PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer
items: The status and influencing factors of abnormal fetal pregnancy outcomes in 265 cases in China: a retrospective study
items: Application of prohexadione-calcium priming affects Brassica napus L. seedlings by regulating morph-physiological characteristics under salt stress
items: Exosomes from uterine fluid promote capacitation of human sperm
items: Natrix natrix after dark: citizen science sheds light on the common grass snake’s nightlife
items: Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador
items: The role of mitophagy in the development of chronic kidney disease
items: Genome‑wide analysis of the MYB gene family in pumpkin
items: Circular RNA circMAN1A2 promotes ovarian cancer progression through the microRNA-135a-3p/IL1RAP/TAK1 pathway
items: Physical activity and sedentary behavior among school-going adolescents in low- and middle-income countries: insights from the global school-based health survey

A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer
type: item
type: AcademicArticle
description: Background Occult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer. Methods The data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach. Results Of the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949…
format: application/pdf
format: text/html
creator: Wei Han
creator: Yingshu Wang
creator: Tao Li
creator: Yuke Dong
creator: Yanwei Dang
creator: Liang He
creator: Lianfang Xu
creator: Yuhao Zhou
creator: Yujie Li
creator: Xudong Wang
subject: Oncology
subject: Otorhinolaryngology
subject: Radiology and Medical Imaging
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17254
publisher: PeerJ Inc.
rights: © 2024 Han et al.
abstract: Background Occult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer. Methods The data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach. Results Of the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949…
bibliographic citation: Han et al. (2024) A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer. PeerJ 12:e17254 https://doi.org/10.7717/peerj.17254
date submitted: 2023-11-29
date accepted: 2024-03-26
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Wei
author list: Agent
  family name: Wang
  given name: Yingshu
author list: Agent
  family name: Li
  given name: Tao
author list: Agent
  family name: Dong
  given name: Yuke
author list: Agent
  family name: Dang
  given name: Yanwei
author list: Agent
  family name: He
  given name: Liang
author list: Agent
  family name: Xu
  given name: Lianfang
author list: Agent
  family name: Zhou
  given name: Yuhao
author list: Agent
  family name: Li
  given name: Yujie
author list: Agent
  family name: Wang
  given name: Xudong
doi: 10.7717/peerj.17254
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Han et al.
attribution name: Han et al.

The status and influencing factors of abnormal fetal pregnancy outcomes in 265 cases in China: a retrospective study
type: item
type: AcademicArticle
description: Background With the advancement of prenatal diagnosis technology, the detection rate of fetal abnormalities continues to increase, imposing a significant burden on both society and families. A retrospective analysis of essential information about pregnant women, such as their pregnancy history and delivery details, is crucial for understanding the primary factors that influence pregnancy outcomes in women with fetal abnormalities. This analysis is of great significance for improving the level of pregnancy management and outcomes in pregnant women with fetal abnormalities. Objective To retrospectively analyze the pregnancy outcomes of women with fetal abnormalities and explore the factors that influence these outcomes. Methods Pregnant women’s pregnancy outcomes were collected from the medical information system and through telephone follow-ups. The chi-square test and logistic regression were used to analyze the factors influencing pregnancy outcomes. Results Among 265 pregnant women diagnosed with fetal abnormalities, 190 chose to continue the pregnancy, while 75 chose to terminate it. Pregnant women with multiple fetal abnormalities (OR = 3.774, 95% CI [1.640–8.683]) were more likely to choose termination of pregnancy (TOP), and pregnant women who were advised to terminate their pregnancy or make a careful choice were more likely to terminate the pregnancy (OR = 41.113, 95% CI [11.028–153.267]). Conclusion The number of organs involved in fetal abnormalities and treatment recommendations were identified as the primary factors influencing pregnancy outcomes. Improving awareness of maternal health care during pregnancy, early pregnancy screening technology, and a multidisciplinary diagnosis and treatment approach are of great significance in assisting pregnant women in making informed decisions and improving fetal prognosis.
format: application/pdf
format: text/html
creator: Jing Ruan
creator: Xuemei Zhong
creator: Jiaxuan Mai
creator: Cuifen Liu
creator: Huiyang Ding
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Pediatrics
subject: Healthcare Services
description: doi:10.7717/peerj.17284
publisher: PeerJ Inc.
rights: © 2024 Ruan et al.
abstract: Background With the advancement of prenatal diagnosis technology, the detection rate of fetal abnormalities continues to increase, imposing a significant burden on both society and families. A retrospective analysis of essential information about pregnant women, such as their pregnancy history and delivery details, is crucial for understanding the primary factors that influence pregnancy outcomes in women with fetal abnormalities. This analysis is of great significance for improving the level of pregnancy management and outcomes in pregnant women with fetal abnormalities. Objective To retrospectively analyze the pregnancy outcomes of women with fetal abnormalities and explore the factors that influence these outcomes. Methods Pregnant women’s pregnancy outcomes were collected from the medical information system and through telephone follow-ups. The chi-square test and logistic regression were used to analyze the factors influencing pregnancy outcomes. Results Among 265 pregnant women diagnosed with fetal abnormalities, 190 chose to continue the pregnancy, while 75 chose to terminate it. Pregnant women with multiple fetal abnormalities (OR = 3.774, 95% CI [1.640–8.683]) were more likely to choose termination of pregnancy (TOP), and pregnant women who were advised to terminate their pregnancy or make a careful choice were more likely to terminate the pregnancy (OR = 41.113, 95% CI [11.028–153.267]). Conclusion The number of organs involved in fetal abnormalities and treatment recommendations were identified as the primary factors influencing pregnancy outcomes. Improving awareness of maternal health care during pregnancy, early pregnancy screening technology, and a multidisciplinary diagnosis and treatment approach are of great significance in assisting pregnant women in making informed decisions and improving fetal prognosis.
bibliographic citation: Ruan et al. (2024) The status and influencing factors of abnormal fetal pregnancy outcomes in 265 cases in China: a retrospective study. PeerJ 12:e17284 https://doi.org/10.7717/peerj.17284
date submitted: 2023-12-28
date accepted: 2024-04-01
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruan
  given name: Jing
author list: Agent
  family name: Zhong
  given name: Xuemei
author list: Agent
  family name: Mai
  given name: Jiaxuan
author list: Agent
  family name: Liu
  given name: Cuifen
author list: Agent
  family name: Ding
  given name: Huiyang
doi: 10.7717/peerj.17284
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Ruan et al.
attribution name: Ruan et al.

Application of prohexadione-calcium priming affects Brassica napus L. seedlings by regulating morph-physiological characteristics under salt stress
type: item
type: AcademicArticle
description: Salinity stress imposes severe constraints on plant growth and development. Here, we explored the impacts of prohexadione-calcium (Pro-Ca) on rapeseed growth under salt stress. We designed a randomized block design pot experiment using two rapeseed varieties, ‘Huayouza 158R’ and ‘Huayouza 62’. We conducted six treatments, S0: non-primed + 0 mM NaCl, Pro-Ca+S0: Pro-Ca primed + 0 mM NaCl, S100: non-primed + 100 mM NaCl, Pro-Ca+S100: Pro-Ca primed + 100 mM NaCl, S150: non-primed + 150 mM NaCl, Pro-Ca+S150: Pro-Ca primed + 150 mM NaCl. The morphophysiological characteristics, and osmoregulatory and antioxidant activities were compared for primed and non-primed varieties. Our data analysis showed that salt stress induced morph-physiological traits and significantly reduced the antioxidant enzyme activities in both rapeseed varieties. The Pro-Ca primed treatment significantly improved seedlings, root, and shoot morphological traits and accumulated more dry matter biomass under salt stress. Compared to Huayouza 158R, Huayouza 62 performed better with the Pro-Ca primed treatment. The Pro-Ca primed treatment significantly enhanced chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and actual photochemical quantum efficiency (ФPSII). Furthermore, the Pro-Ca primed treatment also improved ascorbic acid (ASA) content, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and stimulated the accumulation of soluble proteins. These findings strongly suggested that the Pro-Ca primed treatment may effectively counteract the negative impacts of salinity stress by regulating the morph-physiological and antioxidant traits.
format: application/pdf
format: text/html
creator: Peng Deng
creator: Aaqil Khan
creator: Hang Zhou
creator: Xutong Lu
creator: Huiming Zhao
creator: Youwei Du
creator: Yaxin Wang
creator: Naijie Feng
creator: Dianfeng Zheng
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17312
publisher: PeerJ Inc.
rights: © 2024 Deng et al.
abstract: Salinity stress imposes severe constraints on plant growth and development. Here, we explored the impacts of prohexadione-calcium (Pro-Ca) on rapeseed growth under salt stress. We designed a randomized block design pot experiment using two rapeseed varieties, ‘Huayouza 158R’ and ‘Huayouza 62’. We conducted six treatments, S0: non-primed + 0 mM NaCl, Pro-Ca+S0: Pro-Ca primed + 0 mM NaCl, S100: non-primed + 100 mM NaCl, Pro-Ca+S100: Pro-Ca primed + 100 mM NaCl, S150: non-primed + 150 mM NaCl, Pro-Ca+S150: Pro-Ca primed + 150 mM NaCl. The morphophysiological characteristics, and osmoregulatory and antioxidant activities were compared for primed and non-primed varieties. Our data analysis showed that salt stress induced morph-physiological traits and significantly reduced the antioxidant enzyme activities in both rapeseed varieties. The Pro-Ca primed treatment significantly improved seedlings, root, and shoot morphological traits and accumulated more dry matter biomass under salt stress. Compared to Huayouza 158R, Huayouza 62 performed better with the Pro-Ca primed treatment. The Pro-Ca primed treatment significantly enhanced chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and actual photochemical quantum efficiency (ФPSII). Furthermore, the Pro-Ca primed treatment also improved ascorbic acid (ASA) content, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and stimulated the accumulation of soluble proteins. These findings strongly suggested that the Pro-Ca primed treatment may effectively counteract the negative impacts of salinity stress by regulating the morph-physiological and antioxidant traits.
bibliographic citation: Deng et al. (2024) Application of prohexadione-calcium priming affects Brassica napus L. seedlings by regulating morph-physiological characteristics under salt stress. PeerJ 12:e17312 https://doi.org/10.7717/peerj.17312
date submitted: 2023-09-25
date accepted: 2024-04-08
issued: 2024-04-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Deng
  given name: Peng
author list: Agent
  family name: Khan
  given name: Aaqil
author list: Agent
  family name: Zhou
  given name: Hang
author list: Agent
  family name: Lu
  given name: Xutong
author list: Agent
  family name: Zhao
  given name: Huiming
author list: Agent
  family name: Du
  given name: Youwei
author list: Agent
  family name: Wang
  given name: Yaxin
author list: Agent
  family name: Feng
  given name: Naijie
author list: Agent
  family name: Zheng
  given name: Dianfeng
doi: 10.7717/peerj.17312
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-26
copyright: © 2024 Deng et al.
attribution name: Deng et al.

Exosomes from uterine fluid promote capacitation of human sperm
type: item
type: AcademicArticle
description: Background Extracellular vesicles (EVs) are membrane-bound vesicles containing various proteins, lipids, and nucleic acids. EVs are found in many body fluids, such as blood and urine. The release of EVs can facilitate intercellular communication through fusion with the plasma membrane or endocytosis into the recipient cell or through internalization of the contents. Recent studies have reported that EVs isolated from human endometrial epithelial cells (EECs) promote sperm fertilization ability. EVs from uterine flushing fluid more closely resemble the physiological condition of the uterus. However, it is unclear whether EVs derived directly from uterine flushing fluid have the same effect on sperm. This study aimed to research the effect of EVs from uterine flushing fluid on sperm. Methods EVs were isolated from the uterine flushing fluid. The presence of EVs was confirmed by nanoparticle tracking analysis (NTA), Western blot, and transmission electron microscopy (TEM). EVs were incubated with human sperm for 2 h and 4 h. The effects of EVs on sperm were evaluated by analyzing acrosome reaction, sperm motility, and reactive oxygen species (ROS). Results The EVs fractions isolated from the uterine fluid were observed in cup-shaped vesicles of different sizes by TEM. All isolated vesicles contained similar numbers of vesicles in the expected size range (30–200 nm) by NTA. CD9 and CD63 were detected in EVs by western blot. Comparing the motility of the two groups incubated sperm motility significantly differed at 4 h. The acrosome reactions were promoted by incubating with EVs significantly. ROS were increased in sperm incubated with EVs. Conclusion Our results showed EVs present in the uterine fluid. Acrosome reactions and ROS levels increased in human sperm incubated with EVs. EVs from uterine fluid can promote the capacitation of human sperm. The increased capacitation after sperm interaction with EVs suggests a possible physiological effect during the transit of th…
format: application/pdf
format: text/html
creator: Renbin Deng
creator: Zhao Wu
creator: Chaoyong He
creator: Chuncheng Lu
creator: Danpeng He
creator: Xi Li
creator: Zhenling Duan
creator: Hui Zhao
subject: Cell Biology
subject: Developmental Biology
subject: Anatomy and Physiology
subject: Andrology
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.16875
publisher: PeerJ Inc.
rights: © 2024 Deng et al.
abstract: Background Extracellular vesicles (EVs) are membrane-bound vesicles containing various proteins, lipids, and nucleic acids. EVs are found in many body fluids, such as blood and urine. The release of EVs can facilitate intercellular communication through fusion with the plasma membrane or endocytosis into the recipient cell or through internalization of the contents. Recent studies have reported that EVs isolated from human endometrial epithelial cells (EECs) promote sperm fertilization ability. EVs from uterine flushing fluid more closely resemble the physiological condition of the uterus. However, it is unclear whether EVs derived directly from uterine flushing fluid have the same effect on sperm. This study aimed to research the effect of EVs from uterine flushing fluid on sperm. Methods EVs were isolated from the uterine flushing fluid. The presence of EVs was confirmed by nanoparticle tracking analysis (NTA), Western blot, and transmission electron microscopy (TEM). EVs were incubated with human sperm for 2 h and 4 h. The effects of EVs on sperm were evaluated by analyzing acrosome reaction, sperm motility, and reactive oxygen species (ROS). Results The EVs fractions isolated from the uterine fluid were observed in cup-shaped vesicles of different sizes by TEM. All isolated vesicles contained similar numbers of vesicles in the expected size range (30–200 nm) by NTA. CD9 and CD63 were detected in EVs by western blot. Comparing the motility of the two groups incubated sperm motility significantly differed at 4 h. The acrosome reactions were promoted by incubating with EVs significantly. ROS were increased in sperm incubated with EVs. Conclusion Our results showed EVs present in the uterine fluid. Acrosome reactions and ROS levels increased in human sperm incubated with EVs. EVs from uterine fluid can promote the capacitation of human sperm. The increased capacitation after sperm interaction with EVs suggests a possible physiological effect during the transit of th…
bibliographic citation: Deng et al. (2024) Exosomes from uterine fluid promote capacitation of human sperm. PeerJ 12:e16875 https://doi.org/10.7717/peerj.16875
date submitted: 2023-06-15
date accepted: 2024-01-11
issued: 2024-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Renbin
author list: Agent
  family name: Wu
  given name: Zhao
author list: Agent
  family name: He
  given name: Chaoyong
author list: Agent
  family name: Lu
  given name: Chuncheng
author list: Agent
  family name: He
  given name: Danpeng
author list: Agent
  family name: Li
  given name: Xi
author list: Agent
  family name: Duan
  given name: Zhenling
author list: Agent
  family name: Zhao
  given name: Hui
doi: 10.7717/peerj.16875
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-25
copyright: ©2024 Deng et al.
attribution name: Deng et al.

Natrix natrix after dark: citizen science sheds light on the common grass snake’s nightlife
type: item
type: AcademicArticle
description: Activity patterns in animals are often species-specific, and can be generally categorized as diurnal, crepuscular, or nocturnal. Understanding these patterns provides insight into ecological adaptations and behaviors. The common grass snake (Natrix natrix), one of the most common and widespread European snake species, is traditionally considered diurnal, with scarce evidence of its crepuscular and nocturnal activity. We aimed to document the distribution, environmental conditions, and potential phenotype associations of nighttime activity in N. natrix. We used citizen science data from iNaturalist (1992–2022), Observation.org (2012–2022), together with personal field observations (2010–2023) to collect 127 crepuscular and nocturnal activity records. Most observations occurred between May and August, coinciding with the peak activity period of grass snakes across their distribution range. Statistical analyses revealed no significant difference in mean daily temperatures between crepuscular and nocturnal observations. However, striped individuals displayed nocturnal activity at higher temperatures, consistent with their distribution in warmer regions, but failed to register any difference when tested on a geographic subsample, that accounted for sympatry of the phenotypes. Surprisingly, we found no significant impact of moon presence or moonlight on nighttime activity or age class, contrary to expectations based on other snake species’ responses. While our study reveals that nocturnal activity in the common grass snake is geographically widespread, further research is warranted to understand its drivers and ecological implications. This study highlights the value of citizen science platforms for biological and ecological research, offering unparalleled spatial and temporal coverage by their users. In conclusion, our work extends the knowledge of nocturnal behavior in N. natrix and underlines the critical role of citizen science in discovering behavioral aspects of com…
format: application/pdf
format: text/html
creator: Petronel Spaseni
creator: Tiberiu C. Sahlean
creator: Iulian Gherghel
creator: Ștefan R. Zamfirescu
creator: Ionuț C. Petreanu
creator: Raluca Melenciuc
creator: Cristina F. Alistar
creator: Viorel D. Gavril
creator: Alexandru Strugariu
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.17168
publisher: PeerJ Inc.
rights: © 2024 Spaseni et al.
abstract: Activity patterns in animals are often species-specific, and can be generally categorized as diurnal, crepuscular, or nocturnal. Understanding these patterns provides insight into ecological adaptations and behaviors. The common grass snake (Natrix natrix), one of the most common and widespread European snake species, is traditionally considered diurnal, with scarce evidence of its crepuscular and nocturnal activity. We aimed to document the distribution, environmental conditions, and potential phenotype associations of nighttime activity in N. natrix. We used citizen science data from iNaturalist (1992–2022), Observation.org (2012–2022), together with personal field observations (2010–2023) to collect 127 crepuscular and nocturnal activity records. Most observations occurred between May and August, coinciding with the peak activity period of grass snakes across their distribution range. Statistical analyses revealed no significant difference in mean daily temperatures between crepuscular and nocturnal observations. However, striped individuals displayed nocturnal activity at higher temperatures, consistent with their distribution in warmer regions, but failed to register any difference when tested on a geographic subsample, that accounted for sympatry of the phenotypes. Surprisingly, we found no significant impact of moon presence or moonlight on nighttime activity or age class, contrary to expectations based on other snake species’ responses. While our study reveals that nocturnal activity in the common grass snake is geographically widespread, further research is warranted to understand its drivers and ecological implications. This study highlights the value of citizen science platforms for biological and ecological research, offering unparalleled spatial and temporal coverage by their users. In conclusion, our work extends the knowledge of nocturnal behavior in N. natrix and underlines the critical role of citizen science in discovering behavioral aspects of com…
bibliographic citation: Spaseni et al. (2024) Natrix natrix after dark: citizen science sheds light on the common grass snake’s nightlife. PeerJ 12:e17168 https://doi.org/10.7717/peerj.17168
date submitted: 2023-11-28
date accepted: 2024-03-06
issued: 2024-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spaseni
  given name: Petronel
author list: Agent
  family name: Sahlean
  given name: Tiberiu C.
author list: Agent
  family name: Gherghel
  given name: Iulian
author list: Agent
  family name: Zamfirescu
  given name: Ștefan R.
author list: Agent
  family name: Petreanu
  given name: Ionuț C.
author list: Agent
  family name: Melenciuc
  given name: Raluca
author list: Agent
  family name: Alistar
  given name: Cristina F.
author list: Agent
  family name: Gavril
  given name: Viorel D.
author list: Agent
  family name: Strugariu
  given name: Alexandru
doi: 10.7717/peerj.17168
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-25
copyright: ©2024 Spaseni et al.
attribution name: Spaseni et al.

Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador
type: item
type: AcademicArticle
description: Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates.
format: application/pdf
format: text/html
creator: Nicole Sotomayor
creator: José Eduardo Villacis
creator: Noela Burneo
creator: Jorge Reyes
creator: Sonia Zapata
creator: Rosa de los Ángeles Bayas-Rea
subject: Microbiology
subject: Public Health
description: doi:10.7717/peerj.17199
publisher: PeerJ Inc.
rights: © 2024 Sotomayor et al.
abstract: Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates.
bibliographic citation: Sotomayor et al. (2024) Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador. PeerJ 12:e17199 https://doi.org/10.7717/peerj.17199
date submitted: 2019-02-22
date accepted: 2024-03-14
issued: 2024-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sotomayor
  given name: Nicole
author list: Agent
  family name: Villacis
  given name: José Eduardo
author list: Agent
  family name: Burneo
  given name: Noela
author list: Agent
  family name: Reyes
  given name: Jorge
author list: Agent
  family name: Zapata
  given name: Sonia
author list: Agent
  family name: Bayas-Rea
  given name: Rosa de los Ángeles
doi: 10.7717/peerj.17199
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-25
copyright: © 2024 Sotomayor et al.
attribution name: Sotomayor et al.

The role of mitophagy in the development of chronic kidney disease
type: item
type: AcademicArticle
description: Chronic kidney disease (CKD) represents a significant global health concern, with renal fibrosis emerging as a prevalent and ultimate manifestation of this condition. The absence of targeted therapies presents an ongoing and substantial challenge. Accumulating evidence suggests that the integrity and functionality of mitochondria within renal tubular epithelial cells (RTECs) often become compromised during CKD development, playing a pivotal role in the progression of renal fibrosis. Mitophagy, a specific form of autophagy, assumes responsibility for eliminating damaged mitochondria to uphold mitochondrial equilibrium. Dysregulated mitophagy not only correlates with disrupted mitochondrial dynamics but also contributes to the advancement of renal fibrosis in CKD. While numerous studies have examined mitochondrial metabolism, ROS (reactive oxygen species) production, inflammation, and apoptosis in kidney diseases, the precise pathogenic mechanisms underlying mitophagy in CKD remain elusive. The exact mechanisms through which modulating mitophagy mitigates renal fibrosis, as well as its influence on CKD progression and prognosis, have not undergone systematic investigation. The role of mitophagy in AKI has been relatively clear, but the role of mitophagy in CKD is still rare. This article presents a comprehensive review of the current state of research on regulating mitophagy as a potential treatment for CKD. The objective is to provide fresh perspectives, viable strategies, and practical insights into CKD therapy, thereby contributing to the enhancement of human living conditions and patient well-being.
format: application/pdf
format: text/html
creator: Kexin Yang
creator: Ting Li
creator: Yingpu Geng
creator: Xiangyu Zou
creator: Fujun Peng
creator: Wei Gao
subject: Cell Biology
subject: Nephrology
subject: Pathology
description: doi:10.7717/peerj.17260
publisher: PeerJ Inc.
rights: © 2024 Yang et al.
abstract: Chronic kidney disease (CKD) represents a significant global health concern, with renal fibrosis emerging as a prevalent and ultimate manifestation of this condition. The absence of targeted therapies presents an ongoing and substantial challenge. Accumulating evidence suggests that the integrity and functionality of mitochondria within renal tubular epithelial cells (RTECs) often become compromised during CKD development, playing a pivotal role in the progression of renal fibrosis. Mitophagy, a specific form of autophagy, assumes responsibility for eliminating damaged mitochondria to uphold mitochondrial equilibrium. Dysregulated mitophagy not only correlates with disrupted mitochondrial dynamics but also contributes to the advancement of renal fibrosis in CKD. While numerous studies have examined mitochondrial metabolism, ROS (reactive oxygen species) production, inflammation, and apoptosis in kidney diseases, the precise pathogenic mechanisms underlying mitophagy in CKD remain elusive. The exact mechanisms through which modulating mitophagy mitigates renal fibrosis, as well as its influence on CKD progression and prognosis, have not undergone systematic investigation. The role of mitophagy in AKI has been relatively clear, but the role of mitophagy in CKD is still rare. This article presents a comprehensive review of the current state of research on regulating mitophagy as a potential treatment for CKD. The objective is to provide fresh perspectives, viable strategies, and practical insights into CKD therapy, thereby contributing to the enhancement of human living conditions and patient well-being.
bibliographic citation: Yang et al. (2024) The role of mitophagy in the development of chronic kidney disease. PeerJ 12:e17260 https://doi.org/10.7717/peerj.17260
date submitted: 2023-10-24
date accepted: 2024-03-28
issued: 2024-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Kexin
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Geng
  given name: Yingpu
author list: Agent
  family name: Zou
  given name: Xiangyu
author list: Agent
  family name: Peng
  given name: Fujun
author list: Agent
  family name: Gao
  given name: Wei
doi: 10.7717/peerj.17260
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-25
copyright: ©2024 Yang et al.
attribution name: Yang et al.

Genome‑wide analysis of the MYB gene family in pumpkin
type: item
type: AcademicArticle
description: The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins.
format: application/pdf
format: text/html
creator: Minyan Xu
creator: Jingjing Fu
creator: Ying Ni
creator: Chenchen Zhang
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17304
publisher: PeerJ Inc.
rights: © 2024 Xu et al.
abstract: The MYB gene family exerts significant influence over various biological processes and stress responses in plants. Despite this, a comprehensive analysis of this gene family in pumpkin remains absent. In this study, the MYB genes of Cucurbita moschata were identified and clustered into 33 groups (C1-33), with members of each group being highly conserved in terms of their motif composition. Furthermore, the distribution of 175 CmoMYB genes across all 20 chromosomes was found to be non-uniform. Examination of the promoter regions of these genes revealed the presence of cis-acting elements associated with phytohormone responses and abiotic/biotic stress. Utilizing quantitative real-time polymerase chain reaction (qRT-PCR), the expression patterns of 13 selected CmoMYB genes were validated, particularly in response to exogenous phytohormone exposure and various abiotic stressors, including ABA, SA, MeJA, and drought treatments. Expression analysis in different tissues showed that CmoMYB genes are expressed at different levels in different tissues, suggesting that they are functionally divergent in regulating growth and abiotic stresses. These results provide a basis for future studies to characterize the function of the MYB gene family under abiotic stresses in pumpkins.
bibliographic citation: Xu et al. (2024) Genome‑wide analysis of the MYB gene family in pumpkin. PeerJ 12:e17304 https://doi.org/10.7717/peerj.17304
date submitted: 2023-08-25
date accepted: 2024-04-04
issued: 2024-04-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Minyan
author list: Agent
  family name: Fu
  given name: Jingjing
author list: Agent
  family name: Ni
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Chenchen
doi: 10.7717/peerj.17304
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-25
copyright: © 2024 Xu et al.
attribution name: Xu et al.

Circular RNA circMAN1A2 promotes ovarian cancer progression through the microRNA-135a-3p/IL1RAP/TAK1 pathway
type: item
type: AcademicArticle
description: Background Ovarian cancer (OC) is the most lethal malignancy in women owing to its diagnosis only at the advanced stage. Elucidation of its molecular pathogenesis may help identify new tumor markers and targets for therapy. Circular RNAs (circRNAs) are stable, conserved, and functional biomolecules that can be used as effective biomarkers for various cancers. Methods In this study, a potential circRNA related to early diagnosis of OC, circMAN1A2, was analyzed. Overexpression/knockdown of circMAN1A2 in OC cells was used to decipher its effects on cell proliferation with a Cell Counting Kit-8, 5-ethynyl-2’-deoxyuridine (EdU), cell cycle, clone formation, and wound healing assay. RNA pull-down and Dual luciferase assay were used to explain the underlying mechanism by which circMAN1A2 regulates OC cell proliferation. In vivo, the effect of circMAN1A2 in OC was evaluated using nude mouse xenograft experiments. Results CircMAN1A2 was highly expressed in OC and promoted proliferation, clone formation, and tumorigenicity of OC cells. In addition, we found that circMAN1A2 acted as a sponge for microRNA (miR)-135a-3p; miR-135a-3p directly targeted the 3’ untranslated region of interleukin 1 receptor accessory protein (IL1RAP) in OC cells, thereby regulating the phosphorylation of transforming growth factor-beta activated kinase 1 (TAK1), which resulted in promotion of OC cell growth. Conclusions CircMAN1A2 promotes OC cell proliferation by inhibiting the miR-135a-3p/IL1RAP/TAK1 axis. In conclusion, circMAN1A2 may be a biomarker for early detection of OC and a target for subsequent therapy.
format: application/pdf
format: text/html
creator: Bo Li
creator: Chuancui Hu
creator: Da Zhao
creator: Mingchao Nie
creator: Xiaoli Wang
subject: Evidence Based Medicine
subject: Oncology
description: doi:10.7717/peerj.16967
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Ovarian cancer (OC) is the most lethal malignancy in women owing to its diagnosis only at the advanced stage. Elucidation of its molecular pathogenesis may help identify new tumor markers and targets for therapy. Circular RNAs (circRNAs) are stable, conserved, and functional biomolecules that can be used as effective biomarkers for various cancers. Methods In this study, a potential circRNA related to early diagnosis of OC, circMAN1A2, was analyzed. Overexpression/knockdown of circMAN1A2 in OC cells was used to decipher its effects on cell proliferation with a Cell Counting Kit-8, 5-ethynyl-2’-deoxyuridine (EdU), cell cycle, clone formation, and wound healing assay. RNA pull-down and Dual luciferase assay were used to explain the underlying mechanism by which circMAN1A2 regulates OC cell proliferation. In vivo, the effect of circMAN1A2 in OC was evaluated using nude mouse xenograft experiments. Results CircMAN1A2 was highly expressed in OC and promoted proliferation, clone formation, and tumorigenicity of OC cells. In addition, we found that circMAN1A2 acted as a sponge for microRNA (miR)-135a-3p; miR-135a-3p directly targeted the 3’ untranslated region of interleukin 1 receptor accessory protein (IL1RAP) in OC cells, thereby regulating the phosphorylation of transforming growth factor-beta activated kinase 1 (TAK1), which resulted in promotion of OC cell growth. Conclusions CircMAN1A2 promotes OC cell proliferation by inhibiting the miR-135a-3p/IL1RAP/TAK1 axis. In conclusion, circMAN1A2 may be a biomarker for early detection of OC and a target for subsequent therapy.
bibliographic citation: Li et al. (2024) Circular RNA circMAN1A2 promotes ovarian cancer progression through the microRNA-135a-3p/IL1RAP/TAK1 pathway. PeerJ 12:e16967 https://doi.org/10.7717/peerj.16967
date submitted: 2023-04-14
date accepted: 2024-01-26
issued: 2024-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Bo
author list: Agent
  family name: Hu
  given name: Chuancui
author list: Agent
  family name: Zhao
  given name: Da
author list: Agent
  family name: Nie
  given name: Mingchao
author list: Agent
  family name: Wang
  given name: Xiaoli
doi: 10.7717/peerj.16967
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-24
copyright: ©2024 Li et al.
attribution name: Li et al.

Physical activity and sedentary behavior among school-going adolescents in low- and middle-income countries: insights from the global school-based health survey
type: item
type: AcademicArticle
description: Background The Global School Student Health Survey (GSHS) is being carried out by students in various countries across the globe to advance improved health programs for youth. However, in comparison to high-income countries, adolescents in low- and middle-income countries (LMICs) are generally at an early stage of understanding regarding physical activity (PA) and sedentary behavior (SB), often exhibiting low levels of PA and high levels of SB. Furthermore, there is limited evidence connecting PA and SB in school-going adolescents from LMICs. Purpose The objective of this review was to synthesize the available evidence regarding PA and sedentary behavior among school-going adolescents in LMICs using data from the GSHS. Method On March 18, 2023, a systematic literature search was performed across four electronic databases, namely Web of Science, PubMed, ScienceDirect, and EBSCO with n odaterestrictions. Studies were eligible if they: (1) utilization of data sourced from the Global Student-based Health Survey; (2) exploration of physical activity; (3) specific focus on adolescents; (4) conducted in low- and middle-income countries; (5) study design encompassing observational; (6) published as English journal articles. Results Among the 29 studies included in the analysis, the majority revealed elevated levels of sedentary behavior and diminished levels of PA in low- and middle-income countries. Furthermore, notable disparities in physical engagement and sedentary behavior were noted between male and female adolescents (p < 0.001). Augmented PA among teenagers was observed to correlate with higher consumption of vegetables and fruits (AOR = 1.30; 95% CI [1.13–1.50]; p < 0.001), decreased alcohol consumption, and a reduced prevalence of loneliness and depression (aOR 1.37, 95% CI [1.18–1.59]). Conclusions The results of this review affirm that in contrast to high-income countries, adolescents in low- and middle-income countries (LMICs) are in the early stages of compreh…
format: application/pdf
format: text/html
creator: Hui Li
creator: Wenyu Zhang
creator: Jin Yan
subject: Global Health
subject: Health Policy
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.17097
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background The Global School Student Health Survey (GSHS) is being carried out by students in various countries across the globe to advance improved health programs for youth. However, in comparison to high-income countries, adolescents in low- and middle-income countries (LMICs) are generally at an early stage of understanding regarding physical activity (PA) and sedentary behavior (SB), often exhibiting low levels of PA and high levels of SB. Furthermore, there is limited evidence connecting PA and SB in school-going adolescents from LMICs. Purpose The objective of this review was to synthesize the available evidence regarding PA and sedentary behavior among school-going adolescents in LMICs using data from the GSHS. Method On March 18, 2023, a systematic literature search was performed across four electronic databases, namely Web of Science, PubMed, ScienceDirect, and EBSCO with n odaterestrictions. Studies were eligible if they: (1) utilization of data sourced from the Global Student-based Health Survey; (2) exploration of physical activity; (3) specific focus on adolescents; (4) conducted in low- and middle-income countries; (5) study design encompassing observational; (6) published as English journal articles. Results Among the 29 studies included in the analysis, the majority revealed elevated levels of sedentary behavior and diminished levels of PA in low- and middle-income countries. Furthermore, notable disparities in physical engagement and sedentary behavior were noted between male and female adolescents (p < 0.001). Augmented PA among teenagers was observed to correlate with higher consumption of vegetables and fruits (AOR = 1.30; 95% CI [1.13–1.50]; p < 0.001), decreased alcohol consumption, and a reduced prevalence of loneliness and depression (aOR 1.37, 95% CI [1.18–1.59]). Conclusions The results of this review affirm that in contrast to high-income countries, adolescents in low- and middle-income countries (LMICs) are in the early stages of compreh…
bibliographic citation: Li et al. (2024) Physical activity and sedentary behavior among school-going adolescents in low- and middle-income countries: insights from the global school-based health survey. PeerJ 12:e17097 https://doi.org/10.7717/peerj.17097
date submitted: 2023-11-17
date accepted: 2024-02-21
issued: 2024-04-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Wenyu
author list: Agent
  family name: Yan
  given name: Jin
doi: 10.7717/peerj.17097
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-04-24
copyright: © 2024 Li et al.
attribution name: Li et al.

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