PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of sterile a-motif domain-containing 9-like as a potential biomarker in patients with cutaneous melanoma
items: The mediating role of attention deficit in relationship between insomnia and social cognition tasks among nurses in Saudi Arabia: A cross-sectional study
items: Functionalized nanoparticles crossing the brain–blood barrier to target glioma cells
items: Attitudes of medical students in Khartoum, Sudan towards the doctor-patient relationship: a cross-sectional study
items: Measuring blood glucose before or after lumbar puncture
items: A histological analysis of coloration in the Peruvian mimic poison frog (Ranitomeya imitator)
items: Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity
items: Influencing factors of cardiac valve calcification (CVC) in patients with chronic kidney disease and the impact of CVC on long-term prognosis: a single-center retrospective study
items: MK8617 inhibits M1 macrophage polarization and inflammation via the HIF-1α/GYS1/UDPG/P2Y14 pathway
items: miR-455-3p ameliorates pancreatic acinar cell injury by targeting Slc2a1

Identification of sterile a-motif domain-containing 9-like as a potential biomarker in patients with cutaneous melanoma
type: item
type: AcademicArticle
description: Skin cutaneous melanoma (SKCM) is one of the most aggressive malignancies, accounting for approximately 75% of skin cancer-related fatalities annually. Sterile a-motif domain-containing 9-like (SAMD9L) has been found to regulate cell proliferation and suppress the neoplastic phenotype, but its specific role in SKCM remains unknown. To investigate the cancer-associated immunology of SKCM and the role of SAMD9L in tumor progression, we conducted an integrative bioinformatics analysis that revealed elevated expression levels of SAMD9L in SKCM. ROC curves and survival analyses confirmed the considerable diagnostic and prognostic abilities of SAMD9L. Moreover, a real-world cohort of 35 SKCM patients from the First Affiliated Hospital of Soochow University showed that higher expression levels of SAMD9L were associated with better prognosis. We performed validation experiments, including cell culture, generation of lentiviral-transfected SKCM cell lines, cell proliferation assay, and transwell assay, which demonstrated that down-regulation of SAMD9L significantly promoted proliferation and migration capacities of SKCM cells. Additionally, SAMD9L expression was found to be strongly linked to immune infiltration. Our results revealed a positive correlation between SAMD9L and XAF1 expression, suggesting that SAMD9L may serve as a prospective prognostic indicator of SKCM with co-expressed XAF1 gene. In summary, our findings indicate that SAMD9L may serve as a promising prognostic and therapeutic biomarker and play a critical role in tumor-immune interactions in SKCM.
format: application/pdf
format: text/html
creator: Junsen Ye
creator: Haidan Tang
creator: Chuanrui Xie
creator: Wei Han
creator: Guoliang Shen
creator: Ying Qian
creator: Jin Xu
subject: Bioinformatics
subject: Dermatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.15634
publisher: PeerJ Inc.
rights: © 2023 Ye et al.
abstract: Skin cutaneous melanoma (SKCM) is one of the most aggressive malignancies, accounting for approximately 75% of skin cancer-related fatalities annually. Sterile a-motif domain-containing 9-like (SAMD9L) has been found to regulate cell proliferation and suppress the neoplastic phenotype, but its specific role in SKCM remains unknown. To investigate the cancer-associated immunology of SKCM and the role of SAMD9L in tumor progression, we conducted an integrative bioinformatics analysis that revealed elevated expression levels of SAMD9L in SKCM. ROC curves and survival analyses confirmed the considerable diagnostic and prognostic abilities of SAMD9L. Moreover, a real-world cohort of 35 SKCM patients from the First Affiliated Hospital of Soochow University showed that higher expression levels of SAMD9L were associated with better prognosis. We performed validation experiments, including cell culture, generation of lentiviral-transfected SKCM cell lines, cell proliferation assay, and transwell assay, which demonstrated that down-regulation of SAMD9L significantly promoted proliferation and migration capacities of SKCM cells. Additionally, SAMD9L expression was found to be strongly linked to immune infiltration. Our results revealed a positive correlation between SAMD9L and XAF1 expression, suggesting that SAMD9L may serve as a prospective prognostic indicator of SKCM with co-expressed XAF1 gene. In summary, our findings indicate that SAMD9L may serve as a promising prognostic and therapeutic biomarker and play a critical role in tumor-immune interactions in SKCM.
bibliographic citation: Ye et al. (2023) Identification of sterile a-motif domain-containing 9-like as a potential biomarker in patients with cutaneous melanoma. PeerJ 11:e15634 https://doi.org/10.7717/peerj.15634
date submitted: 2023-03-10
date accepted: 2023-06-05
issued: 2023-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ye
  given name: Junsen
author list: Agent
  family name: Tang
  given name: Haidan
author list: Agent
  family name: Xie
  given name: Chuanrui
author list: Agent
  family name: Han
  given name: Wei
author list: Agent
  family name: Shen
  given name: Guoliang
author list: Agent
  family name: Qian
  given name: Ying
author list: Agent
  family name: Xu
  given name: Jin
doi: 10.7717/peerj.15634
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-05
copyright: © 2023 Ye et al.
attribution name: Ye et al.

The mediating role of attention deficit in relationship between insomnia and social cognition tasks among nurses in Saudi Arabia: A cross-sectional study
type: item
type: AcademicArticle
description: Purpose Insomnia-related affective functional disorder may negatively affect social cognition such as empathy, altruism, and attitude toward providing care. No previous studies have ever investigated the mediating role of attention deficit in the relationship between insomnia and social cognition. Methods A cross-sectional survey was carried out among 664 nurses (Mage = 33.03 years; SD ± 6.93 years) from December 2020 to September 2021. They completed the Scale of Attitude towards the Patient (SAtP), the Athens Insomnia Scale (AIS), a single-item numeric rating scale assessing the increasing severity of attention complaints, and questions relating to socio-demographic information. The analysis was carried out by examining the mediating role of attention deficit in the relationship between insomnia and social cognition. Results The prevalence of insomnia symptoms was high (52% insomnia using the AIS). Insomnia was significantly correlated with attention problems (b = 0.18, standard error (SE) = 0.02, p < 0.001). Attention problems were significantly negatively correlated with nurses’ attitudes towards patients (b = −0.56, SE = 0.08, p < 0.001), respect for autonomy (b = −0.18, SE = 0.03, p < 0.001), holism (b = −0.14, SE = 0.03, p < 0.001), empathy (b = −0.15, SE = 0.03, p < 0.001), and altruism (b = −0.10, SE = 0.02, p < 0.001). Attention problems indirectly mediated the effect of insomnia on attitudes toward patients (99% CI = −0.10 [−0.16 to −0.05]), respect for autonomy (99% CI = −0.03 [−0.05 to −0.02]), holism (99% CI = −0.02 [−0.04 to −0.01]) empathy (99% CI = −0.03 [−0.04 to −0.01]), and altruism (99% CI = −0.02 [−0.03 to −0.01]). Conclusion Nurses with insomnia-related attention problems are likely to have poor explicit social cognition such as attitude toward patients, altruism, empathy, respect for autonomy, and holism.
format: application/pdf
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creator: Md. Dilshad Manzar
creator: Faizan Kashoo
creator: Abdulrhman Albougami
creator: Majed Alamri
creator: Jazi Shaydied Alotaibi
creator: Bader A. Alrasheadi
creator: Ahmed Mansour Almansour
creator: Mehrunnisha Ahmad
creator: Mohamed Sherif Sirajudeen
creator: Mohamed Yacin Sikkandar
creator: Mark D. Griffiths
subject: Nursing
subject: Psychiatry and Psychology
subject: Healthcare Services
description: doi:10.7717/peerj.15508
publisher: PeerJ Inc.
rights: © 2023 Manzar et al.
abstract: Purpose Insomnia-related affective functional disorder may negatively affect social cognition such as empathy, altruism, and attitude toward providing care. No previous studies have ever investigated the mediating role of attention deficit in the relationship between insomnia and social cognition. Methods A cross-sectional survey was carried out among 664 nurses (Mage = 33.03 years; SD ± 6.93 years) from December 2020 to September 2021. They completed the Scale of Attitude towards the Patient (SAtP), the Athens Insomnia Scale (AIS), a single-item numeric rating scale assessing the increasing severity of attention complaints, and questions relating to socio-demographic information. The analysis was carried out by examining the mediating role of attention deficit in the relationship between insomnia and social cognition. Results The prevalence of insomnia symptoms was high (52% insomnia using the AIS). Insomnia was significantly correlated with attention problems (b = 0.18, standard error (SE) = 0.02, p < 0.001). Attention problems were significantly negatively correlated with nurses’ attitudes towards patients (b = −0.56, SE = 0.08, p < 0.001), respect for autonomy (b = −0.18, SE = 0.03, p < 0.001), holism (b = −0.14, SE = 0.03, p < 0.001), empathy (b = −0.15, SE = 0.03, p < 0.001), and altruism (b = −0.10, SE = 0.02, p < 0.001). Attention problems indirectly mediated the effect of insomnia on attitudes toward patients (99% CI = −0.10 [−0.16 to −0.05]), respect for autonomy (99% CI = −0.03 [−0.05 to −0.02]), holism (99% CI = −0.02 [−0.04 to −0.01]) empathy (99% CI = −0.03 [−0.04 to −0.01]), and altruism (99% CI = −0.02 [−0.03 to −0.01]). Conclusion Nurses with insomnia-related attention problems are likely to have poor explicit social cognition such as attitude toward patients, altruism, empathy, respect for autonomy, and holism.
bibliographic citation: Manzar et al. (2023) The mediating role of attention deficit in relationship between insomnia and social cognition tasks among nurses in Saudi Arabia: A cross-sectional study. PeerJ 11:e15508 https://doi.org/10.7717/peerj.15508
date submitted: 2022-12-19
date accepted: 2023-05-15
issued: 2023-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manzar
  given name: Md. Dilshad
author list: Agent
  family name: Kashoo
  given name: Faizan
author list: Agent
  family name: Albougami
  given name: Abdulrhman
author list: Agent
  family name: Alamri
  given name: Majed
author list: Agent
  family name: Alotaibi
  given name: Jazi Shaydied
author list: Agent
  family name: Alrasheadi
  given name: Bader A.
author list: Agent
  family name: Almansour
  given name: Ahmed Mansour
author list: Agent
  family name: Ahmad
  given name: Mehrunnisha
author list: Agent
  family name: Sirajudeen
  given name: Mohamed Sherif
author list: Agent
  family name: Sikkandar
  given name: Mohamed Yacin
author list: Agent
  family name: Griffiths
  given name: Mark D.
doi: 10.7717/peerj.15508
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-04
copyright: © 2023 Manzar et al.
attribution name: Manzar et al.

Functionalized nanoparticles crossing the brain–blood barrier to target glioma cells
type: item
type: AcademicArticle
description: Glioma is the most common tumor of the central nervous system (CNS), with a 5-year survival rate of <35%. Drug therapy, such as chemotherapeutic and immunotherapeutic agents, remains one of the main treatment modalities for glioma, including temozolomide, doxorubicin, bortezomib, cabazitaxel, dihydroartemisinin, immune checkpoint inhibitors, as well as other approaches such as siRNA, ferroptosis induction, etc. However, the filter function of the blood-brain barrier (BBB) reduces the amount of drugs needed to effectively target CNS tumors, making it one of the main reasons for poor drug efficacies in glioma. Thus, finding a suitable drug delivery platform that can cross the BBB, increase drug aggregation and retainment in tumoral areas and avoid accumulation in non-targeted areas remains an unsolved challenge in glioma drug therapy. An ideal drug delivery system for glioma therapy should have the following features: (1) prolonged drug life in circulation and effective penetration through the BBB; (2) adequate accumulation within the tumor (3) controlled-drug release modulation; (4) good clearance from the body without significant toxicity and immunogenicity, etc. In this regard, due to their unique structural features, nanocarriers can effectively span the BBB and target glioma cells through surface functionalization, providing a new and effective strategy for drug delivery. In this article, we discuss the characteristics and pathways of different nanocarriers for crossing the BBB and targeting glioma by listing different materials for drug delivery platforms, including lipid materials, polymers, nanocrystals, inorganic nanomaterials, etc.
format: application/pdf
format: text/html
creator: Yongyan Wu
creator: Yufeng Qian
creator: Wei Peng
creator: Xuchen Qi
subject: Biochemistry
subject: Hematology
subject: Neurology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.15571
publisher: PeerJ Inc.
rights: © 2023 Wu et al.
abstract: Glioma is the most common tumor of the central nervous system (CNS), with a 5-year survival rate of <35%. Drug therapy, such as chemotherapeutic and immunotherapeutic agents, remains one of the main treatment modalities for glioma, including temozolomide, doxorubicin, bortezomib, cabazitaxel, dihydroartemisinin, immune checkpoint inhibitors, as well as other approaches such as siRNA, ferroptosis induction, etc. However, the filter function of the blood-brain barrier (BBB) reduces the amount of drugs needed to effectively target CNS tumors, making it one of the main reasons for poor drug efficacies in glioma. Thus, finding a suitable drug delivery platform that can cross the BBB, increase drug aggregation and retainment in tumoral areas and avoid accumulation in non-targeted areas remains an unsolved challenge in glioma drug therapy. An ideal drug delivery system for glioma therapy should have the following features: (1) prolonged drug life in circulation and effective penetration through the BBB; (2) adequate accumulation within the tumor (3) controlled-drug release modulation; (4) good clearance from the body without significant toxicity and immunogenicity, etc. In this regard, due to their unique structural features, nanocarriers can effectively span the BBB and target glioma cells through surface functionalization, providing a new and effective strategy for drug delivery. In this article, we discuss the characteristics and pathways of different nanocarriers for crossing the BBB and targeting glioma by listing different materials for drug delivery platforms, including lipid materials, polymers, nanocrystals, inorganic nanomaterials, etc.
bibliographic citation: Wu et al. (2023) Functionalized nanoparticles crossing the brain–blood barrier to target glioma cells. PeerJ 11:e15571 https://doi.org/10.7717/peerj.15571
date submitted: 2023-04-13
date accepted: 2023-05-25
issued: 2023-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wu
  given name: Yongyan
author list: Agent
  family name: Qian
  given name: Yufeng
author list: Agent
  family name: Peng
  given name: Wei
author list: Agent
  family name: Qi
  given name: Xuchen
doi: 10.7717/peerj.15571
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-04
copyright: ©2023 Wu et al.
attribution name: Wu et al.

Attitudes of medical students in Khartoum, Sudan towards the doctor-patient relationship: a cross-sectional study
type: item
type: AcademicArticle
description: Background/Objectives The doctor-patient relationship is essential to the delivery of high-quality medical care. A strong doctor-patient relationship that improves patient outcomes and satisfaction depends on effective communication. The purpose of this study was to assess medical students’ attitudes toward the doctor-patient relationship during their clinical years at the University of Khartoum. We also looked at how gender and study year affected patient-centeredness. Participants/Setting The study was conducted on medical students in their clinical years from December 2020 to March 2021. Students were selected from years 3 to 6. A total of 353 medical students constituted the study sample. Design The cross-sectional study utilized the Patient Practitioner Orientation Scale (PPOS) for the measurement of student attitudes towards the doctor-patient relationship. PPOS scores are calculated as a mean score that ranges from 1 (indicating doctor or disease-centered inclinations) to 6 (indicating patient-centered or egalitarian inclinations). Medical students’ demographic data was collected, including their gender, age and study year. Results A total of 313 students completed the survey (response rate: 89%). The average total PPOS score and the scores for the caring and sharing subscales for the entire cohort were 4.08 ± 0.53, 4.43 ± 0.58, and 3.72 ± 0.72, respectively. Female gender was significantly associated with more patient-centered attitudes (p < 0.001). When compared to the start of their clinical curriculum, students’ attitudes were significantly more patient-centered by the conclusion of their studies (p < 0.001). Conclusion A satisfactory level of patient-centeredness was demonstrated by medical students at the University of Khartoum, and gender had an impact on this quality. Additional consideration should be given to the finding that students’ orientations were more patient-centered in the caring dimension and less so in the sharing one. Once addressed, imp…
format: application/pdf
format: text/html
creator: Aya M. Haiba
creator: Marwan M. Haiba
subject: Health Policy
subject: Ethical Issues
subject: Science and Medical Education
description: doi:10.7717/peerj.15434
publisher: PeerJ Inc.
rights: © 2023 Haiba and Haiba
abstract: Background/Objectives The doctor-patient relationship is essential to the delivery of high-quality medical care. A strong doctor-patient relationship that improves patient outcomes and satisfaction depends on effective communication. The purpose of this study was to assess medical students’ attitudes toward the doctor-patient relationship during their clinical years at the University of Khartoum. We also looked at how gender and study year affected patient-centeredness. Participants/Setting The study was conducted on medical students in their clinical years from December 2020 to March 2021. Students were selected from years 3 to 6. A total of 353 medical students constituted the study sample. Design The cross-sectional study utilized the Patient Practitioner Orientation Scale (PPOS) for the measurement of student attitudes towards the doctor-patient relationship. PPOS scores are calculated as a mean score that ranges from 1 (indicating doctor or disease-centered inclinations) to 6 (indicating patient-centered or egalitarian inclinations). Medical students’ demographic data was collected, including their gender, age and study year. Results A total of 313 students completed the survey (response rate: 89%). The average total PPOS score and the scores for the caring and sharing subscales for the entire cohort were 4.08 ± 0.53, 4.43 ± 0.58, and 3.72 ± 0.72, respectively. Female gender was significantly associated with more patient-centered attitudes (p < 0.001). When compared to the start of their clinical curriculum, students’ attitudes were significantly more patient-centered by the conclusion of their studies (p < 0.001). Conclusion A satisfactory level of patient-centeredness was demonstrated by medical students at the University of Khartoum, and gender had an impact on this quality. Additional consideration should be given to the finding that students’ orientations were more patient-centered in the caring dimension and less so in the sharing one. Once addressed, imp…
bibliographic citation: Haiba et al. (2023) Attitudes of medical students in Khartoum, Sudan towards the doctor-patient relationship: a cross-sectional study. PeerJ 11:e15434 https://doi.org/10.7717/peerj.15434
date submitted: 2022-11-07
date accepted: 2023-04-26
issued: 2023-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haiba
  given name: Aya M.
author list: Agent
  family name: Haiba
  given name: Marwan M.
doi: 10.7717/peerj.15434
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-03
copyright: ©2023 Haiba and Haiba
attribution name: Haiba and Haiba

Measuring blood glucose before or after lumbar puncture
type: item
type: AcademicArticle
description: Background The ratio of cerebrospinal fluid (CSF) to peripheral blood glucose at the same period is an important index for diagnosing and monitoring the efficacy of central nervous system infection, especially bacterial meningitis. Some guidelines refer that blood glucose measurement should be carried out before lumbar puncture. The main reason is to avoid possible effect of stress response induced by lumbar puncture on the level of blood glucose. However, there is no consensus on whether it should be followed in actual clinical work, since up to now no research work having been published on whether lumbar puncture will induce the changes on blood glucose. Our study aimed to investigate the changes of peripheral blood glucose before and after lumbar puncture. Methods In order to clarify the influence of timing of peripheral blood glucose measurement at the same period of lumbar puncture, a prospective study was conducted including children with an age range from 2 months to 12 years old in the neurology department of a medical center. For those children who need lumbar puncture due to their illness, their blood glucose was measured within 5 min before and after lumbar puncture, respectively. The blood glucose level and the ratio of CSF to blood glucose before and after lumbar puncture were compared. Meanwhile, the patients were divided into different groups according to the factors of sex, age and sedation or not for further comparison. All statistical analyses of the data were performed using SPSS version 26.0 for Windows. Results In total, 101 children who needed lumbar puncture during hospitalization from January 1, 2021, to October 1, 2021, were recruited with 65 male and 36 female respectively. There was no significant difference on the level of blood glucose, CSF to blood glucose ratio before and after lumbar puncture among the children (p > 0.05). No differences were observed within different groups (sex, age, sedation or not) either. Conclusion It is unneces…
format: application/pdf
format: text/html
creator: Kaili Shi
creator: Xue Li
creator: Ying Li
creator: Xiaohua Tan
creator: Kelu Zheng
creator: Wenxiong Chen
creator: Xiaojing Li
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Hematology
subject: Neurology
subject: Pediatrics
description: doi:10.7717/peerj.15544
publisher: PeerJ Inc.
rights: © 2023 Shi et al.
abstract: Background The ratio of cerebrospinal fluid (CSF) to peripheral blood glucose at the same period is an important index for diagnosing and monitoring the efficacy of central nervous system infection, especially bacterial meningitis. Some guidelines refer that blood glucose measurement should be carried out before lumbar puncture. The main reason is to avoid possible effect of stress response induced by lumbar puncture on the level of blood glucose. However, there is no consensus on whether it should be followed in actual clinical work, since up to now no research work having been published on whether lumbar puncture will induce the changes on blood glucose. Our study aimed to investigate the changes of peripheral blood glucose before and after lumbar puncture. Methods In order to clarify the influence of timing of peripheral blood glucose measurement at the same period of lumbar puncture, a prospective study was conducted including children with an age range from 2 months to 12 years old in the neurology department of a medical center. For those children who need lumbar puncture due to their illness, their blood glucose was measured within 5 min before and after lumbar puncture, respectively. The blood glucose level and the ratio of CSF to blood glucose before and after lumbar puncture were compared. Meanwhile, the patients were divided into different groups according to the factors of sex, age and sedation or not for further comparison. All statistical analyses of the data were performed using SPSS version 26.0 for Windows. Results In total, 101 children who needed lumbar puncture during hospitalization from January 1, 2021, to October 1, 2021, were recruited with 65 male and 36 female respectively. There was no significant difference on the level of blood glucose, CSF to blood glucose ratio before and after lumbar puncture among the children (p > 0.05). No differences were observed within different groups (sex, age, sedation or not) either. Conclusion It is unneces…
bibliographic citation: Shi et al. (2023) Measuring blood glucose before or after lumbar puncture. PeerJ 11:e15544 https://doi.org/10.7717/peerj.15544
date submitted: 2023-03-07
date accepted: 2023-05-21
issued: 2023-07-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Kaili
author list: Agent
  family name: Li
  given name: Xue
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Tan
  given name: Xiaohua
author list: Agent
  family name: Zheng
  given name: Kelu
author list: Agent
  family name: Chen
  given name: Wenxiong
author list: Agent
  family name: Li
  given name: Xiaojing
doi: 10.7717/peerj.15544
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-03
copyright: ©2023 Shi et al.
attribution name: Shi et al.

A histological analysis of coloration in the Peruvian mimic poison frog (Ranitomeya imitator)
type: item
type: AcademicArticle
description: Aposematism continues to be a phenomenon of central interest in evolutionary biology. The life history of the mimic poison frog, Ranitomeya imitator, relies heavily on aposematism. In order for aposematic signals to be effective, predators must be able to learn to avoid the associated phenotype. However, in R. imitator, aposematism is associated with four different color phenotypes that mimic a complex of congeneric species occurring across the mimic frog’s geographic range. Investigations of the underlying mechanics of color production in these frogs can provide insights into how and why these different morphs evolved. We used histological samples to examine divergence in the color production mechanisms used by R. imitator to produce effective aposematic signals across its geographic range. We measured the coverage of melanophores and xanthophores (the area covered by chromatophores divided by total area of the skin section) in each color morph. We find that morphs that produce orange skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce yellow skin. In turn, morphs that produce yellow skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce green skin. Generally, across the morphs, a high ratio of xanthophores to melanophores is associated with colors of brighter spectral reflectance. Together, our results contribute to the understanding of color production in amphibians and document divergence in the histology of a species that is subject to divergent selection associated with aposematism.
format: application/pdf
format: text/html
creator: Mallory de Araujo Miles
creator: Mikayla Joyce Johnson
creator: Adam M. M. Stuckert
creator: Kyle Summers
subject: Evolutionary Studies
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.15533
publisher: PeerJ Inc.
rights: © 2023 de Araujo Miles et al.
abstract: Aposematism continues to be a phenomenon of central interest in evolutionary biology. The life history of the mimic poison frog, Ranitomeya imitator, relies heavily on aposematism. In order for aposematic signals to be effective, predators must be able to learn to avoid the associated phenotype. However, in R. imitator, aposematism is associated with four different color phenotypes that mimic a complex of congeneric species occurring across the mimic frog’s geographic range. Investigations of the underlying mechanics of color production in these frogs can provide insights into how and why these different morphs evolved. We used histological samples to examine divergence in the color production mechanisms used by R. imitator to produce effective aposematic signals across its geographic range. We measured the coverage of melanophores and xanthophores (the area covered by chromatophores divided by total area of the skin section) in each color morph. We find that morphs that produce orange skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce yellow skin. In turn, morphs that produce yellow skin exhibit a higher coverage of xanthophores and lower coverage of melanophores than those that produce green skin. Generally, across the morphs, a high ratio of xanthophores to melanophores is associated with colors of brighter spectral reflectance. Together, our results contribute to the understanding of color production in amphibians and document divergence in the histology of a species that is subject to divergent selection associated with aposematism.
bibliographic citation: de Araujo Miles et al. (2023) A histological analysis of coloration in the Peruvian mimic poison frog (Ranitomeya imitator). PeerJ 11:e15533 https://doi.org/10.7717/peerj.15533
date submitted: 2022-11-09
date accepted: 2023-05-19
issued: 2023-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Araujo Miles
  given name: Mallory
author list: Agent
  family name: Johnson
  given name: Mikayla Joyce
author list: Agent
  family name: Stuckert
  given name: Adam M. M.
author list: Agent
  family name: Summers
  given name: Kyle
doi: 10.7717/peerj.15533
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-30
copyright: © 2023 de Araujo Miles et al.
attribution name: de Araujo Miles et al.

Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity
type: item
type: AcademicArticle
description: Respiratory diseases are among the major health problems causing a burden on hospitals. Diagnosis of infection and rapid prediction of severity without time-consuming clinical tests could be beneficial in preventing the spread and progression of the disease, especially in countries where health systems remain incapable. Personalized medicine studies involving statistics and computer technologies could help to address this need. In addition to individual studies, competitions are also held such as Dialogue for Reverse Engineering Assessment and Methods (DREAM) challenge which is a community-driven organization with a mission to research biology, bioinformatics, and biomedicine. One of these competitions was the Respiratory Viral DREAM Challenge, which aimed to develop early predictive biomarkers for respiratory virus infections. These efforts are promising, however, the prediction performance of the computational methods developed for detecting respiratory diseases still has room for improvement. In this study, we focused on improving the performance of predicting the infection and symptom severity of individuals infected with various respiratory viruses using gene expression data collected before and after exposure. The publicly available gene expression dataset in the Gene Expression Omnibus, named GSE73072, containing samples exposed to four respiratory viruses (H1N1, H3N2, human rhinovirus (HRV), and respiratory syncytial virus (RSV)) was used as input data. Various preprocessing methods and machine learning algorithms were implemented and compared to achieve the best prediction performance. The experimental results showed that the proposed approaches obtained a prediction performance of 0.9746 area under the precision-recall curve (AUPRC) for infection (i.e., shedding) prediction (SC-1), 0.9182 AUPRC for symptom class prediction (SC-2), and 0.6733 Pearson correlation for symptom score prediction (SC-3) by outperforming the best leaderboard scores of Respiratory …
format: application/pdf
format: text/html
creator: Yunus Emre Işık
creator: Zafer Aydın
subject: Bioinformatics
subject: Computational Biology
subject: Virology
description: doi:10.7717/peerj.15552
publisher: PeerJ Inc.
rights: © 2023 Işık and Aydın
abstract: Respiratory diseases are among the major health problems causing a burden on hospitals. Diagnosis of infection and rapid prediction of severity without time-consuming clinical tests could be beneficial in preventing the spread and progression of the disease, especially in countries where health systems remain incapable. Personalized medicine studies involving statistics and computer technologies could help to address this need. In addition to individual studies, competitions are also held such as Dialogue for Reverse Engineering Assessment and Methods (DREAM) challenge which is a community-driven organization with a mission to research biology, bioinformatics, and biomedicine. One of these competitions was the Respiratory Viral DREAM Challenge, which aimed to develop early predictive biomarkers for respiratory virus infections. These efforts are promising, however, the prediction performance of the computational methods developed for detecting respiratory diseases still has room for improvement. In this study, we focused on improving the performance of predicting the infection and symptom severity of individuals infected with various respiratory viruses using gene expression data collected before and after exposure. The publicly available gene expression dataset in the Gene Expression Omnibus, named GSE73072, containing samples exposed to four respiratory viruses (H1N1, H3N2, human rhinovirus (HRV), and respiratory syncytial virus (RSV)) was used as input data. Various preprocessing methods and machine learning algorithms were implemented and compared to achieve the best prediction performance. The experimental results showed that the proposed approaches obtained a prediction performance of 0.9746 area under the precision-recall curve (AUPRC) for infection (i.e., shedding) prediction (SC-1), 0.9182 AUPRC for symptom class prediction (SC-2), and 0.6733 Pearson correlation for symptom score prediction (SC-3) by outperforming the best leaderboard scores of Respiratory …
bibliographic citation: Işık et al. (2023) Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity. PeerJ 11:e15552 https://doi.org/10.7717/peerj.15552
date submitted: 2022-11-11
date accepted: 2023-05-23
issued: 2023-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Işık
  given name: Yunus Emre
author list: Agent
  family name: Aydın
  given name: Zafer
doi: 10.7717/peerj.15552
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-30
copyright: © 2023 Işık and Aydın
attribution name: Işık and Aydın

Influencing factors of cardiac valve calcification (CVC) in patients with chronic kidney disease and the impact of CVC on long-term prognosis: a single-center retrospective study
type: item
type: AcademicArticle
description: Objective To investigate the effect of cardiac valve calcification (CVC) on the prognosis of patients with chronic kidney disease (CKD). Methods A total of 343 CKD patients were retrospectively analyzed, and divided into two groups according to the presence or absence of cardiac valve calcification. All patients were followed until death, loss to follow-up, or the end point of the study (December 2021). Results The incidence of CVC among the 343 CKD patients was 29.7%, including 21 cases of mitral valve calcification, 63 cases of aortic valve calcification, and 18 cases of mitral valve combined with aortic valve calcification. The incidence of CVC in CKD stages 1–2 was 0.3%, 5.2% in CKD stages 3–4, and 24.2% in CKD stage 5 (P < 0.05). Advanced age, higher serum albumin, higher cystatin C and lower uric acid levels were all associated with a higher risk of CVC. After six years of follow-up, 77 patients (22.4%) died. The causes of death were cardiovascular and cerebrovascular diseases in 36 cases (46.7%), infection in 29 cases (37.7%), gastrointestinal bleeding in nine cases (11.7%), and “other” in the remaining three cases (3.9%). A Kaplan Meier survival analysis showed that the overall survival rate of patients with CVC was lower than that of patients without CVC. Conclusion The incidence of CVC, mainly aortic calcification, is high in patients with CKD. Advanced age, higher serum albumin and higher cystatin C levels were associated with a higher risk of CVC. Hyperuricemia was associated with a lower risk of CVC. The overall survival rate of patients with CVC was lower than that of patients without CVC.
format: application/pdf
format: text/html
creator: Ju Wang
creator: Jianping Xiao
creator: Ruifeng Wang
creator: Deguang Wang
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.15569
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Objective To investigate the effect of cardiac valve calcification (CVC) on the prognosis of patients with chronic kidney disease (CKD). Methods A total of 343 CKD patients were retrospectively analyzed, and divided into two groups according to the presence or absence of cardiac valve calcification. All patients were followed until death, loss to follow-up, or the end point of the study (December 2021). Results The incidence of CVC among the 343 CKD patients was 29.7%, including 21 cases of mitral valve calcification, 63 cases of aortic valve calcification, and 18 cases of mitral valve combined with aortic valve calcification. The incidence of CVC in CKD stages 1–2 was 0.3%, 5.2% in CKD stages 3–4, and 24.2% in CKD stage 5 (P < 0.05). Advanced age, higher serum albumin, higher cystatin C and lower uric acid levels were all associated with a higher risk of CVC. After six years of follow-up, 77 patients (22.4%) died. The causes of death were cardiovascular and cerebrovascular diseases in 36 cases (46.7%), infection in 29 cases (37.7%), gastrointestinal bleeding in nine cases (11.7%), and “other” in the remaining three cases (3.9%). A Kaplan Meier survival analysis showed that the overall survival rate of patients with CVC was lower than that of patients without CVC. Conclusion The incidence of CVC, mainly aortic calcification, is high in patients with CKD. Advanced age, higher serum albumin and higher cystatin C levels were associated with a higher risk of CVC. Hyperuricemia was associated with a lower risk of CVC. The overall survival rate of patients with CVC was lower than that of patients without CVC.
bibliographic citation: Wang et al. (2023) Influencing factors of cardiac valve calcification (CVC) in patients with chronic kidney disease and the impact of CVC on long-term prognosis: a single-center retrospective study. PeerJ 11:e15569 https://doi.org/10.7717/peerj.15569
date submitted: 2022-11-25
date accepted: 2023-05-25
issued: 2023-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ju
author list: Agent
  family name: Xiao
  given name: Jianping
author list: Agent
  family name: Wang
  given name: Ruifeng
author list: Agent
  family name: Wang
  given name: Deguang
doi: 10.7717/peerj.15569
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-30
copyright: ©2023 Wang et al.
attribution name: Wang et al.

MK8617 inhibits M1 macrophage polarization and inflammation via the HIF-1α/GYS1/UDPG/P2Y14 pathway
type: item
type: AcademicArticle
description: Background Nonresolving inflammation is a major driver of disease and needs to be taken seriously. Hypoxia-inducible factor (HIF) is closely associated with inflammation. Hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHIs), as stabilizers of HIF, have recently been reported to have the ability to block inflammation. We used MK8617, a novel HIF-PHI, to study its effect on macrophage inflammation and to explore its possible mechanisms. Methods Cell viability after MK8617 and lipopolysaccharide (LPS) addition was assessed by Cell Counting Kit-8 (CCK8) to find the appropriate drug concentration. MK8617 pretreated or unpretreated cells were then stimulated with LPS to induce macrophage polarization and inflammation. Inflammatory indicators in cells were assessed by real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR), western blot (WB) and immunofluorescence (IF). The level of uridine diphosphate glucose (UDPG) in the cell supernatant was measured by ELISA. Purinergic G protein-coupled receptor P2Y14, as well as hypoxia-inducible factor-1α (HIF-1α) and glycogen synthase 1 (GYS1) were detected by qRT-PCR and WB. After UDPG inhibition with glycogen phosphorylase inhibitor (GPI) or knockdown of HIF-1α and GYS1 with lentivirus, P2Y14 and inflammatory indexes of macrophages were detected by qRT-PCR and WB. Results MK8617 reduced LPS-induced release of pro-inflammatory factors as well as UDPG secretion and P2Y14 expression. UDPG upregulated P2Y14 and inflammatory indicators, while inhibition of UDPG suppressed LPS-induced inflammation. In addition, HIF-1α directly regulated GYS1, which encoded glycogen synthase, an enzyme that mediated the synthesis of glycogen by UDPG, thereby affecting UDPG secretion. Knockdown of HIF-1α and GYS1 disrupted the anti-inflammatory effect of MK8617. Conclusions Our study demonstrated the role of MK8617 in macrophage inflammation and revealed that its mechanism of action may be related to the HIF-1α/GYS1/…
format: application/pdf
format: text/html
creator: Lingling Qian
creator: Xiao-qin Chen
creator: Deyang Kong
creator: Gaoyuan Wang
creator: Yun Cao
creator: Yingchun Xiao
creator: Jing-yuan Cao
creator: Chunbo Zou
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15591
publisher: PeerJ Inc.
rights: © 2023 Qian et al.
abstract: Background Nonresolving inflammation is a major driver of disease and needs to be taken seriously. Hypoxia-inducible factor (HIF) is closely associated with inflammation. Hypoxia-inducible factor-prolyl hydroxylase inhibitors (HIF-PHIs), as stabilizers of HIF, have recently been reported to have the ability to block inflammation. We used MK8617, a novel HIF-PHI, to study its effect on macrophage inflammation and to explore its possible mechanisms. Methods Cell viability after MK8617 and lipopolysaccharide (LPS) addition was assessed by Cell Counting Kit-8 (CCK8) to find the appropriate drug concentration. MK8617 pretreated or unpretreated cells were then stimulated with LPS to induce macrophage polarization and inflammation. Inflammatory indicators in cells were assessed by real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR), western blot (WB) and immunofluorescence (IF). The level of uridine diphosphate glucose (UDPG) in the cell supernatant was measured by ELISA. Purinergic G protein-coupled receptor P2Y14, as well as hypoxia-inducible factor-1α (HIF-1α) and glycogen synthase 1 (GYS1) were detected by qRT-PCR and WB. After UDPG inhibition with glycogen phosphorylase inhibitor (GPI) or knockdown of HIF-1α and GYS1 with lentivirus, P2Y14 and inflammatory indexes of macrophages were detected by qRT-PCR and WB. Results MK8617 reduced LPS-induced release of pro-inflammatory factors as well as UDPG secretion and P2Y14 expression. UDPG upregulated P2Y14 and inflammatory indicators, while inhibition of UDPG suppressed LPS-induced inflammation. In addition, HIF-1α directly regulated GYS1, which encoded glycogen synthase, an enzyme that mediated the synthesis of glycogen by UDPG, thereby affecting UDPG secretion. Knockdown of HIF-1α and GYS1 disrupted the anti-inflammatory effect of MK8617. Conclusions Our study demonstrated the role of MK8617 in macrophage inflammation and revealed that its mechanism of action may be related to the HIF-1α/GYS1/…
bibliographic citation: Qian et al. (2023) MK8617 inhibits M1 macrophage polarization and inflammation via the HIF-1α/GYS1/UDPG/P2Y14 pathway. PeerJ 11:e15591 https://doi.org/10.7717/peerj.15591
date submitted: 2022-12-16
date accepted: 2023-05-29
issued: 2023-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qian
  given name: Lingling
author list: Agent
  family name: Chen
  given name: Xiao-qin
author list: Agent
  family name: Kong
  given name: Deyang
author list: Agent
  family name: Wang
  given name: Gaoyuan
author list: Agent
  family name: Cao
  given name: Yun
author list: Agent
  family name: Xiao
  given name: Yingchun
author list: Agent
  family name: Cao
  given name: Jing-yuan
author list: Agent
  family name: Zou
  given name: Chunbo
doi: 10.7717/peerj.15591
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-30
copyright: © 2023 Qian et al.
attribution name: Qian et al.

miR-455-3p ameliorates pancreatic acinar cell injury by targeting Slc2a1
type: item
type: AcademicArticle
description: Objective With the number of patients with acute pancreatitis (AP) increasing year by year, it is pressing to explore new key genes and markers for the treatment of AP. miR-455-3p/solute carrier family 2 member 1 (Slc2a1) obtained through bioinformatics analysis may participate in the progression of AP. Materials and Methods The C57BL/6 mouse model of AP was constructed for subsequent studies. Through bioinformatics analysis, the differentially expressed genes related to AP were screened and hub genes were identified. A caerulein-induced AP animal model was constructed to detect the pathological changes of mouse pancreas by HE staining. The concentrations of amylase and lipase were measured. Primary mouse pancreatic acinar cells were isolated and subjected to microscopy to observe their morphology. The enzymatic activities of trypsin and amylase were detected. The secretion of inflammatory cytokines in mouse were measured with the ELISA kits of TNF-α, IL-6 and IL-1β to determine pancreatic acinar cell damage. A binding site between the Slc2a1 3′ UTR region and the miR-455-3p sequence was verified by dual-luciferase reporter assay. The expression of miR-455-3p was quantified by qRT-PCR, and Slc2a1 were detected by western blot. Results A total of five (Fyn, Gadd45a, Sdc1, Slc2a1, and Src) were identified by bioinformatics analysis, and miR-455-3p/Slc2a1 were further studied. HE staining results showed that the AP models were successfully established by caerulein induction. In mice with AP, the expression of miR-455-3p was reduced, while that of Slc2a1 was increased. In the caerulein-induced cell model, the expression of Slc2a1 was significantly reduced after intervention of miR-455-3p mimics, whereas increased after miR-455-3p inhibitor treatment. miR-455-3p decreased the secretion of inflammatory cytokines in the cell supernatant, reduced the activity of trypsin and amylase, and alleviated the cell damage induced by caerulein. In addition, Slc2a1 3’UTR region was bo…
format: application/pdf
format: text/html
creator: Yinchu Zhan
creator: Chenlin Chen
creator: Zhiqiang Wu
creator: Feng Zhou
creator: Xinping Yu
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.15612
publisher: PeerJ Inc.
rights: © 2023 Zhan et al.
abstract: Objective With the number of patients with acute pancreatitis (AP) increasing year by year, it is pressing to explore new key genes and markers for the treatment of AP. miR-455-3p/solute carrier family 2 member 1 (Slc2a1) obtained through bioinformatics analysis may participate in the progression of AP. Materials and Methods The C57BL/6 mouse model of AP was constructed for subsequent studies. Through bioinformatics analysis, the differentially expressed genes related to AP were screened and hub genes were identified. A caerulein-induced AP animal model was constructed to detect the pathological changes of mouse pancreas by HE staining. The concentrations of amylase and lipase were measured. Primary mouse pancreatic acinar cells were isolated and subjected to microscopy to observe their morphology. The enzymatic activities of trypsin and amylase were detected. The secretion of inflammatory cytokines in mouse were measured with the ELISA kits of TNF-α, IL-6 and IL-1β to determine pancreatic acinar cell damage. A binding site between the Slc2a1 3′ UTR region and the miR-455-3p sequence was verified by dual-luciferase reporter assay. The expression of miR-455-3p was quantified by qRT-PCR, and Slc2a1 were detected by western blot. Results A total of five (Fyn, Gadd45a, Sdc1, Slc2a1, and Src) were identified by bioinformatics analysis, and miR-455-3p/Slc2a1 were further studied. HE staining results showed that the AP models were successfully established by caerulein induction. In mice with AP, the expression of miR-455-3p was reduced, while that of Slc2a1 was increased. In the caerulein-induced cell model, the expression of Slc2a1 was significantly reduced after intervention of miR-455-3p mimics, whereas increased after miR-455-3p inhibitor treatment. miR-455-3p decreased the secretion of inflammatory cytokines in the cell supernatant, reduced the activity of trypsin and amylase, and alleviated the cell damage induced by caerulein. In addition, Slc2a1 3’UTR region was bo…
bibliographic citation: Zhan et al. (2023) miR-455-3p ameliorates pancreatic acinar cell injury by targeting Slc2a1. PeerJ 11:e15612 https://doi.org/10.7717/peerj.15612
date submitted: 2022-12-27
date accepted: 2023-06-01
issued: 2023-06-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhan
  given name: Yinchu
author list: Agent
  family name: Chen
  given name: Chenlin
author list: Agent
  family name: Wu
  given name: Zhiqiang
author list: Agent
  family name: Zhou
  given name: Feng
author list: Agent
  family name: Yu
  given name: Xinping
doi: 10.7717/peerj.15612
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-30
copyright: ©2023 Zhan et al.
attribution name: Zhan et al.

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