugahara
  given name: Kazuma
author list: Agent
  family name: Takemoto
  given name: Yosuke
author list: Agent
  family name: Tsuda
  given name: Junko
author list: Agent
  family name: Hirose
  given name: Yoshinobu
author list: Agent
  family name: Hashimoto
  given name: Makoto
author list: Agent
  family name: Yamashita
  given name: Hiroshi
doi: 10.7717/peerj.15562
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Kobayashi et al.
attribution name: Kobayashi et al.

Ferrostatin-1 post-treatment attenuates acute kidney injury in mice by inhibiting ferritin production and regulating iron uptake-related proteins
type: item
type: AcademicArticle
description: Background Acute kidney injury (AKI) is a common and serious medical condition with high morbidity and mortality. Recent research has highlighted ferroptosis, a novel form of programmed cell death, as a potential therapeutic target in mitigating renal tubular injury in AKI. Ferrostatin-1, a specific ferroptosis inhibitor, has been demonstrated to prevent renal injury through ferroptosis inhibition. Methods Utilizing a murine AKI model, we investigated the effects of Ferrostatin-1 by administering it post-injury. Through high-throughput sequencing and pathological analysis, we focused on the critical role of ferroptosis-related pathways in the treatment. Results Ferrostatin-1 post-conditioning effectively mitigated oxidative damage and reduced iron content associated with AKI. Additionally, critical ferroptosis-related proteins, such as GPX4, SLC7A11, NRF2, and FTH1, exhibited increased expression levels. In vitro, Ferrostatin-1 treatment of HK-2 cells significantly diminished lipid peroxidation and iron accumulation. Furthermore, Ferrostatin-1 was found to downregulate the PI3K signalling pathway. Conclusion Ferrostatin-1 acted as a potential ferroptosis inhibitor with the capacity to enhance antioxidant defences. This study suggests that Ferrostatin-1 could serve as a promising novel strategy for improving the treatment of AKI and promoting recovery from the condition.
format: application/pdf
format: text/html
creator: Yanxiu Zhao
creator: Binhua Jiang
creator: Dinghui Huang
creator: Juxiang Lou
creator: Guoshun Li
creator: Jianqi Liu
creator: Fuhui Duan
creator: Yuan Yuan
creator: Xiaoyan Su
subject: Evidence Based Medicine
subject: Nephrology
subject: Pathology
description: doi:10.7717/peerj.15786
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Background Acute kidney injury (AKI) is a common and serious medical condition with high morbidity and mortality. Recent research has highlighted ferroptosis, a novel form of programmed cell death, as a potential therapeutic target in mitigating renal tubular injury in AKI. Ferrostatin-1, a specific ferroptosis inhibitor, has been demonstrated to prevent renal injury through ferroptosis inhibition. Methods Utilizing a murine AKI model, we investigated the effects of Ferrostatin-1 by administering it post-injury. Through high-throughput sequencing and pathological analysis, we focused on the critical role of ferroptosis-related pathways in the treatment. Results Ferrostatin-1 post-conditioning effectively mitigated oxidative damage and reduced iron content associated with AKI. Additionally, critical ferroptosis-related proteins, such as GPX4, SLC7A11, NRF2, and FTH1, exhibited increased expression levels. In vitro, Ferrostatin-1 treatment of HK-2 cells significantly diminished lipid peroxidation and iron accumulation. Furthermore, Ferrostatin-1 was found to downregulate the PI3K signalling pathway. Conclusion Ferrostatin-1 acted as a potential ferroptosis inhibitor with the capacity to enhance antioxidant defences. This study suggests that Ferrostatin-1 could serve as a promising novel strategy for improving the treatment of AKI and promoting recovery from the condition.
bibliographic citation: Zhao et al. (2023) Ferrostatin-1 post-treatment attenuates acute kidney injury in mice by inhibiting ferritin production and regulating iron uptake-related proteins. PeerJ 11:e15786 https://doi.org/10.7717/peerj.15786
date submitted: 2023-04-14
date accepted: 2023-07-04
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yanxiu
author list: Agent
  family name: Jiang
  given name: Binhua
author list: Agent
  family name: Huang
  given name: Dinghui
author list: Agent
  family name: Lou
  given name: Juxiang
author list: Agent
  family name: Li
  given name: Guoshun
author list: Agent
  family name: Liu
  given name: Jianqi
author list: Agent
  family name: Duan
  given name: Fuhui
author list: Agent
  family name: Yuan
  given name: Yuan
author list: Agent
  family name: Su
  given name: Xiaoyan
doi: 10.7717/peerj.15786
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: © 2023 Zhao et al.
attribution name: Zhao et al.

Evolution of fertilization ability in obligatorily outcrossing populations of Caenorhabditis elegans
type: item
type: AcademicArticle
description: In species reproducing by selfing, the traits connected with outcrossing typically undergo degeneration, a phenomenon called selfing syndrome. In Caenorhabditis elegans nematodes, selfing syndrome affects many traits involved in mating, rendering cross-fertilization highly inefficient. In this study, we investigated the evolution of cross-fertilization efficiency in populations genetically modified to reproduce by obligatory outcrossing. Following the genetic modification, replicate obligatorily outcrossing were maintained for over 100 generations, at either optimal (20 °C) or elevated (24 °C) temperatures, as a part of a broader experimental evolution program. Subsequently, fertilization rates were assayed in the evolving populations, as well as their ancestors who had the obligatory outcrossing introduced but did not go through experimental evolution. Fertilization effectivity was measured by tracking the fractions of fertilized females in age-synchronized populations, through 8 h since reaching adulthood. In order to check the robustness of our measurements, each evolving population was assayed in two or three independent replicate blocks. Indeed, we found high levels of among-block variability in the fertilization trajectories, and in the estimates of divergence between evolving populations and their ancestors. We also identified five populations which appear to have evolved increased fertilization efficiency, relative to their ancestors. However, due to the abovementioned high variability, this set of populations should be treated as candidate, with further replications needed to either confirm or disprove their divergence from ancestors. Furthermore, we also discuss additional observations we have made concerning fertilization trajectories.
format: application/pdf
format: text/html
creator: Joanna K. Palka
creator: Alicja Dyba
creator: Julia Brzozowska
creator: Weronika Antoł
creator: Karolina Sychta
creator: Zofia M. Prokop
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.15825
publisher: PeerJ Inc.
rights: © 2023 Palka et al.
abstract: In species reproducing by selfing, the traits connected with outcrossing typically undergo degeneration, a phenomenon called selfing syndrome. In Caenorhabditis elegans nematodes, selfing syndrome affects many traits involved in mating, rendering cross-fertilization highly inefficient. In this study, we investigated the evolution of cross-fertilization efficiency in populations genetically modified to reproduce by obligatory outcrossing. Following the genetic modification, replicate obligatorily outcrossing were maintained for over 100 generations, at either optimal (20 °C) or elevated (24 °C) temperatures, as a part of a broader experimental evolution program. Subsequently, fertilization rates were assayed in the evolving populations, as well as their ancestors who had the obligatory outcrossing introduced but did not go through experimental evolution. Fertilization effectivity was measured by tracking the fractions of fertilized females in age-synchronized populations, through 8 h since reaching adulthood. In order to check the robustness of our measurements, each evolving population was assayed in two or three independent replicate blocks. Indeed, we found high levels of among-block variability in the fertilization trajectories, and in the estimates of divergence between evolving populations and their ancestors. We also identified five populations which appear to have evolved increased fertilization efficiency, relative to their ancestors. However, due to the abovementioned high variability, this set of populations should be treated as candidate, with further replications needed to either confirm or disprove their divergence from ancestors. Furthermore, we also discuss additional observations we have made concerning fertilization trajectories.
bibliographic citation: Palka et al. (2023) Evolution of fertilization ability in obligatorily outcrossing populations of Caenorhabditis elegans. PeerJ 11:e15825 https://doi.org/10.7717/peerj.15825
date submitted: 2023-02-17
date accepted: 2023-07-10
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palka
  given name: Joanna K.
author list: Agent
  family name: Dyba
  given name: Alicja
author list: Agent
  family name: Brzozowska
  given name: Julia
author list: Agent
  family name: Antoł
  given name: Weronika
author list: Agent
  family name: Sychta
  given name: Karolina
author list: Agent
  family name: Prokop
  given name: Zofia M.
doi: 10.7717/peerj.15825
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Palka et al.
attribution name: Palka et al.

Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods
type: item
type: AcademicArticle
description: Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
format: application/pdf
format: text/html
creator: Ivan Bulygin
creator: Vladislav Shatov
creator: Anton Rykachevskiy
creator: Arsenii Raiko
creator: Alexander Bernstein
creator: Evgeny Burnaev
creator: Mikhail S. Gelfand
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Data Science
description: doi:10.7717/peerj.15838
publisher: PeerJ Inc.
rights: © 2023 Bulygin et al.
abstract: Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
bibliographic citation: Bulygin et al. (2023) Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods. PeerJ 11:e15838 https://doi.org/10.7717/peerj.15838
date submitted: 2022-11-02
date accepted: 2023-07-12
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bulygin
  given name: Ivan
author list: Agent
  family name: Shatov
  given name: Vladislav
author list: Agent
  family name: Rykachevskiy
  given name: Anton
author list: Agent
  family name: Raiko
  given name: Arsenii
author list: Agent
  family name: Bernstein
  given name: Alexander
author list: Agent
  family name: Burnaev
  given name: Evgeny
author list: Agent
  family name: Gelfand
  given name: Mikhail S.
doi: 10.7717/peerj.15838
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Bulygin et al.
attribution name: Bulygin et al.

EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is a common malignant tumor. There are few studies on EXOSC10 (exosome component 10) in HCC; however, the importance of EXOSC10 for HCC remains unclear. Methods In the study, the prognosis value of EXOSC10 and the immune correlation were explored by bioinformatics. The expression of EXOSC10 was verified by tissue samples from clinical patients and in vitro experiment (liver cancer cell lines HepG2, MHCC97H and Huh-7; normal human liver cell line LO2). Immunohistochemistry (IHC) was used to detect EXOSC10 protein expression in clinical tissue from HCC. Huh-7 cells with siEXOSC10 were constructed using lipofectamine 3000. Cell counting kit 8 (CCK-8) and colony formation were used to test cell proliferation. The wound healing and transwell were used to analyze the cell migration capacity. Mitochondrial membrane potential, Hoechst 33342 dye, and flow cytometer were used to detect the change in cell apoptosis, respectively. Differential expression genes (DEGs) analysis and gene set enrichment analysis (GSEA) were used to investigate the potential mechanism of EXOSC10 and were verified by western blotting. Results EXOSC10 was highly expressed in tissues from patients with HCC and was an independent prognostic factor for overall survival (OS) in HCC. Increased expression of EXOSC10 was significantly related to histological grade, T stage, and pathological stage. Multivariate analysis indicated that the high expression level of EXOSC10 was correlated with poor overall survival (OS) in HCC. GO and GSEA analysis showed enrichment of the cell cycle and p53-related signaling pathway. Immune analysis showed that EXOSC10 expression was a significant positive correlation with immune infiltration in HCC. In vitro experiments, cell proliferation and migration were inhibited by the elimination of EXOSC10. Furthermore, the elimination of EXOSC10 induced cell apoptosis, suppressed PARP, N-cadherin and Bcl-2 protein expression levels, while incr…
format: application/pdf
format: text/html
creator: Zhi-Yong Meng
creator: Yu-Chun Fan
creator: Chao-Sheng Zhang
creator: Lin-Li Zhang
creator: Tong Wu
creator: Min-Yu Nong
creator: Tian Wang
creator: Chuang Chen
creator: Li-He Jiang
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.15860
publisher: PeerJ Inc.
rights: © 2023 Meng et al.
abstract: Background Hepatocellular carcinoma (HCC) is a common malignant tumor. There are few studies on EXOSC10 (exosome component 10) in HCC; however, the importance of EXOSC10 for HCC remains unclear. Methods In the study, the prognosis value of EXOSC10 and the immune correlation were explored by bioinformatics. The expression of EXOSC10 was verified by tissue samples from clinical patients and in vitro experiment (liver cancer cell lines HepG2, MHCC97H and Huh-7; normal human liver cell line LO2). Immunohistochemistry (IHC) was used to detect EXOSC10 protein expression in clinical tissue from HCC. Huh-7 cells with siEXOSC10 were constructed using lipofectamine 3000. Cell counting kit 8 (CCK-8) and colony formation were used to test cell proliferation. The wound healing and transwell were used to analyze the cell migration capacity. Mitochondrial membrane potential, Hoechst 33342 dye, and flow cytometer were used to detect the change in cell apoptosis, respectively. Differential expression genes (DEGs) analysis and gene set enrichment analysis (GSEA) were used to investigate the potential mechanism of EXOSC10 and were verified by western blotting. Results EXOSC10 was highly expressed in tissues from patients with HCC and was an independent prognostic factor for overall survival (OS) in HCC. Increased expression of EXOSC10 was significantly related to histological grade, T stage, and pathological stage. Multivariate analysis indicated that the high expression level of EXOSC10 was correlated with poor overall survival (OS) in HCC. GO and GSEA analysis showed enrichment of the cell cycle and p53-related signaling pathway. Immune analysis showed that EXOSC10 expression was a significant positive correlation with immune infiltration in HCC. In vitro experiments, cell proliferation and migration were inhibited by the elimination of EXOSC10. Furthermore, the elimination of EXOSC10 induced cell apoptosis, suppressed PARP, N-cadherin and Bcl-2 protein expression levels, while incr…
bibliographic citation: Meng et al. (2023) EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification. PeerJ 11:e15860 https://doi.org/10.7717/peerj.15860
date submitted: 2023-01-13
date accepted: 2023-07-17
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Zhi-Yong
author list: Agent
  family name: Fan
  given name: Yu-Chun
author list: Agent
  family name: Zhang
  given name: Chao-Sheng
author list: Agent
  family name: Zhang
  given name: Lin-Li
author list: Agent
  family name: Wu
  given name: Tong
author list: Agent
  family name: Nong
  given name: Min-Yu
author list: Agent
  family name: Wang
  given name: Tian
author list: Agent
  family name: Chen
  given name: Chuang
author list: Agent
  family name: Jiang
  given name: Li-He
doi: 10.7717/peerj.15860
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Meng et al.
attribution name: Meng et al.

Dieting alleviates hyperuricemia and organ injuries in uricase-deficient rats via down-regulating cell cycle pathway
type: item
type: AcademicArticle
description: Dieting is a basic treatment for lowering hyperuricemia. Here, we aimed to determine the optimal amount of dietary food that lowers serum uric acid (SUA) without modifying the dietary ingredients in rats. Increased SUA was found in food-deprived 45-day-old uricase-deficient rats (Kunming-DY rats), and the optimal amount of dietary food (75% dietary intake) to lower SUA was established by controlling the amount of food given daily from 25% to 100% for 2 weeks. In addition to lowering SUA by approximately 22.5 ± 20.5%, the optimal amount of dietary food given for 2 weeks inhibited urine uric acid excretion, lowered the uric acid content in multiple organs, improved renal function, lowered serum triglyceride, alleviated organ injuries (e.g., liver, kidney and intestinal tract) at the histological level, and down-regulated the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway of the cell cycle (ko04110). Taken together, these results demonstrate that 75% dietary food effectively lowers the SUA level without modifying dietary ingredients and alleviates the injuries resulting from uricase deficiency or hyperuricemia, the mechanism of which is associated with the down-regulation of the cell cycle pathway.
format: application/pdf
format: text/html
creator: Yun Yu
creator: Xulian Wan
creator: Dan Li
creator: Yalin Qi
creator: Ning Li
creator: Guangyun Luo
creator: Hua Yin
creator: Lei Wang
creator: Wan Qin
creator: Yongkun Li
creator: Lvyu Li
creator: Weigang Duan
subject: Food Science and Technology
subject: Urology
subject: Metabolic Sciences
description: doi:10.7717/peerj.15999
publisher: PeerJ Inc.
rights: © 2023 Yu et al.
abstract: Dieting is a basic treatment for lowering hyperuricemia. Here, we aimed to determine the optimal amount of dietary food that lowers serum uric acid (SUA) without modifying the dietary ingredients in rats. Increased SUA was found in food-deprived 45-day-old uricase-deficient rats (Kunming-DY rats), and the optimal amount of dietary food (75% dietary intake) to lower SUA was established by controlling the amount of food given daily from 25% to 100% for 2 weeks. In addition to lowering SUA by approximately 22.5 ± 20.5%, the optimal amount of dietary food given for 2 weeks inhibited urine uric acid excretion, lowered the uric acid content in multiple organs, improved renal function, lowered serum triglyceride, alleviated organ injuries (e.g., liver, kidney and intestinal tract) at the histological level, and down-regulated the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway of the cell cycle (ko04110). Taken together, these results demonstrate that 75% dietary food effectively lowers the SUA level without modifying dietary ingredients and alleviates the injuries resulting from uricase deficiency or hyperuricemia, the mechanism of which is associated with the down-regulation of the cell cycle pathway.
bibliographic citation: Yu et al. (2023) Dieting alleviates hyperuricemia and organ injuries in uricase-deficient rats via down-regulating cell cycle pathway. PeerJ 11:e15999 https://doi.org/10.7717/peerj.15999
date submitted: 2023-04-19
date accepted: 2023-08-09
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yun
author list: Agent
  family name: Wan
  given name: Xulian
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Qi
  given name: Yalin
author list: Agent
  family name: Li
  given name: Ning
author list: Agent
  family name: Luo
  given name: Guangyun
author list: Agent
  family name: Yin
  given name: Hua
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Qin
  given name: Wan
author list: Agent
  family name: Li
  given name: Yongkun
author list: Agent
  family name: Li
  given name: Lvyu
author list: Agent
  family name: Duan
  given name: Weigang
doi: 10.7717/peerj.15999
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Yu et al.
attribution name: Yu et al.

Predictors of one-year mortality following hip fracture surgery in elderly
type: item
type: AcademicArticle
description: Background Understanding mortality risk factors is critical to reducing mortality among elderly hip fracture patients. To investigate the effects of admission and post-operative levels of distribution width of red blood cells (RDW), albumin, and RDW/albumin (RA) ratio on predicting 1-year mortality following hip fracture surgery. Methods A retrospective study was conducted on 275 elderly patients who underwent hip fracture surgery in a tertiary hospital between January 2018 and January 2022. Deaths within one year of hip fracture were defined as the deceased group. The survivors were defined as those who survived for at least one year. The relationship between admission and post-operative levels of RDW, albumin, RA, and mortality within one year after hip surgery was assessed statistically, including binary logistic regression analysis. The study also assessed other factors related to mortality. Results One-year mortality was 34.7%. There was a 3.03-year (95% CI [1.32–4.75]) difference between the deceased (79.55 ± 8.36 years) and survivors (82.58 ± 7.41 years) (p < 0.001). In the deceased group, the mean hemoglobin (HGB) values at admission (p = 0.022) and post-operative (p = 0.04) were significantly lower. RDW values at admission (p = 0.001) and post-op (p = 0.001) were significantly lower in the survivor group. The mean albumin values at admission (p < 0.001) and post-operative (p < 0.001) in the survivor group were significantly higher than in the deceased group. A significant difference was found between the survivor group and the deceased group in terms of mean RA ratio at admission and post-operative (p < 0.001). Based on binary logistic regression analysis, presence of chronic obstructive pulmonary disease (COPD) (OR 3.73, 95% CI [1.8–7.76]), RDW (OR 1.78, 95% CI [1.48–2.14]), and albumin (OR 0.81, 95% CI [0.75–0.87]), values at admission were found to be independent predictors of 1-year mortality in elderly patients with hip fracture. Conclusion Based on th…
format: application/pdf
format: text/html
creator: Mehmet Özel
creator: Mustafa Altıntaş
creator: Ali Cankut Tatlıparmak
subject: Epidemiology
subject: Geriatrics
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.16008
publisher: PeerJ Inc.
rights: © 2023 Özel et al.
abstract: Background Understanding mortality risk factors is critical to reducing mortality among elderly hip fracture patients. To investigate the effects of admission and post-operative levels of distribution width of red blood cells (RDW), albumin, and RDW/albumin (RA) ratio on predicting 1-year mortality following hip fracture surgery. Methods A retrospective study was conducted on 275 elderly patients who underwent hip fracture surgery in a tertiary hospital between January 2018 and January 2022. Deaths within one year of hip fracture were defined as the deceased group. The survivors were defined as those who survived for at least one year. The relationship between admission and post-operative levels of RDW, albumin, RA, and mortality within one year after hip surgery was assessed statistically, including binary logistic regression analysis. The study also assessed other factors related to mortality. Results One-year mortality was 34.7%. There was a 3.03-year (95% CI [1.32–4.75]) difference between the deceased (79.55 ± 8.36 years) and survivors (82.58 ± 7.41 years) (p < 0.001). In the deceased group, the mean hemoglobin (HGB) values at admission (p = 0.022) and post-operative (p = 0.04) were significantly lower. RDW values at admission (p = 0.001) and post-op (p = 0.001) were significantly lower in the survivor group. The mean albumin values at admission (p < 0.001) and post-operative (p < 0.001) in the survivor group were significantly higher than in the deceased group. A significant difference was found between the survivor group and the deceased group in terms of mean RA ratio at admission and post-operative (p < 0.001). Based on binary logistic regression analysis, presence of chronic obstructive pulmonary disease (COPD) (OR 3.73, 95% CI [1.8–7.76]), RDW (OR 1.78, 95% CI [1.48–2.14]), and albumin (OR 0.81, 95% CI [0.75–0.87]), values at admission were found to be independent predictors of 1-year mortality in elderly patients with hip fracture. Conclusion Based on th…
bibliographic citation: Özel et al. (2023) Predictors of one-year mortality following hip fracture surgery in elderly. PeerJ 11:e16008 https://doi.org/10.7717/peerj.16008
date submitted: 2023-06-03
date accepted: 2023-08-09
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Özel
  given name: Mehmet
author list: Agent
  family name: Altıntaş
  given name: Mustafa
author list: Agent
  family name: Tatlıparmak
  given name: Ali Cankut
doi: 10.7717/peerj.16008
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Özel et al.
attribution name: Özel et al.

Retrospective study: risk assessment model for osteoporosis—a detailed exploration involving 4,552 Shanghai dwellers
type: item
type: AcademicArticle
description: Background Osteoporosis, a prevalent orthopedic issue, significantly influences patients’ quality of life and results in considerable financial burden. The objective of this study was to develop and validate a clinical prediction model for osteoporosis risk, utilizing computer algorithms and demographic data. Method In this research, a total of 4,552 residents from Shanghai were retrospectively included. LASSO regression analysis was executed on the sample’s basic characteristics, and logistic regression was employed for analyzing clinical characteristics and building a predictive model. The model’s diagnostic capacity for predicting osteoporosis risk was assessed using R software and computer algorithms. Results The predictive nomogram model for bone loss risk, derived from the LASSO analysis, comprised factors including BMI, TC, TG, HDL, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes. The nomogram prediction model demonstrated impressive discriminative capability, with a C-index of 0.908 (training set), 0.908 (validation set), and 0.910 (entire cohort). The area under the ROC curve (AUC) of the model was 0.909 (training set), 0.903 (validation set), and applicable to the entire cohort. The decision curve analysis further corroborated that the model could efficiently predict the risk of bone loss in patients. Conclusion The nomogram, based on essential demographic and health factors (Body Mass Index, Total Cholesterol, Triglycerides, High-Density Lipoprotein, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes), offered accurate predictions for the risk of bone loss within the studied population.
format: application/pdf
format: text/html
creator: Dan Han
creator: Zhongcheng Fan
creator: Yi-sheng Chen
creator: Zichao Xue
creator: Zhenwei Yang
creator: Danping Liu
creator: Rong Zhou
creator: Hong Yuan
subject: Epidemiology
subject: Geriatrics
subject: Orthopedics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.16017
publisher: PeerJ Inc.
rights: © 2023 Han et al.
abstract: Background Osteoporosis, a prevalent orthopedic issue, significantly influences patients’ quality of life and results in considerable financial burden. The objective of this study was to develop and validate a clinical prediction model for osteoporosis risk, utilizing computer algorithms and demographic data. Method In this research, a total of 4,552 residents from Shanghai were retrospectively included. LASSO regression analysis was executed on the sample’s basic characteristics, and logistic regression was employed for analyzing clinical characteristics and building a predictive model. The model’s diagnostic capacity for predicting osteoporosis risk was assessed using R software and computer algorithms. Results The predictive nomogram model for bone loss risk, derived from the LASSO analysis, comprised factors including BMI, TC, TG, HDL, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes. The nomogram prediction model demonstrated impressive discriminative capability, with a C-index of 0.908 (training set), 0.908 (validation set), and 0.910 (entire cohort). The area under the ROC curve (AUC) of the model was 0.909 (training set), 0.903 (validation set), and applicable to the entire cohort. The decision curve analysis further corroborated that the model could efficiently predict the risk of bone loss in patients. Conclusion The nomogram, based on essential demographic and health factors (Body Mass Index, Total Cholesterol, Triglycerides, High-Density Lipoprotein, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes), offered accurate predictions for the risk of bone loss within the studied population.
bibliographic citation: Han et al. (2023) Retrospective study: risk assessment model for osteoporosis—a detailed exploration involving 4,552 Shanghai dwellers. PeerJ 11:e16017 https://doi.org/10.7717/peerj.16017
date submitted: 2023-02-07
date accepted: 2023-08-10
issued: 2023-09-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Dan
author list: Agent
  family name: Fan
  given name: Zhongcheng
author list: Agent
  family name: Chen
  given name: Yi-sheng
author list: Agent
  family name: Xue
  given name: Zichao
author list: Agent
  family name: Yang
  given name: Zhenwei
author list: Agent
  family name: Liu
  given name: Danping
author list: Agent
  family name: Zhou
  given name: Rong
author list: Agent
  family name: Yuan
  given name: Hong
doi: 10.7717/peerj.16017
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-08
copyright: ©2023 Han et al.
attribution name: Han et al.

Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes
type: item
type: AcademicArticle
description: Background Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. Methods In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). Results A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens–Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulati…
format: application/pdf
format: text/html
creator: Varun Hiremath
creator: Kanwar Pal Singh
creator: Neelu Jain
creator: Kishan Swaroop
creator: Pradeep Kumar Jain
creator: Sapna Panwar
creator: Nivedita Sinha
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15820
publisher: PeerJ Inc.
rights: © 2023 Hiremath et al.
abstract: Background Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. Methods In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). Results A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens–Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulati…
bibliographic citation: Hiremath et al. (2023) Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes. PeerJ 11:e15820 https://doi.org/10.7717/peerj.15820
date submitted: 2023-03-14
date accepted: 2023-07-10
issued: 2023-09-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hiremath
  given name: Varun
author list: Agent
  family name: Singh
  given name: Kanwar Pal
author list: Agent
  family name: Jain
  given name: Neelu
author list: Agent
  family name: Swaroop
  given name: Kishan
author list: Agent
  family name: Jain
  given name: Pradeep Kumar
author list: Agent
  family name: Panwar
  given name: Sapna
author list: Agent
  family name: Sinha
  given name: Nivedita
doi: 10.7717/peerj.15820
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-07
copyright: © 2023 Hiremath et al.
attribution name: Hiremath et al.

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