PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice
items: Habitual tea consumption is associated with a lower prevalence of kidney stone disease in postmenopausal women
items: Effects of defeat and entrapment on suicide risk in university population: the role of rumination and sex
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

Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice
type: item
type: AcademicArticle
description: Context AMD3100, a CXCR4 antagonist, has beneficial effects immaculate in the treatment of acute lung injury (ALI). Objective ALI is a severe inflammatory condition associated with poor prognosis and limited treatment options. AMD3100, has therapeutic effects that reduce ALI. Our study explored the regulatory mechanisms of AMD3100 in alleviating the injury of lipopolysaccharide (LPS)-induced ALI in mice. Materials and Methods Male ICR mice were randomly divided into control, LPS-treated, AMD3100-treated, and LPS + AMD3100-treatment groups. The histological changes of lung tissues from different groups were evaluated using hematoxylin and eosin staining. Lung injury was measured by ELISA and lung wet/dry ratio. Moreover, lung tissues from the four groups were subjected to transcriptome sequencing followed by differential expression, functional enrichment, protein-protein interaction (PPI) networks, and transcription factor analyses. The validation of mRNAs and protein levels were conducted with qRT-PCR and ELISA. Results Hematoxylin and eosin staining combined with the concentration of IL-1 and IL1-β and lung wet/dry ratios revealed that AMD3100 reduced the level of LPS-induced lung injury. Analysis of the transcriptome sequencing data identified 294 differentially expressed genes in the LPS-induced ALI mouse model. Based on the PPI network and module analysis, hub targets of AMD3100, such as Cxcl10 and Cxcl9, were identified in module 1, and hub targets, such as Cxcl12 and Cxcl1, were identified in module 2. Cxcl10 and Cxcl9 are involved in the Toll-like receptor signaling pathway, and Cxcl12 and Cxcl1 arae enriched in the nuclear factor-kappa B signaling pathway. Cxcl19, Cxcl10, and Cxcl1 are targeted by transcription factors like NF-κB. The validation of mRNAs and protein levels conducted by PCR and ELISA supported our transcriptome data. Conclusions Our findings indicate that AMD3100 may exhibit a therapeutic effect on LPS-induced ALI in mice by modulating multip…
format: application/pdf
format: text/html
creator: Zhou Lv
creator: Bohan Zhang
creator: Hui Zhang
creator: Yanfei Mao
creator: Qihong Yu
creator: Wenwen Dong
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Respiratory Medicine
subject: Histology
description: doi:10.7717/peerj.18698
publisher: PeerJ Inc.
rights: © 2024 Lv et al.
abstract: Context AMD3100, a CXCR4 antagonist, has beneficial effects immaculate in the treatment of acute lung injury (ALI). Objective ALI is a severe inflammatory condition associated with poor prognosis and limited treatment options. AMD3100, has therapeutic effects that reduce ALI. Our study explored the regulatory mechanisms of AMD3100 in alleviating the injury of lipopolysaccharide (LPS)-induced ALI in mice. Materials and Methods Male ICR mice were randomly divided into control, LPS-treated, AMD3100-treated, and LPS + AMD3100-treatment groups. The histological changes of lung tissues from different groups were evaluated using hematoxylin and eosin staining. Lung injury was measured by ELISA and lung wet/dry ratio. Moreover, lung tissues from the four groups were subjected to transcriptome sequencing followed by differential expression, functional enrichment, protein-protein interaction (PPI) networks, and transcription factor analyses. The validation of mRNAs and protein levels were conducted with qRT-PCR and ELISA. Results Hematoxylin and eosin staining combined with the concentration of IL-1 and IL1-β and lung wet/dry ratios revealed that AMD3100 reduced the level of LPS-induced lung injury. Analysis of the transcriptome sequencing data identified 294 differentially expressed genes in the LPS-induced ALI mouse model. Based on the PPI network and module analysis, hub targets of AMD3100, such as Cxcl10 and Cxcl9, were identified in module 1, and hub targets, such as Cxcl12 and Cxcl1, were identified in module 2. Cxcl10 and Cxcl9 are involved in the Toll-like receptor signaling pathway, and Cxcl12 and Cxcl1 arae enriched in the nuclear factor-kappa B signaling pathway. Cxcl19, Cxcl10, and Cxcl1 are targeted by transcription factors like NF-κB. The validation of mRNAs and protein levels conducted by PCR and ELISA supported our transcriptome data. Conclusions Our findings indicate that AMD3100 may exhibit a therapeutic effect on LPS-induced ALI in mice by modulating multip…
bibliographic citation: Lv et al. (2024) Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice. PeerJ 12:e18698 https://doi.org/10.7717/peerj.18698
date submitted: 2024-04-30
date accepted: 2024-11-21
issued: 2024-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Zhou
author list: Agent
  family name: Zhang
  given name: Bohan
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Mao
  given name: Yanfei
author list: Agent
  family name: Yu
  given name: Qihong
author list: Agent
  family name: Dong
  given name: Wenwen
doi: 10.7717/peerj.18698
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-12
copyright: © 2024 Lv et al.
attribution name: Lv et al.

Habitual tea consumption is associated with a lower prevalence of kidney stone disease in postmenopausal women
type: item
type: AcademicArticle
description: Background Menopause is associated with an increased risk of kidney stone disease (KSD). However, for postmenopausal women, how to avoid KSD has rarely been studied. The aim of this study was to explore whether drinking tea is associated with a reduction in the prevalence of KSD in postmenopausal women. Methods We collected 11,484 postmenopausal women from the Taiwan Biobank, and used questionnaires to obtain information on tea drinking, KSD, and comorbidities. The participants were divided into two groups according to habitual tea consumption: tea-drinking and non-tea-drinking groups. The association between habitual tea consumption and KSD was examined by logistic regression analysis. Results There were 2,035 postmenopausal women in the tea-drinking group and 9,449 postmenopausal women in the non-tea-drinking group. The mean age of all participants was 61 years. Compared to the non-tea-drinking group, the tea-drinking group had a significantly lower prevalence of KSD (7% vs. 5%). The odds ratio (OR) of KSD was lower in those who habitually drank tea than in those who did not (OR = 0.78; 95% confidence interval [CI] [0.63 to 0.96]) after adjusting for confounders. Moreover, postmenopausal women with a daily intake of two cups of tea or more had a 30% reduced risk of KSD compared to those who did not habitually drink tea (OR = 0.71, 95% CI [0.56 to 0.90]). Conclusions Our results suggest that habitual tea drinking may be associated with a reduction in the prevalence of KSD in postmenopausal women. Further studies are warranted to investigate the protective effect of tea on the development of KSD.
format: application/pdf
format: text/html
creator: Kuan-Hsien Wu
creator: Jia-In Lee
creator: Yung-Chin Lee
creator: Jung-Tsung Shen
creator: Hsun-Shuan Wang
creator: Yao-Hsuan Tsao
creator: Yi-Hsuan Wu
creator: Shu-Pin Huang
creator: Szu-Chia Chen
creator: Jhen-Hao Jhan
creator: Jiun-Hung Geng
subject: Epidemiology
subject: Nutrition
subject: Public Health
subject: Urology
subject: Women’s Health
description: doi:10.7717/peerj.18639
publisher: PeerJ Inc.
rights: © 2024 Wu et al.
abstract: Background Menopause is associated with an increased risk of kidney stone disease (KSD). However, for postmenopausal women, how to avoid KSD has rarely been studied. The aim of this study was to explore whether drinking tea is associated with a reduction in the prevalence of KSD in postmenopausal women. Methods We collected 11,484 postmenopausal women from the Taiwan Biobank, and used questionnaires to obtain information on tea drinking, KSD, and comorbidities. The participants were divided into two groups according to habitual tea consumption: tea-drinking and non-tea-drinking groups. The association between habitual tea consumption and KSD was examined by logistic regression analysis. Results There were 2,035 postmenopausal women in the tea-drinking group and 9,449 postmenopausal women in the non-tea-drinking group. The mean age of all participants was 61 years. Compared to the non-tea-drinking group, the tea-drinking group had a significantly lower prevalence of KSD (7% vs. 5%). The odds ratio (OR) of KSD was lower in those who habitually drank tea than in those who did not (OR = 0.78; 95% confidence interval [CI] [0.63 to 0.96]) after adjusting for confounders. Moreover, postmenopausal women with a daily intake of two cups of tea or more had a 30% reduced risk of KSD compared to those who did not habitually drink tea (OR = 0.71, 95% CI [0.56 to 0.90]). Conclusions Our results suggest that habitual tea drinking may be associated with a reduction in the prevalence of KSD in postmenopausal women. Further studies are warranted to investigate the protective effect of tea on the development of KSD.
bibliographic citation: Wu et al. (2024) Habitual tea consumption is associated with a lower prevalence of kidney stone disease in postmenopausal women. PeerJ 12:e18639 https://doi.org/10.7717/peerj.18639
date submitted: 2024-07-02
date accepted: 2024-11-13
issued: 2024-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wu
  given name: Kuan-Hsien
author list: Agent
  family name: Lee
  given name: Jia-In
author list: Agent
  family name: Lee
  given name: Yung-Chin
author list: Agent
  family name: Shen
  given name: Jung-Tsung
author list: Agent
  family name: Wang
  given name: Hsun-Shuan
author list: Agent
  family name: Tsao
  given name: Yao-Hsuan
author list: Agent
  family name: Wu
  given name: Yi-Hsuan
author list: Agent
  family name: Huang
  given name: Shu-Pin
author list: Agent
  family name: Chen
  given name: Szu-Chia
author list: Agent
  family name: Jhan
  given name: Jhen-Hao
author list: Agent
  family name: Geng
  given name: Jiun-Hung
doi: 10.7717/peerj.18639
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-11
copyright: © 2024 Wu et al.
attribution name: Wu et al.

Effects of defeat and entrapment on suicide risk in university population: the role of rumination and sex
type: item
type: AcademicArticle
description: Background Suicide is recognized as a significant public health issue, with adolescents/young people being a risk group of concern. Taking the integrated motivational-volitional model as a reference, this study focuses on analyzing the association between defeat and entrapment, on the one hand, and suicide risk, on the other, in a university population without depressive symptoms, while also considering the role of rumination and sex. Method The survey study involved a community sample of 650 Spanish university students. A total of 524 students (150 men (Mage = 20.6, SD = 3.7) and 374 women (Mage = 20.4, SD = 3.6)) completed self-report measures of suicide risk, defeat, entrapment, and rumination. Results Defeat and entrapment were significantly associated with suicide risk, and higher rumination was both directly and indirectly associated with higher levels of entrapment through the variable of defeat. However, the effect of rumination on entrapment varied by sex. Conclusion Despite being a cross-sectional preliminary study, this work identifies important variables in the trajectory of suicidal ideation. Adolescence and young adulthood are a critical stage for intervening to reduce the risk of death by suicide, and this study provides findings that may inform preventive approaches.
format: application/pdf
format: text/html
creator: Inmaculada Nayara Silvestre Vidal
creator: Marta Nieto
creator: Jorge Ricarte
creator: María Dolores Vizcaíno Alcantud
creator: David Hallford
creator: Laura Ros
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.18673
publisher: PeerJ Inc.
rights: © 2024 Silvestre Vidal et al.
abstract: Background Suicide is recognized as a significant public health issue, with adolescents/young people being a risk group of concern. Taking the integrated motivational-volitional model as a reference, this study focuses on analyzing the association between defeat and entrapment, on the one hand, and suicide risk, on the other, in a university population without depressive symptoms, while also considering the role of rumination and sex. Method The survey study involved a community sample of 650 Spanish university students. A total of 524 students (150 men (Mage = 20.6, SD = 3.7) and 374 women (Mage = 20.4, SD = 3.6)) completed self-report measures of suicide risk, defeat, entrapment, and rumination. Results Defeat and entrapment were significantly associated with suicide risk, and higher rumination was both directly and indirectly associated with higher levels of entrapment through the variable of defeat. However, the effect of rumination on entrapment varied by sex. Conclusion Despite being a cross-sectional preliminary study, this work identifies important variables in the trajectory of suicidal ideation. Adolescence and young adulthood are a critical stage for intervening to reduce the risk of death by suicide, and this study provides findings that may inform preventive approaches.
bibliographic citation: Silvestre Vidal et al. (2024) Effects of defeat and entrapment on suicide risk in university population: the role of rumination and sex. PeerJ 12:e18673 https://doi.org/10.7717/peerj.18673
date submitted: 2024-05-14
date accepted: 2024-11-19
issued: 2024-12-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silvestre Vidal
  given name: Inmaculada Nayara
author list: Agent
  family name: Nieto
  given name: Marta
author list: Agent
  family name: Ricarte
  given name: Jorge
author list: Agent
  family name: Vizcaíno Alcantud
  given name: María Dolores
author list: Agent
  family name: Hallford
  given name: David
author list: Agent
  family name: Ros
  given name: Laura
doi: 10.7717/peerj.18673
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-11
copyright: © 2024 Silvestre Vidal et al.
attribution name: Silvestre Vidal et al.

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.

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