PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Characterization and clinical outcomes of outpatients with subacute or chronic post COVID-19 cough: a real-world study
items: Differential circulating miRNA profiles identified miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers for cholangiocarcinoma diagnosis
items: Comparative leaf anatomy of two species of Ipomoea L. (Convolvulaceae): taxonomic importance and adaptations to xeric conditions of the cangas
items: Endorsement of reporting guidelines and clinical trial registration across urological medical journals: a cross-sectional study
items: Interspecies differences in the transcriptome response of corals to acute heat stress
items: Construction and validation of a predictive model for the risk of malnutrition in hospitalized patients over 65 years of age with malignant tumours: a single-centre retrospective cross-sectional study
items: Spectrum analysis of inborn errors of metabolism for expanded newborn screening in Xinjiang, China
items: Accuracy of augmented reality navigated surgery for placement of zygomatic implants: a human cadaver study
items: The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment
items: Observation of peri-implant bone loss rates in patients visiting dentist—A retrospective evaluation of patients of a faculty hospital for one year

Characterization and clinical outcomes of outpatients with subacute or chronic post COVID-19 cough: a real-world study
type: item
type: AcademicArticle
description: Background Limited research exists on the features and management of post-COVID cough. This real-world study investigates outpatients with subacute or chronic post-COVID cough, aiming to delineate characteristics and regimen responses within the population. Method We enrolled eligible patients from our outpatient unit between August 2023 and February 2024. Comprehensive clinical data, prescriptions, and patient-reported cough severity were collected during the primary visit and subsequent follow-ups. Result A total of 141 patients, aged: 42 ± 14 years old, were included, with 70% being female. The median cough duration was 8 weeks (interquartile range 4–12 weeks). Sixty percent presented with a dry cough, while the rest had coughs with phlegm. Over half reported abnormal laryngeal sensations (54%). Twenty-one percent coughed during the day, while 32% coughed constantly, and 48% experienced nocturnal episodes. Compound methoxyphenamine capsules were the most prescribed, but our study found ICS/LABA to be the most effective, followed by compound methoxyphenamine capsules, montelukast, and Chinese patent drugs. Conclusion Females exhibit a higher prevalence of post-COVID cough, and our study recommends ICS/LABA as the preferred treatment. These findings warrant validation through larger, prospectively designed studies.
format: application/pdf
format: text/html
creator: Chun Yao
creator: Dongliang Cheng
creator: Wenhong Yang
creator: Yun Guo
creator: Tong Zhou
subject: Evidence Based Medicine
subject: Infectious Diseases
subject: Internal Medicine
subject: COVID-19
description: doi:10.7717/peerj.18705
publisher: PeerJ Inc.
rights: © 2024 Yao et al.
abstract: Background Limited research exists on the features and management of post-COVID cough. This real-world study investigates outpatients with subacute or chronic post-COVID cough, aiming to delineate characteristics and regimen responses within the population. Method We enrolled eligible patients from our outpatient unit between August 2023 and February 2024. Comprehensive clinical data, prescriptions, and patient-reported cough severity were collected during the primary visit and subsequent follow-ups. Result A total of 141 patients, aged: 42 ± 14 years old, were included, with 70% being female. The median cough duration was 8 weeks (interquartile range 4–12 weeks). Sixty percent presented with a dry cough, while the rest had coughs with phlegm. Over half reported abnormal laryngeal sensations (54%). Twenty-one percent coughed during the day, while 32% coughed constantly, and 48% experienced nocturnal episodes. Compound methoxyphenamine capsules were the most prescribed, but our study found ICS/LABA to be the most effective, followed by compound methoxyphenamine capsules, montelukast, and Chinese patent drugs. Conclusion Females exhibit a higher prevalence of post-COVID cough, and our study recommends ICS/LABA as the preferred treatment. These findings warrant validation through larger, prospectively designed studies.
bibliographic citation: Yao et al. (2024) Characterization and clinical outcomes of outpatients with subacute or chronic post COVID-19 cough: a real-world study. PeerJ 12:e18705 https://doi.org/10.7717/peerj.18705
date submitted: 2024-06-20
date accepted: 2024-11-22
issued: 2024-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Chun
author list: Agent
  family name: Cheng
  given name: Dongliang
author list: Agent
  family name: Yang
  given name: Wenhong
author list: Agent
  family name: Guo
  given name: Yun
author list: Agent
  family name: Zhou
  given name: Tong
doi: 10.7717/peerj.18705
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-11
copyright: © 2024 Yao et al.
attribution name: Yao et al.

Differential circulating miRNA profiles identified miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers for cholangiocarcinoma diagnosis
type: item
type: AcademicArticle
description: Background Cholangiocarcinoma (CCA) is high in morbidity and mortality rates which may be due to asymptomatic and effective diagnostic methods not available. Therefore, an effective diagnosis is urgently needed. Methods Investigation of plasma circulating miRNA (cir-miRNA) was divided into two phases, including the discovery phase (pooled 10 samples each from three pools in each group) and the validation phase (17, 16, and 35 subjects of healthy control (HC), O. viverrini (OV), and CCA groups, respectively). The plasma from healthy control subjects, O. viverrini infected subjects, and CCA subjects was used. In the discovery phase, plasma was pooled by adding an equal volume of plasma, and cir-miRNA was isolated and analyzed with the nCounter® SPRINT Profiler. The significantly different cir-miRNAs were selected for the validation phase. In the validation phase, cir-miRNA was isolated and analyzed using real time-quantitative polymerase chain reaction (RT-qPCR). Subsequently, statistical analysis was conducted, and diagnostic parameters were calculated. Results Differential plasma cir-miRNA profile showed at least three candidates including miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers. From validation of these cir-miRNAs by RT-qPCR, the result showed that the satisfied sensitivity and specificity to differential CCA group from HC and OV group was obtained from miR-4532 (P < 0.05) while miR-423-5p and miR-93-5p can be used for differential CCA from OV and HC group (P < 0.05) with high specificity but limited the sensitivity. In conclusion, candidate cir-miRNAs have been identified as potential biomarkers including miR-423-5p, miR-93-5p and miR-4532. Screening by miR-4532 and confirmed with miR-423-5p, miR-93-5p were suggested for differential CCA patients in the endemic area of O. viverrini.
format: application/pdf
format: text/html
creator: Kittiya Supradit
creator: Sattrachai Prasopdee
creator: Teva Phanaksri
creator: Sithichoke Tangphatsornruang
creator: Montinee Pholhelm
creator: Siraphatsorn Yusuk
creator: Kritiya Butthongkomvong
creator: Kanokpan Wongprasert
creator: Jutharat Kulsantiwong
creator: Amnat Chukan
creator: Smarn Tesana
creator: Veerachai Thitapakorn
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Parasitology
subject: Oncology
description: doi:10.7717/peerj.18367
publisher: PeerJ Inc.
rights: © 2024 Supradit et al.
abstract: Background Cholangiocarcinoma (CCA) is high in morbidity and mortality rates which may be due to asymptomatic and effective diagnostic methods not available. Therefore, an effective diagnosis is urgently needed. Methods Investigation of plasma circulating miRNA (cir-miRNA) was divided into two phases, including the discovery phase (pooled 10 samples each from three pools in each group) and the validation phase (17, 16, and 35 subjects of healthy control (HC), O. viverrini (OV), and CCA groups, respectively). The plasma from healthy control subjects, O. viverrini infected subjects, and CCA subjects was used. In the discovery phase, plasma was pooled by adding an equal volume of plasma, and cir-miRNA was isolated and analyzed with the nCounter® SPRINT Profiler. The significantly different cir-miRNAs were selected for the validation phase. In the validation phase, cir-miRNA was isolated and analyzed using real time-quantitative polymerase chain reaction (RT-qPCR). Subsequently, statistical analysis was conducted, and diagnostic parameters were calculated. Results Differential plasma cir-miRNA profile showed at least three candidates including miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers. From validation of these cir-miRNAs by RT-qPCR, the result showed that the satisfied sensitivity and specificity to differential CCA group from HC and OV group was obtained from miR-4532 (P < 0.05) while miR-423-5p and miR-93-5p can be used for differential CCA from OV and HC group (P < 0.05) with high specificity but limited the sensitivity. In conclusion, candidate cir-miRNAs have been identified as potential biomarkers including miR-423-5p, miR-93-5p and miR-4532. Screening by miR-4532 and confirmed with miR-423-5p, miR-93-5p were suggested for differential CCA patients in the endemic area of O. viverrini.
bibliographic citation: Supradit et al. (2024) Differential circulating miRNA profiles identified miR-423-5p, miR-93-5p, and miR-4532 as potential biomarkers for cholangiocarcinoma diagnosis. PeerJ 12:e18367 https://doi.org/10.7717/peerj.18367
date submitted: 2024-04-01
date accepted: 2024-09-30
issued: 2024-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Supradit
  given name: Kittiya
author list: Agent
  family name: Prasopdee
  given name: Sattrachai
author list: Agent
  family name: Phanaksri
  given name: Teva
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
author list: Agent
  family name: Pholhelm
  given name: Montinee
author list: Agent
  family name: Yusuk
  given name: Siraphatsorn
author list: Agent
  family name: Butthongkomvong
  given name: Kritiya
author list: Agent
  family name: Wongprasert
  given name: Kanokpan
author list: Agent
  family name: Kulsantiwong
  given name: Jutharat
author list: Agent
  family name: Chukan
  given name: Amnat
author list: Agent
  family name: Tesana
  given name: Smarn
author list: Agent
  family name: Thitapakorn
  given name: Veerachai
doi: 10.7717/peerj.18367
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-10
copyright: © 2024 Supradit et al.
attribution name: Supradit et al.

Comparative leaf anatomy of two species of Ipomoea L. (Convolvulaceae): taxonomic importance and adaptations to xeric conditions of the cangas
type: item
type: AcademicArticle
description: Background Accurate species identification is the first step towards establishing conservation strategies, especially regarding rare and threatened species, such as those studied here. Moreover, understanding the responses to the environment and growing conditions of endemic species is necessary for its conservation. This study compares the leaf anatomy of Ipomoea cavalcantei and I. marabaensis, which grow on the Brazilian ironstone outcrops (cangas) and exhibit morphological convergence. Methods Leaf anatomical characters of the species were described. Additionally, the leaf adaptive potential of I. cavalcantei was evaluated, comparing individuals grown in natural canga areas (in situ) and cultivated in topsoil (ex situ). Quantitative analysis evaluated stomatal density, polar and equatorial diameter of stomata, and thickness of the epidermis and mesophyll. Results Ipomoea cavalcantei and I. marabaensis can be distinguished by the mesophyll type. Ipomoea marabaensis is also characterized by the presence of lateral protuberances on the abaxial surface of the midrib. Individuals of I. cavalcantei under cultivation have lower stomatal density, although their functionality (polar/equatorial diameter) is more significant than those grown in a natural environment; these individuals also exhibit leaves with a thinner cuticle, abaxial epidermal cells with more sinuous walls, a lower occurrence of trichomes and secretory cells (laticifers), and more druse-containing idioblasts in the mesophyll. All these traits are adaptations to growing conditions that include lower light and the absence of water stress. Conclusions Leaf anatomical traits showed to be useful to delimit Ipomoea cavalcantei and I. marabaensis in the non-reproductive stage. For individuals of I. cavalcantei cultivated in topsoil, some features, especially of the epidermis, respond to light and water supply.
format: application/pdf
format: text/html
creator: Joyce C. R. Silva
creator: Kleber R. Silva
creator: Cecilio F. Caldeira
creator: Aline Oriani
creator: Mauricio T. C. Watanabe
subject: Biodiversity
subject: Developmental Biology
subject: Ecology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.18599
publisher: PeerJ Inc.
rights: © 2024 Silva et al.
abstract: Background Accurate species identification is the first step towards establishing conservation strategies, especially regarding rare and threatened species, such as those studied here. Moreover, understanding the responses to the environment and growing conditions of endemic species is necessary for its conservation. This study compares the leaf anatomy of Ipomoea cavalcantei and I. marabaensis, which grow on the Brazilian ironstone outcrops (cangas) and exhibit morphological convergence. Methods Leaf anatomical characters of the species were described. Additionally, the leaf adaptive potential of I. cavalcantei was evaluated, comparing individuals grown in natural canga areas (in situ) and cultivated in topsoil (ex situ). Quantitative analysis evaluated stomatal density, polar and equatorial diameter of stomata, and thickness of the epidermis and mesophyll. Results Ipomoea cavalcantei and I. marabaensis can be distinguished by the mesophyll type. Ipomoea marabaensis is also characterized by the presence of lateral protuberances on the abaxial surface of the midrib. Individuals of I. cavalcantei under cultivation have lower stomatal density, although their functionality (polar/equatorial diameter) is more significant than those grown in a natural environment; these individuals also exhibit leaves with a thinner cuticle, abaxial epidermal cells with more sinuous walls, a lower occurrence of trichomes and secretory cells (laticifers), and more druse-containing idioblasts in the mesophyll. All these traits are adaptations to growing conditions that include lower light and the absence of water stress. Conclusions Leaf anatomical traits showed to be useful to delimit Ipomoea cavalcantei and I. marabaensis in the non-reproductive stage. For individuals of I. cavalcantei cultivated in topsoil, some features, especially of the epidermis, respond to light and water supply.
bibliographic citation: Silva et al. (2024) Comparative leaf anatomy of two species of Ipomoea L. (Convolvulaceae): taxonomic importance and adaptations to xeric conditions of the cangas. PeerJ 12:e18599 https://doi.org/10.7717/peerj.18599
date submitted: 2024-09-10
date accepted: 2024-11-06
issued: 2024-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Joyce C. R.
author list: Agent
  family name: Silva
  given name: Kleber R.
author list: Agent
  family name: Caldeira
  given name: Cecilio F.
author list: Agent
  family name: Oriani
  given name: Aline
author list: Agent
  family name: Watanabe
  given name: Mauricio T. C.
doi: 10.7717/peerj.18599
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-10
copyright: © 2024 Silva et al.
attribution name: Silva et al.

Endorsement of reporting guidelines and clinical trial registration across urological medical journals: a cross-sectional study
type: item
type: AcademicArticle
description: Introduction Over the years, funding for urologic diseases has witnessed a steady rise, reaching $587 million in 2020 from $541 million in 2018. In parallel, there has been a notable increase in the total number of urology journals from 2011 to 2018. This surge in research funding and journal publications calls for urologists to effectively navigate through a vast body of evidence to make the best evidence-based clinical decisions. Our primary objective was to assess the “instructions for authors” of these journals to determine the extent of endorsement of reporting guidelines for common study designs in medical research. Methods Top urology journals were identified using the 2021 Scopus CiteScore and confirmed via Google Scholar Metrics h5-index. In a masked, duplicate manner, two investigators retrieved data from the “instructions for authors” webpages of the included journals. For each journal investigated in our study, the following data were extracted: journal title, 5-year impact factor, email responses of journal editors, mention of the EQUATOR Network in the “instructions for authors,” mention of the ICMJE in the “instruction for authors,” geographical region of publication and statements about clinical trial registration. Results Of the 92 urology journals examined, only one-third (32/92) mentioned the EQUATOR network in their “instructions for authors.” A total of 17 journals (17/92, 18.5%) did not mention a single reporting guideline. The most endorsed guideline was CONSORT at 67.4% (62/92). Clinical trial registration was not mentioned by 28 (30%), recommended by 27 (29%), and required by 37 journals (40%). Conclusion Our findings indicate that urology journals inconsistently endorse reporting guidelines and clinical trial registration. Based on these results, we propose that urology journals adopt a standardized approach, incorporating explicit requirements for reporting guidelines such as those listed on the EQUATOR Network and clinical trial registrat…
format: application/pdf
format: text/html
creator: Alex Hagood
creator: Joseph Case
creator: Trevor Magee
creator: Caleb Smith
creator: Danya Nees
creator: Griffin Hughes
creator: Matt Vassar
subject: Urology
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.18619
publisher: PeerJ Inc.
rights: © 2024 Hagood et al.
abstract: Introduction Over the years, funding for urologic diseases has witnessed a steady rise, reaching $587 million in 2020 from $541 million in 2018. In parallel, there has been a notable increase in the total number of urology journals from 2011 to 2018. This surge in research funding and journal publications calls for urologists to effectively navigate through a vast body of evidence to make the best evidence-based clinical decisions. Our primary objective was to assess the “instructions for authors” of these journals to determine the extent of endorsement of reporting guidelines for common study designs in medical research. Methods Top urology journals were identified using the 2021 Scopus CiteScore and confirmed via Google Scholar Metrics h5-index. In a masked, duplicate manner, two investigators retrieved data from the “instructions for authors” webpages of the included journals. For each journal investigated in our study, the following data were extracted: journal title, 5-year impact factor, email responses of journal editors, mention of the EQUATOR Network in the “instructions for authors,” mention of the ICMJE in the “instruction for authors,” geographical region of publication and statements about clinical trial registration. Results Of the 92 urology journals examined, only one-third (32/92) mentioned the EQUATOR network in their “instructions for authors.” A total of 17 journals (17/92, 18.5%) did not mention a single reporting guideline. The most endorsed guideline was CONSORT at 67.4% (62/92). Clinical trial registration was not mentioned by 28 (30%), recommended by 27 (29%), and required by 37 journals (40%). Conclusion Our findings indicate that urology journals inconsistently endorse reporting guidelines and clinical trial registration. Based on these results, we propose that urology journals adopt a standardized approach, incorporating explicit requirements for reporting guidelines such as those listed on the EQUATOR Network and clinical trial registrat…
bibliographic citation: Hagood et al. (2024) Endorsement of reporting guidelines and clinical trial registration across urological medical journals: a cross-sectional study. PeerJ 12:e18619 https://doi.org/10.7717/peerj.18619
date submitted: 2024-01-10
date accepted: 2024-11-11
issued: 2024-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hagood
  given name: Alex
author list: Agent
  family name: Case
  given name: Joseph
author list: Agent
  family name: Magee
  given name: Trevor
author list: Agent
  family name: Smith
  given name: Caleb
author list: Agent
  family name: Nees
  given name: Danya
author list: Agent
  family name: Hughes
  given name: Griffin
author list: Agent
  family name: Vassar
  given name: Matt
doi: 10.7717/peerj.18619
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-10
copyright: © 2024 Hagood et al.
attribution name: Hagood et al.

Interspecies differences in the transcriptome response of corals to acute heat stress
type: item
type: AcademicArticle
description: Rising sea surface temperatures threaten the survival of corals worldwide, with coral bleaching events becoming more commonplace. However, different coral species are known to exhibit variable levels of susceptibility to thermal stress. To elucidate genetic mechanisms that may underlie these differences, we compared the gene repertoire of four coral species, Favites colemani, Montipora digitata, Acropora digitifera, and Seriatopora caliendrum, that were previously demonstrated to have differing responses to acute thermal stress. We found that more tolerant species, like F. colemani and M. digitata, possess a greater abundance of antioxidant protein families and chaperones. Under acute thermal stress conditions, only S. caliendrum showed a significant bleaching response, which was accompanied by activation of the DNA damage response network and drastic upregulation of stress response genes (SRGs). This suggests that differences in SRG orthologs, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stability of physiological functions required to survive shifts in seawater temperature.
format: application/pdf
format: text/html
creator: Jeric Da-Anoy
creator: Niño Posadas
creator: Cecilia Conaco
subject: Genomics
subject: Marine Biology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.18627
publisher: PeerJ Inc.
rights: © 2024 Da-Anoy et al.
abstract: Rising sea surface temperatures threaten the survival of corals worldwide, with coral bleaching events becoming more commonplace. However, different coral species are known to exhibit variable levels of susceptibility to thermal stress. To elucidate genetic mechanisms that may underlie these differences, we compared the gene repertoire of four coral species, Favites colemani, Montipora digitata, Acropora digitifera, and Seriatopora caliendrum, that were previously demonstrated to have differing responses to acute thermal stress. We found that more tolerant species, like F. colemani and M. digitata, possess a greater abundance of antioxidant protein families and chaperones. Under acute thermal stress conditions, only S. caliendrum showed a significant bleaching response, which was accompanied by activation of the DNA damage response network and drastic upregulation of stress response genes (SRGs). This suggests that differences in SRG orthologs, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stability of physiological functions required to survive shifts in seawater temperature.
bibliographic citation: Da-Anoy et al. (2024) Interspecies differences in the transcriptome response of corals to acute heat stress. PeerJ 12:e18627 https://doi.org/10.7717/peerj.18627
date submitted: 2024-08-26
date accepted: 2024-11-11
issued: 2024-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Da-Anoy
  given name: Jeric
author list: Agent
  family name: Posadas
  given name: Niño
author list: Agent
  family name: Conaco
  given name: Cecilia
doi: 10.7717/peerj.18627
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-10
copyright: ©2024 Da-Anoy et al.
attribution name: Da-Anoy et al.

Construction and validation of a predictive model for the risk of malnutrition in hospitalized patients over 65 years of age with malignant tumours: a single-centre retrospective cross-sectional study
type: item
type: AcademicArticle
description: Background Nutritional status is a critical indicator of overall health in individuals suffering from malignant tumours, reflecting the complex interplay of various contributing factors. This research focused on identifying and analysing the factors influencing malnutrition among older patients aged ≥65 with malignant tumours and aimed to develop a comprehensive risk model for predicting malnutrition. Methods This study conducted a retrospective analysis of clinical data from 3,387 older inpatients aged ≥65 years with malignant tumours collected at our hospital from July 1, 2021, to December 31, 2023. The dataset was subsequently divided into training and validation sets at an 8:2 ratio. The nutritional status of these patients was evaluated using the Nutritional Risk Screening Tool 2002 (NRS-2002) and the 2018 Global Leadership Initiative on Malnutrition (GLIM) Standards for Clinical Nutrition and Metabolism. Based on these assessments, patients were categorized into either malnutrition or non-malnutrition groups. Subsequently, a risk prediction model was developed and presented through a nomogram for practical application. Results The analysis encompassed 2,715 individuals in the development cohort and 672 in the validation cohort, with a malnutrition prevalence of 40.42%. A significant positive correlation between the incidence of malnutrition and age was observed. Independent risk factors identified included systemic factors, tumour staging (TNM stage), age, Karnofsky Performance Status (KPS) score, history of alcohol consumption, co-infections, presence of ascites or pleural effusion, haemoglobin (HGB) levels, creatinine (Cr), and the neutrophil-to-lymphocyte ratio (NLR). The predictive model exhibited areas under the curve (AUC) of 0.793 (95% confidence interval (CI) [0.776–0.810]) for the development cohort and 0.832 (95% CI [0.801–0.863]) for the validation cohort. Calibration curves indicated Brier scores of 0.186 and 0.190, while the Hosmer–Lemeshow test y…
format: application/pdf
format: text/html
creator: Xuexing Wang
creator: Jie Chu
creator: Chunmei Wei
creator: Jinsong Xu
creator: Yuan He
creator: Chunmei Chen
subject: Gastroenterology and Hepatology
subject: Geriatrics
subject: Nutrition
subject: Oncology
subject: Metabolic Sciences
description: doi:10.7717/peerj.18685
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background Nutritional status is a critical indicator of overall health in individuals suffering from malignant tumours, reflecting the complex interplay of various contributing factors. This research focused on identifying and analysing the factors influencing malnutrition among older patients aged ≥65 with malignant tumours and aimed to develop a comprehensive risk model for predicting malnutrition. Methods This study conducted a retrospective analysis of clinical data from 3,387 older inpatients aged ≥65 years with malignant tumours collected at our hospital from July 1, 2021, to December 31, 2023. The dataset was subsequently divided into training and validation sets at an 8:2 ratio. The nutritional status of these patients was evaluated using the Nutritional Risk Screening Tool 2002 (NRS-2002) and the 2018 Global Leadership Initiative on Malnutrition (GLIM) Standards for Clinical Nutrition and Metabolism. Based on these assessments, patients were categorized into either malnutrition or non-malnutrition groups. Subsequently, a risk prediction model was developed and presented through a nomogram for practical application. Results The analysis encompassed 2,715 individuals in the development cohort and 672 in the validation cohort, with a malnutrition prevalence of 40.42%. A significant positive correlation between the incidence of malnutrition and age was observed. Independent risk factors identified included systemic factors, tumour staging (TNM stage), age, Karnofsky Performance Status (KPS) score, history of alcohol consumption, co-infections, presence of ascites or pleural effusion, haemoglobin (HGB) levels, creatinine (Cr), and the neutrophil-to-lymphocyte ratio (NLR). The predictive model exhibited areas under the curve (AUC) of 0.793 (95% confidence interval (CI) [0.776–0.810]) for the development cohort and 0.832 (95% CI [0.801–0.863]) for the validation cohort. Calibration curves indicated Brier scores of 0.186 and 0.190, while the Hosmer–Lemeshow test y…
bibliographic citation: Wang et al. (2024) Construction and validation of a predictive model for the risk of malnutrition in hospitalized patients over 65 years of age with malignant tumours: a single-centre retrospective cross-sectional study. PeerJ 12:e18685 https://doi.org/10.7717/peerj.18685
date submitted: 2024-06-27
date accepted: 2024-11-20
issued: 2024-12-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xuexing
author list: Agent
  family name: Chu
  given name: Jie
author list: Agent
  family name: Wei
  given name: Chunmei
author list: Agent
  family name: Xu
  given name: Jinsong
author list: Agent
  family name: He
  given name: Yuan
author list: Agent
  family name: Chen
  given name: Chunmei
doi: 10.7717/peerj.18685
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-10
copyright: © 2024 Wang et al.
attribution name: Wang et al.

Spectrum analysis of inborn errors of metabolism for expanded newborn screening in Xinjiang, China
type: item
type: AcademicArticle
description: To determine the disease spectrum and genetic characteristics of inborn errors of metabolism (IEM) in Xinjiang province in the northwest of China, 41,690 newborn babies were screening by tandem mass spectrometry from November 2018 to December 2021. Of these, 57 newborn babies were referred for genetic analysis by next-generation sequencing, which was validated by Sanger sequencing. A total of 36 newborn babies and one relative were diagnosed with IEM, and the overall positive predictive value was 29.03%. The overall incidence of IEM in Xinjiang was 1:1,158 (36/41,690). The incidence of amino acidemias, organic acidemias, and fatty acid oxidation disorder were 1:1,668 (25/41,690), 1:4,632 (9/41,690), and 1:20,845 (2/41,690), respectively. Phenylketonuria and methylmalonic acidemia were the two most common inborn errors of metabolism (IEM), accounting for 83% (30/36) of all confirmed cases. Some hotspot mutations were observed for several IEMs, including PAH gene c.158G > A (p.Arg53His) and c.688G > A (p.Val230Ile) for hyperphenylalaninemia. Four mutation types of the MMACHC gene (e.g., c.609G > A (p.Trp203Ter), c.567dupT (p.Ile190fs)) and six mutation types of the MMUT gene (e.g., c.729_730insT (p.Asp244fs)) were found for methylmalonic acidemia. We also found 11 mutations in six genes: PCCB, IVD, GCDH, MCCC1, SLC22A5, and ACADS in this region. This study combined tandem mass spectrometry and next-generation sequencing technology for the screening and diagnosis of IEM. The study provides effective clinical guidance, and the data provide a basis for expanding newborn screening, genetic screening, and IEM gene consultation in Xinjiang, China.
format: application/pdf
format: text/html
creator: Jingying Zhu
creator: Li Han
creator: Pingjingwen Yang
creator: Ziyi Feng
creator: Shuyuan Xue
subject: Pediatrics
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.18173
publisher: PeerJ Inc.
rights: © 2024 Zhu et al.
abstract: To determine the disease spectrum and genetic characteristics of inborn errors of metabolism (IEM) in Xinjiang province in the northwest of China, 41,690 newborn babies were screening by tandem mass spectrometry from November 2018 to December 2021. Of these, 57 newborn babies were referred for genetic analysis by next-generation sequencing, which was validated by Sanger sequencing. A total of 36 newborn babies and one relative were diagnosed with IEM, and the overall positive predictive value was 29.03%. The overall incidence of IEM in Xinjiang was 1:1,158 (36/41,690). The incidence of amino acidemias, organic acidemias, and fatty acid oxidation disorder were 1:1,668 (25/41,690), 1:4,632 (9/41,690), and 1:20,845 (2/41,690), respectively. Phenylketonuria and methylmalonic acidemia were the two most common inborn errors of metabolism (IEM), accounting for 83% (30/36) of all confirmed cases. Some hotspot mutations were observed for several IEMs, including PAH gene c.158G > A (p.Arg53His) and c.688G > A (p.Val230Ile) for hyperphenylalaninemia. Four mutation types of the MMACHC gene (e.g., c.609G > A (p.Trp203Ter), c.567dupT (p.Ile190fs)) and six mutation types of the MMUT gene (e.g., c.729_730insT (p.Asp244fs)) were found for methylmalonic acidemia. We also found 11 mutations in six genes: PCCB, IVD, GCDH, MCCC1, SLC22A5, and ACADS in this region. This study combined tandem mass spectrometry and next-generation sequencing technology for the screening and diagnosis of IEM. The study provides effective clinical guidance, and the data provide a basis for expanding newborn screening, genetic screening, and IEM gene consultation in Xinjiang, China.
bibliographic citation: Zhu et al. (2024) Spectrum analysis of inborn errors of metabolism for expanded newborn screening in Xinjiang, China. PeerJ 12:e18173 https://doi.org/10.7717/peerj.18173
date submitted: 2023-08-28
date accepted: 2024-09-04
issued: 2024-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Jingying
author list: Agent
  family name: Han
  given name: Li
author list: Agent
  family name: Yang
  given name: Pingjingwen
author list: Agent
  family name: Feng
  given name: Ziyi
author list: Agent
  family name: Xue
  given name: Shuyuan
doi: 10.7717/peerj.18173
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-09
copyright: © 2024 Zhu et al.
attribution name: Zhu et al.

Accuracy of augmented reality navigated surgery for placement of zygomatic implants: a human cadaver study
type: item
type: AcademicArticle
description: Purpose Placement of zygomatic implants in the most optimal prosthetic position is considered challenging due to limited bone mass of the zygoma, limited visibility, length of the drilling path and proximity to critical anatomical structures. Augmented reality (AR) navigation can eliminate some of the disadvantages of surgical guides and conventional surgical navigation, while potentially improving accuracy. In this human cadaver study, we evaluated a developed AR navigation approach for placement of zygomatic implants after total maxillectomy. Methods The developed AR navigation interface connects a commercial navigation system with the Microsoft HoloLens. AR navigated surgery was performed to place 20 zygomatic implants using five human cadaver skulls after total maxillectomy. To determine accuracy, postoperative scans were virtually matched with preoperative three-dimensional virtual surgical planning, and distances in mm from entry-exit points and angular deviations were calculated as outcome measures. Results were compared with a previously conducted study in which zygomatic implants were positioned with 3D printed surgical guides. Results The mean entry point deviation was 2.43 ± 1.33 mm and a 3D angle deviation of 5.80 ± 4.12° (range 1.39–19.16°). The mean exit point deviation was 3.28 mm (±2.17). The abutment height deviation was on average 2.20 ± 1.35 mm. The accuracy of the abutment in the occlusal plane was 4.13 ± 2.53 mm. Surgical guides perform significantly better for the entry-point (P = 0.012) and 3D angle (P = 0.05); however, there is no significant difference in accuracy for the exit-point (P = 0.143) when using 3D printed drill guides or AR navigated surgery. Conclusion Despite the higher precision of surgical guides, AR navigation demonstrated acceptable accuracy, with potential for improvement and specialized applications. The study highlights the feasibility of AR navigation for zygomatic implant placement, offering an alternative to convention…
format: application/pdf
format: text/html
creator: Sander Tabernée Heijtmeijer
creator: Haye Glas
creator: Nard Janssen
creator: Nathalie Vosselman
creator: Sebastiaan de Visscher
creator: Fred Spijkervet
creator: Gerry Raghoebar
creator: Remco de Bree
creator: Antoine Rosenberg
creator: Max Witjes
creator: Joep Kraeima
subject: Dentistry
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18468
publisher: PeerJ Inc.
rights: © 2024 Tabernée Heijtmeijer et al.
abstract: Purpose Placement of zygomatic implants in the most optimal prosthetic position is considered challenging due to limited bone mass of the zygoma, limited visibility, length of the drilling path and proximity to critical anatomical structures. Augmented reality (AR) navigation can eliminate some of the disadvantages of surgical guides and conventional surgical navigation, while potentially improving accuracy. In this human cadaver study, we evaluated a developed AR navigation approach for placement of zygomatic implants after total maxillectomy. Methods The developed AR navigation interface connects a commercial navigation system with the Microsoft HoloLens. AR navigated surgery was performed to place 20 zygomatic implants using five human cadaver skulls after total maxillectomy. To determine accuracy, postoperative scans were virtually matched with preoperative three-dimensional virtual surgical planning, and distances in mm from entry-exit points and angular deviations were calculated as outcome measures. Results were compared with a previously conducted study in which zygomatic implants were positioned with 3D printed surgical guides. Results The mean entry point deviation was 2.43 ± 1.33 mm and a 3D angle deviation of 5.80 ± 4.12° (range 1.39–19.16°). The mean exit point deviation was 3.28 mm (±2.17). The abutment height deviation was on average 2.20 ± 1.35 mm. The accuracy of the abutment in the occlusal plane was 4.13 ± 2.53 mm. Surgical guides perform significantly better for the entry-point (P = 0.012) and 3D angle (P = 0.05); however, there is no significant difference in accuracy for the exit-point (P = 0.143) when using 3D printed drill guides or AR navigated surgery. Conclusion Despite the higher precision of surgical guides, AR navigation demonstrated acceptable accuracy, with potential for improvement and specialized applications. The study highlights the feasibility of AR navigation for zygomatic implant placement, offering an alternative to convention…
bibliographic citation: Tabernée Heijtmeijer et al. (2024) Accuracy of augmented reality navigated surgery for placement of zygomatic implants: a human cadaver study. PeerJ 12:e18468 https://doi.org/10.7717/peerj.18468
date submitted: 2024-07-01
date accepted: 2024-10-15
issued: 2024-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tabernée Heijtmeijer
  given name: Sander
author list: Agent
  family name: Glas
  given name: Haye
author list: Agent
  family name: Janssen
  given name: Nard
author list: Agent
  family name: Vosselman
  given name: Nathalie
author list: Agent
  family name: de Visscher
  given name: Sebastiaan
author list: Agent
  family name: Spijkervet
  given name: Fred
author list: Agent
  family name: Raghoebar
  given name: Gerry
author list: Agent
  family name: de Bree
  given name: Remco
author list: Agent
  family name: Rosenberg
  given name: Antoine
author list: Agent
  family name: Witjes
  given name: Max
author list: Agent
  family name: Kraeima
  given name: Joep
doi: 10.7717/peerj.18468
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-09
copyright: © 2024 Tabernée Heijtmeijer et al.
attribution name: Tabernée Heijtmeijer et al.

The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment
type: item
type: AcademicArticle
description: Background Cluster of differentiation 47 (CD47), a transmembrane protein, plays a critical role in regulating cellular functions and maintaining immune homeostasis. Its expression has been shown to influence cancer prognosis. In this study, we investigated the role of CD47 in tumor progression in colon adenocarcinoma (COAD) and evaluated its potential as a target for immunotherapy. Materials and Methods We analyzed surgical samples from 96 COAD patients. Immunohistochemical analysis was performed on 90 samples, while the remaining 6 were subjected to multiplex immunofluorescence. To explore the association between CD47 expression and clinicopathological characteristics, we integrated transcriptome data from The Cancer Genome Atlas and the Gene Expression Omnibus using R software. The Tumor Immune Estimation Resource and Kaplan-Meier plotter were utilized to assess the relationship between CD47 expression, patient prognosis, and immune infiltration. Furthermore, the single-cell Tumor Immune System Interaction Database was used to examine the correlation between CD47 expression and the tumor microenvironment (TME). All included patients gave oral and written informed consent. The study was approved by the Ethics Committee of 3201 Hospital (full name: Medical Ethics Committee of 3201 Hospital). Results CD47 was found to be overexpressed in various tumors, including COAD. Higher CD47 expression was significantly associated with more advanced tumor stages, including TNM staging, T staging, and N staging (P < 0.05). A robust correlation was observed between CD47 expression and immune cell infiltration in COAD. Patients with elevated CD47 expression tended to have longer disease-free intervals, although this benefit was diminished in cases with high infiltration of M1 macrophages. The immunosuppressive function of CD47 primarily acted through the CD47/SIRPα pathway. Additionally, distinct cellular compositions and distributions were identified between primary and metastati…
format: application/pdf
format: text/html
creator: Qiu-Si Tian
creator: ChunMei Zhang
creator: Zhi-Jun Bao
creator: ZhiGang Pei
subject: Bioinformatics
subject: Cell Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.18579
publisher: PeerJ Inc.
rights: © 2024 Tian et al.
abstract: Background Cluster of differentiation 47 (CD47), a transmembrane protein, plays a critical role in regulating cellular functions and maintaining immune homeostasis. Its expression has been shown to influence cancer prognosis. In this study, we investigated the role of CD47 in tumor progression in colon adenocarcinoma (COAD) and evaluated its potential as a target for immunotherapy. Materials and Methods We analyzed surgical samples from 96 COAD patients. Immunohistochemical analysis was performed on 90 samples, while the remaining 6 were subjected to multiplex immunofluorescence. To explore the association between CD47 expression and clinicopathological characteristics, we integrated transcriptome data from The Cancer Genome Atlas and the Gene Expression Omnibus using R software. The Tumor Immune Estimation Resource and Kaplan-Meier plotter were utilized to assess the relationship between CD47 expression, patient prognosis, and immune infiltration. Furthermore, the single-cell Tumor Immune System Interaction Database was used to examine the correlation between CD47 expression and the tumor microenvironment (TME). All included patients gave oral and written informed consent. The study was approved by the Ethics Committee of 3201 Hospital (full name: Medical Ethics Committee of 3201 Hospital). Results CD47 was found to be overexpressed in various tumors, including COAD. Higher CD47 expression was significantly associated with more advanced tumor stages, including TNM staging, T staging, and N staging (P < 0.05). A robust correlation was observed between CD47 expression and immune cell infiltration in COAD. Patients with elevated CD47 expression tended to have longer disease-free intervals, although this benefit was diminished in cases with high infiltration of M1 macrophages. The immunosuppressive function of CD47 primarily acted through the CD47/SIRPα pathway. Additionally, distinct cellular compositions and distributions were identified between primary and metastati…
bibliographic citation: Tian et al. (2024) The role of CD47 in immune escape of colon cancer and its correlation with heterogeneity of tumor immune microenvironment. PeerJ 12:e18579 https://doi.org/10.7717/peerj.18579
date submitted: 2024-06-13
date accepted: 2024-11-04
issued: 2024-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tian
  given name: Qiu-Si
author list: Agent
  family name: Zhang
  given name: ChunMei
author list: Agent
  family name: Bao
  given name: Zhi-Jun
author list: Agent
  family name: Pei
  given name: ZhiGang
doi: 10.7717/peerj.18579
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-09
copyright: ©2024 Tian et al.
attribution name: Tian et al.

Observation of peri-implant bone loss rates in patients visiting dentist—A retrospective evaluation of patients of a faculty hospital for one year
type: item
type: AcademicArticle
description: Background Many studies have been published on the relationship between different parameters with marginal bone loss around implants. The results of these studies vary, but some variables such as smoking or certain systemic conditions are more likely to predispose or exacerbate the resorption around implants. The aim of this study was to determine the rates of implants with radiographically detected marginal bone loss and to determine whether there is a relationship between the severity of destruction and certain risk factors like location of implant, restoration type, systemic condition, age, sex or smoking habits. Materials and Methods Panoramic radiographs obtained for 1 year were examined. Patients with bone loss around the implant were classified according to the region of implant placement, type of restoration on implants, systemic diseases, and smoking habits. The rate of bone loss around the implants was recorded as the resorption score. Double and multiple comparison tests were applied to observe whether the resorption scores were related to the variables. Results Of 17,352 patients, 1,465 had at least one implant, and 1,116 of these had no bone loss. A total of 181 patients (863 implants) included in the study, there was a weak correlation between age (p = 0.017) and resorption rate. Implants supporting bridge restorations had higher resorption scores. Gender, age, and systemic conditions alone are not effective in increasing peri-implant bone loss (p < 0.05); therefore, placing implants in the mandible (p = 0.020) or using implants to support bridge restorations(p = 0.027) may make implants more vulnerable to resorption.
format: application/pdf
format: text/html
creator: Ilkim Karadag
creator: Halis Kurnaz
creator: Mehmet Murat Akkaya
creator: İrem Karadag
creator: Zeynep Ilayda Konukçu Kurnaz
subject: Dentistry
subject: Epidemiology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18643
publisher: PeerJ Inc.
rights: © 2024 Karadag et al.
abstract: Background Many studies have been published on the relationship between different parameters with marginal bone loss around implants. The results of these studies vary, but some variables such as smoking or certain systemic conditions are more likely to predispose or exacerbate the resorption around implants. The aim of this study was to determine the rates of implants with radiographically detected marginal bone loss and to determine whether there is a relationship between the severity of destruction and certain risk factors like location of implant, restoration type, systemic condition, age, sex or smoking habits. Materials and Methods Panoramic radiographs obtained for 1 year were examined. Patients with bone loss around the implant were classified according to the region of implant placement, type of restoration on implants, systemic diseases, and smoking habits. The rate of bone loss around the implants was recorded as the resorption score. Double and multiple comparison tests were applied to observe whether the resorption scores were related to the variables. Results Of 17,352 patients, 1,465 had at least one implant, and 1,116 of these had no bone loss. A total of 181 patients (863 implants) included in the study, there was a weak correlation between age (p = 0.017) and resorption rate. Implants supporting bridge restorations had higher resorption scores. Gender, age, and systemic conditions alone are not effective in increasing peri-implant bone loss (p < 0.05); therefore, placing implants in the mandible (p = 0.020) or using implants to support bridge restorations(p = 0.027) may make implants more vulnerable to resorption.
bibliographic citation: Karadag et al. (2024) Observation of peri-implant bone loss rates in patients visiting dentist—A retrospective evaluation of patients of a faculty hospital for one year. PeerJ 12:e18643 https://doi.org/10.7717/peerj.18643
date submitted: 2024-07-23
date accepted: 2024-11-14
issued: 2024-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karadag
  given name: Ilkim
author list: Agent
  family name: Kurnaz
  given name: Halis
author list: Agent
  family name: Akkaya
  given name: Mehmet Murat
author list: Agent
  family name: Karadag
  given name: İrem
author list: Agent
  family name: Konukçu Kurnaz
  given name: Zeynep Ilayda
doi: 10.7717/peerj.18643
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-09
copyright: © 2024 Karadag et al.
attribution name: Karadag et al.

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