PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bridging the gap between sustainability and profitability: unveiling the untapped potential of sea cucumber viscera
items: Beneficial effects of upgrading to His-Purkinje system pacing in patients with pacing-induced cardiomyopathy: a systematic review and meta-analysis
items: Physical activity, problematic smartphone use, and burnout among Chinese college students
items: Conservation spillover effect of UNESCO World Heritage Sites into surrounding landscapes
items: Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps
items: Molecular and phenotypic distinctions of macrophages in tolerant and susceptible to hypoxia rats
items: Dynamic analysis and control of a rice-pest system under transcritical bifurcations
items: Validation of the HeLD-14 functional oral health literacy instrument in a general population
items: Sociodemographic distributions and molecular characterization of colonized Enterococcus faecium isolates from locality hospitals in Khartoum, Sudan
items: Identification of ACHE as the hub gene targeting solasonine associated with non-small cell lung cancer (NSCLC) using integrated bioinformatics analysis

Bridging the gap between sustainability and profitability: unveiling the untapped potential of sea cucumber viscera
type: item
type: AcademicArticle
description: Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land and water pollution. However, discarded sea cucumber viscera contain various nutrients that can be used in many applications. Therefore, this review highlights the biological and economic aspects of sea cucumbers, followed by a critical discussion of the nutritional value of their internal organs and possible applications, including as functional feed additives in the aquaculture industry, sources of natural testosterone for application in sex reversal and production of monosex population, of neuroprotective agents against central nervous system disorders and of cosmetic ingredients, especially for skin whitening and anti-ageing products. The review further highlights the valorisation potential of viscera to maximize their economic potential, thus providing an enormous prospect for reusing sea cucumber waste, thereby reducing the negative impact of the sea cucumber fishery sector on the environment.
format: application/pdf
format: text/html
creator: Muhammad Fatratullah Muhsin
creator: Yushinta Fujaya
creator: Andi Aliah Hidayani
creator: Hanafiah Fazhan
creator: Wan Adibah Wan Mahari
creator: Su Shiung Lam
creator: Alexander Chong Shu-Chien
creator: Youji Wang
creator: Nor Afiqah-Aleng
creator: Nita Rukminasari
creator: Khor Waiho
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.16252
publisher: PeerJ Inc.
rights: © 2023 Muhsin et al.
abstract: Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land and water pollution. However, discarded sea cucumber viscera contain various nutrients that can be used in many applications. Therefore, this review highlights the biological and economic aspects of sea cucumbers, followed by a critical discussion of the nutritional value of their internal organs and possible applications, including as functional feed additives in the aquaculture industry, sources of natural testosterone for application in sex reversal and production of monosex population, of neuroprotective agents against central nervous system disorders and of cosmetic ingredients, especially for skin whitening and anti-ageing products. The review further highlights the valorisation potential of viscera to maximize their economic potential, thus providing an enormous prospect for reusing sea cucumber waste, thereby reducing the negative impact of the sea cucumber fishery sector on the environment.
bibliographic citation: Muhsin et al. (2023) Bridging the gap between sustainability and profitability: unveiling the untapped potential of sea cucumber viscera. PeerJ 11:e16252 https://doi.org/10.7717/peerj.16252
date submitted: 2023-05-31
date accepted: 2023-09-18
issued: 2023-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muhsin
  given name: Muhammad Fatratullah
author list: Agent
  family name: Fujaya
  given name: Yushinta
author list: Agent
  family name: Hidayani
  given name: Andi Aliah
author list: Agent
  family name: Fazhan
  given name: Hanafiah
author list: Agent
  family name: Wan Mahari
  given name: Wan Adibah
author list: Agent
  family name: Lam
  given name: Su Shiung
author list: Agent
  family name: Shu-Chien
  given name: Alexander Chong
author list: Agent
  family name: Wang
  given name: Youji
author list: Agent
  family name: Afiqah-Aleng
  given name: Nor
author list: Agent
  family name: Rukminasari
  given name: Nita
author list: Agent
  family name: Waiho
  given name: Khor
doi: 10.7717/peerj.16252
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-11
copyright: © 2023 Muhsin et al.
attribution name: Muhsin et al.

Beneficial effects of upgrading to His-Purkinje system pacing in patients with pacing-induced cardiomyopathy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background The purpose of this study was to evaluate the effectiveness of His-Purkinje system pacing (HPSP) in the management of patients with pace-induced cardiomyopathy (PICM). Methods PubMed, Embase, Web of Science, and the Cochrane Library were searched comprehensively to collect related studies published from the inception of databases to June 1, 2022. R 4.04 software, including the Metafor package, matrix package, and the Meta package, was utilized to conduct the singe-arm meta-analysis. The methodology index for non-randomized studies (MINORS) was used to assess the methodological quality of the included studies. Results A total of seven studies were included, involving 164 PICM patients. The meta-analysis showed that HPSP ameliorated the left ventricular ejection fraction (LVEF) by 13.41% (95% CI [11.21–15.61]), improved the New York Heart Association (NYHA) classification by 1.02 (95% CI [−1.41 to −0.63]), and shortened the QRS duration (QRSd) by 60.85 ms (95% CI [−63.94 to −57.75]), resulting in improved cardiac functions in PICM patients. Besides, HPSP reversed the ventricular remodeling, with a 32.46 ml (95% CI [−53.18 to −11.75]) decrease in left ventricular end systolic volume (LVESV) and a 5.93 mm (95% CI [−7.68 to −4.19]) decrease in left ventricular end-diastolic dimension (LVEDD). HPSP also showed stable electrical parameters of pacemakers, with a 0.07 V (95% CI [0.01–0.13]) increase in pacing threshold, a 0.02 mV (95% CI [−0.85 to 0.90]) increase in sensed R-wave amplitude, and a 31.12 Ω reduction in impedance (95% CI [−69.62 to 7.39]). Compared with LBBP, HBP improved LVEF by 13.28% (95% CI [−11.64 to 14.92]) vs 14.43% (95% CI [−13.01 to 15.85]), ameliorated NHYA classification by 1.18 (95% CI [−1.97 to −0.39]) vs 0.95 (95% CI [−1.33 to −0.58]), shortened QRSd by 63.16 ms (95% CI [−67.00 to −59.32]) vs 57.98 ms (95% CI [−62.52 to −53.25]), and decreased LVEDD by 4.12 mm (95% CI [−5.79 to −2.45]) vs 6.26 mm (95% CI [−62.52 to −53.25]). The electri…
format: application/pdf
format: text/html
creator: Nian Tang
creator: Xiaoxiao Chen
creator: Hongfei Li
creator: Denghong Zhang
subject: Cardiology
subject: Drugs and Devices
description: doi:10.7717/peerj.16268
publisher: PeerJ Inc.
rights: © 2023 Tang et al.
abstract: Background The purpose of this study was to evaluate the effectiveness of His-Purkinje system pacing (HPSP) in the management of patients with pace-induced cardiomyopathy (PICM). Methods PubMed, Embase, Web of Science, and the Cochrane Library were searched comprehensively to collect related studies published from the inception of databases to June 1, 2022. R 4.04 software, including the Metafor package, matrix package, and the Meta package, was utilized to conduct the singe-arm meta-analysis. The methodology index for non-randomized studies (MINORS) was used to assess the methodological quality of the included studies. Results A total of seven studies were included, involving 164 PICM patients. The meta-analysis showed that HPSP ameliorated the left ventricular ejection fraction (LVEF) by 13.41% (95% CI [11.21–15.61]), improved the New York Heart Association (NYHA) classification by 1.02 (95% CI [−1.41 to −0.63]), and shortened the QRS duration (QRSd) by 60.85 ms (95% CI [−63.94 to −57.75]), resulting in improved cardiac functions in PICM patients. Besides, HPSP reversed the ventricular remodeling, with a 32.46 ml (95% CI [−53.18 to −11.75]) decrease in left ventricular end systolic volume (LVESV) and a 5.93 mm (95% CI [−7.68 to −4.19]) decrease in left ventricular end-diastolic dimension (LVEDD). HPSP also showed stable electrical parameters of pacemakers, with a 0.07 V (95% CI [0.01–0.13]) increase in pacing threshold, a 0.02 mV (95% CI [−0.85 to 0.90]) increase in sensed R-wave amplitude, and a 31.12 Ω reduction in impedance (95% CI [−69.62 to 7.39]). Compared with LBBP, HBP improved LVEF by 13.28% (95% CI [−11.64 to 14.92]) vs 14.43% (95% CI [−13.01 to 15.85]), ameliorated NHYA classification by 1.18 (95% CI [−1.97 to −0.39]) vs 0.95 (95% CI [−1.33 to −0.58]), shortened QRSd by 63.16 ms (95% CI [−67.00 to −59.32]) vs 57.98 ms (95% CI [−62.52 to −53.25]), and decreased LVEDD by 4.12 mm (95% CI [−5.79 to −2.45]) vs 6.26 mm (95% CI [−62.52 to −53.25]). The electri…
bibliographic citation: Tang et al. (2023) Beneficial effects of upgrading to His-Purkinje system pacing in patients with pacing-induced cardiomyopathy: a systematic review and meta-analysis. PeerJ 11:e16268 https://doi.org/10.7717/peerj.16268
date submitted: 2023-06-28
date accepted: 2023-09-19
issued: 2023-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Nian
author list: Agent
  family name: Chen
  given name: Xiaoxiao
author list: Agent
  family name: Li
  given name: Hongfei
author list: Agent
  family name: Zhang
  given name: Denghong
doi: 10.7717/peerj.16268
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-11
copyright: © 2023 Tang et al.
attribution name: Tang et al.

Physical activity, problematic smartphone use, and burnout among Chinese college students
type: item
type: AcademicArticle
description: The aim of this study was to investigate the association between physical activity (PA), problematic smartphone use (PSU), and burnout, as well as to identify whether there is a mediating role for PSU. We recruited 823 college students (Mage = 18.55, SD = 0.83) from Wuhan, China, in December 2022, including 499 males and 324 females. Demographic information, the International Physical Activity Questionnaire-Short Form (IPAQ-SF), the Smartphone Addiction Scale-Short Version (SAS-SV), and the Maslach Burnout Inventory-Student Survey (MBI-SS) were used for assessments. Pearson correlation analysis showed that PA was significantly associated with PSU (r = −0.151, p < 0.001), PSU was significantly associated with burnout (r = 0.421, p < 0.001), and the association between PA and burnout was not statistically significant (r = −0.046, p > 0.05). The results of the mediation model test showed that PA could not predict burnout directly; it instead predicted burnout entirely indirectly through PSU. Furthermore, PSU mediated the predictive effect of PA on exhaustion and cynicism. In conclusion, there is no direct connection between PA levels and burnout. PA indirectly affects burnout through PSU, but does not fully apply to the three different dimensions of exhaustion, cynicism, and professional efficacy.
format: application/pdf
format: text/html
creator: Lianghao Zhu
creator: Junli Hou
creator: Bojun Zhou
creator: Xi Xiao
creator: Jingqiang Wang
creator: Wanping Jia
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Mental Health
subject: Sports Medicine
description: doi:10.7717/peerj.16270
publisher: PeerJ Inc.
rights: © 2023 Zhu et al.
abstract: The aim of this study was to investigate the association between physical activity (PA), problematic smartphone use (PSU), and burnout, as well as to identify whether there is a mediating role for PSU. We recruited 823 college students (Mage = 18.55, SD = 0.83) from Wuhan, China, in December 2022, including 499 males and 324 females. Demographic information, the International Physical Activity Questionnaire-Short Form (IPAQ-SF), the Smartphone Addiction Scale-Short Version (SAS-SV), and the Maslach Burnout Inventory-Student Survey (MBI-SS) were used for assessments. Pearson correlation analysis showed that PA was significantly associated with PSU (r = −0.151, p < 0.001), PSU was significantly associated with burnout (r = 0.421, p < 0.001), and the association between PA and burnout was not statistically significant (r = −0.046, p > 0.05). The results of the mediation model test showed that PA could not predict burnout directly; it instead predicted burnout entirely indirectly through PSU. Furthermore, PSU mediated the predictive effect of PA on exhaustion and cynicism. In conclusion, there is no direct connection between PA levels and burnout. PA indirectly affects burnout through PSU, but does not fully apply to the three different dimensions of exhaustion, cynicism, and professional efficacy.
bibliographic citation: Zhu et al. (2023) Physical activity, problematic smartphone use, and burnout among Chinese college students. PeerJ 11:e16270 https://doi.org/10.7717/peerj.16270
date submitted: 2023-06-07
date accepted: 2023-09-19
issued: 2023-10-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Lianghao
author list: Agent
  family name: Hou
  given name: Junli
author list: Agent
  family name: Zhou
  given name: Bojun
author list: Agent
  family name: Xiao
  given name: Xi
author list: Agent
  family name: Wang
  given name: Jingqiang
author list: Agent
  family name: Jia
  given name: Wanping
doi: 10.7717/peerj.16270
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-11
copyright: © 2023 Zhu et al.
attribution name: Zhu et al.

Conservation spillover effect of UNESCO World Heritage Sites into surrounding landscapes
type: item
type: AcademicArticle
description: Protected areas (PA) are one of the primary tools for conserving and protecting biodiversity, but their goals have evolved overtime beyond nature conservation to include supporting human communities within and adjacent to the PA. UNESCO World Heritage Sites (WHS) offer a unique perspective on the success of PAs as they fall under three categories, cultural, natural, and mixed heritage sites. The nature of these categories encapsulates the inclusion of human communities in the goals of the WHS. To understand the impact and relationship the WHS has with its surrounding landscape, we assessed changes in three indicators, land use and land cover (LULC), human footprint (HF), and forest landscape integrity index (FLII), across three spatial scales, 1, 10, 100 km from the WHS boundary. We found that there is a conservation spillover effect at least within 1 km of the WHS boundary. In this buffer zone, HF was low and FLII was high. FLII was lower and HF was higher at larger spatial scales. The relationship between the WHS and its surrounding landscape is one reason to support the WHS network, however, management of PAs should be more explicit about this relationship as well as relationships between individual PAs.
format: application/pdf
format: text/html
creator: Emilia B. Hyland
creator: John E. Quinn
subject: Ecology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.15858
publisher: PeerJ Inc.
rights: © 2023 Hyland and Quinn
abstract: Protected areas (PA) are one of the primary tools for conserving and protecting biodiversity, but their goals have evolved overtime beyond nature conservation to include supporting human communities within and adjacent to the PA. UNESCO World Heritage Sites (WHS) offer a unique perspective on the success of PAs as they fall under three categories, cultural, natural, and mixed heritage sites. The nature of these categories encapsulates the inclusion of human communities in the goals of the WHS. To understand the impact and relationship the WHS has with its surrounding landscape, we assessed changes in three indicators, land use and land cover (LULC), human footprint (HF), and forest landscape integrity index (FLII), across three spatial scales, 1, 10, 100 km from the WHS boundary. We found that there is a conservation spillover effect at least within 1 km of the WHS boundary. In this buffer zone, HF was low and FLII was high. FLII was lower and HF was higher at larger spatial scales. The relationship between the WHS and its surrounding landscape is one reason to support the WHS network, however, management of PAs should be more explicit about this relationship as well as relationships between individual PAs.
bibliographic citation: Hyland et al. (2023) Conservation spillover effect of UNESCO World Heritage Sites into surrounding landscapes. PeerJ 11:e15858 https://doi.org/10.7717/peerj.15858
date submitted: 2022-07-13
date accepted: 2023-07-17
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hyland
  given name: Emilia B.
author list: Agent
  family name: Quinn
  given name: John E.
doi: 10.7717/peerj.15858
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: © 2023 Hyland and Quinn
attribution name: Hyland and Quinn

Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps
type: item
type: AcademicArticle
description: Background Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method. Methods We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O–MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH–MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies. Results Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH–MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 we…
format: application/pdf
format: text/html
creator: Lucas Sire
creator: Paul Schmidt Yáñez
creator: Annie Bézier
creator: Béatrice Courtial
creator: Susan Mbedi
creator: Sarah Sparmann
creator: Laurent Larrieu
creator: Rodolphe Rougerie
creator: Christophe Bouget
creator: Michael T. Monaghan
creator: Elisabeth A. Herniou
creator: Carlos Lopez-Vaamonde
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.16022
publisher: PeerJ Inc.
rights: © 2023 Sire et al.
abstract: Background Broad-scale monitoring of arthropods is often carried out with passive traps (e.g., Malaise traps) that can collect thousands of specimens per sample. The identification of individual specimens requires time and taxonomic expertise, limiting the geographical and temporal scale of research and monitoring studies. DNA metabarcoding of bulk-sample homogenates has been found to be faster, efficient and reliable, but the destruction of samples prevents a posteriori validation of species occurrences and relative abundances. Non-destructive metabarcoding of DNA extracted from collection medium has been applied in a limited number of studies, but further tests of efficiency are required with different trap types and collection media to assess the consistency of the method. Methods We quantified the detection rate of arthropod species when applying non-destructive DNA metabarcoding with a short (127-bp) fragment of mitochondrial COI on two combinations of passive traps and collection media: (1) water with monopropylene glycol (H2O–MPG) used in window-flight traps (WFT, 53 in total); (2) ethanol with monopropylene glycol (EtOH–MPG) used in Malaise traps (MT, 27 in total). We then compared our results with those obtained for the same samples using morphological identification (for WFTs) or destructive metabarcoding of bulk homogenate (for MTs). This comparison was applied as part of a larger study of arthropod species richness in silver fir (Abies alba Mill., 1759) stands across a range of climate-induced tree dieback levels and forest management strategies. Results Of the 53 H2O-MPG samples from WFTs, 16 produced no metabarcoding results, while the remaining 37 samples yielded 77 arthropod MOTUs in total, of which none matched any of the 343 beetle species morphologically identified from the same traps. Metabarcoding of 26 EtOH–MPG samples from MTs detected more arthropod MOTUs (233) than destructive metabarcoding of homogenate (146 MOTUs, 8 orders), of which 71 we…
bibliographic citation: Sire et al. (2023) Persisting roadblocks in arthropod monitoring using non-destructive metabarcoding from collection media of passive traps. PeerJ 11:e16022 https://doi.org/10.7717/peerj.16022
date submitted: 2023-02-17
date accepted: 2023-08-11
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sire
  given name: Lucas
author list: Agent
  family name: Schmidt Yáñez
  given name: Paul
author list: Agent
  family name: Bézier
  given name: Annie
author list: Agent
  family name: Courtial
  given name: Béatrice
author list: Agent
  family name: Mbedi
  given name: Susan
author list: Agent
  family name: Sparmann
  given name: Sarah
author list: Agent
  family name: Larrieu
  given name: Laurent
author list: Agent
  family name: Rougerie
  given name: Rodolphe
author list: Agent
  family name: Bouget
  given name: Christophe
author list: Agent
  family name: Monaghan
  given name: Michael T.
author list: Agent
  family name: Herniou
  given name: Elisabeth A.
author list: Agent
  family name: Lopez-Vaamonde
  given name: Carlos
doi: 10.7717/peerj.16022
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: ©2023 Sire et al.
attribution name: Sire et al.

Molecular and phenotypic distinctions of macrophages in tolerant and susceptible to hypoxia rats
type: item
type: AcademicArticle
description: Individual hypoxia tolerance is a major influence on the course and outcome of infectious and inflammatory diseases. Macrophages, which play central roles in systemic inflammatory response and other immunity reactions, are subject to functional activation orchestrated by several transcription factors including hypoxia inducible factors (HIFs). HIF-1 expression levels and the lipopolysaccharide (LPS)-induced systemic inflammatory response severity have been shown to correlate with hypoxia tolerance. Molecular and functional features of macrophages, depending on the organisms resistance to hypoxia, can determine the severity of the course of infectious and inflammatory diseases, including the systemic inflammatory response. The purpose is the comparative molecular and functional characterization of non-activated and LPS-activated bone marrow-derived macrophages under normoxia in rats with different tolerance to oxygen deprivation. Hypoxia resistance was assessed by gasping time measurement in an 11,500 m altitude-equivalent hypobaric decompression chamber. Based on the outcome, the animals were assigned to three groups termed ‘tolerant to hypoxia’ (n = 12), ‘normal’, and ‘susceptible to hypoxia’ (n = 13). The ‘normal’ group was excluded from subsequent experiments. One month after hypoxia resistance test, the blood was collected from the tail vein to isolate monocytes. Non-activated and LPS-activated macrophage cultures were investigated by PCR, flow cytometry and Western blot methods. Gene expression patterns of non-activated cultured macrophages from tolerant and susceptible to hypoxia animals differed. We observed higher expression of VEGF and CD11b and lower expression of Tnfa, Il1b and Epas1 in non-activated cultures obtained from tolerant to hypoxia animals, whereas HIF-1α mRNA and protein expression levels were similar. LPS-activated macrophage cultures derived from susceptible to hypoxia animals expressed higher levels of Hif1a and CCR7 than the tolerant group…
format: application/pdf
format: text/html
creator: Dzhuliia Dzhalilova
creator: Anna Kosyreva
creator: Anastasiya Lokhonina
creator: Ivan Tsvetkov
creator: Polina Vishnyakova
creator: Olga Makarova
creator: Timur Fatkhudinov
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.16052
publisher: PeerJ Inc.
rights: © 2023 Dzhalilova et al.
abstract: Individual hypoxia tolerance is a major influence on the course and outcome of infectious and inflammatory diseases. Macrophages, which play central roles in systemic inflammatory response and other immunity reactions, are subject to functional activation orchestrated by several transcription factors including hypoxia inducible factors (HIFs). HIF-1 expression levels and the lipopolysaccharide (LPS)-induced systemic inflammatory response severity have been shown to correlate with hypoxia tolerance. Molecular and functional features of macrophages, depending on the organisms resistance to hypoxia, can determine the severity of the course of infectious and inflammatory diseases, including the systemic inflammatory response. The purpose is the comparative molecular and functional characterization of non-activated and LPS-activated bone marrow-derived macrophages under normoxia in rats with different tolerance to oxygen deprivation. Hypoxia resistance was assessed by gasping time measurement in an 11,500 m altitude-equivalent hypobaric decompression chamber. Based on the outcome, the animals were assigned to three groups termed ‘tolerant to hypoxia’ (n = 12), ‘normal’, and ‘susceptible to hypoxia’ (n = 13). The ‘normal’ group was excluded from subsequent experiments. One month after hypoxia resistance test, the blood was collected from the tail vein to isolate monocytes. Non-activated and LPS-activated macrophage cultures were investigated by PCR, flow cytometry and Western blot methods. Gene expression patterns of non-activated cultured macrophages from tolerant and susceptible to hypoxia animals differed. We observed higher expression of VEGF and CD11b and lower expression of Tnfa, Il1b and Epas1 in non-activated cultures obtained from tolerant to hypoxia animals, whereas HIF-1α mRNA and protein expression levels were similar. LPS-activated macrophage cultures derived from susceptible to hypoxia animals expressed higher levels of Hif1a and CCR7 than the tolerant group…
bibliographic citation: Dzhalilova et al. (2023) Molecular and phenotypic distinctions of macrophages in tolerant and susceptible to hypoxia rats. PeerJ 11:e16052 https://doi.org/10.7717/peerj.16052
date submitted: 2023-05-15
date accepted: 2023-08-16
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dzhalilova
  given name: Dzhuliia
author list: Agent
  family name: Kosyreva
  given name: Anna
author list: Agent
  family name: Lokhonina
  given name: Anastasiya
author list: Agent
  family name: Tsvetkov
  given name: Ivan
author list: Agent
  family name: Vishnyakova
  given name: Polina
author list: Agent
  family name: Makarova
  given name: Olga
author list: Agent
  family name: Fatkhudinov
  given name: Timur
doi: 10.7717/peerj.16052
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: ©2023 Dzhalilova et al.
attribution name: Dzhalilova et al.

Dynamic analysis and control of a rice-pest system under transcritical bifurcations
type: item
type: AcademicArticle
description: A decision model is developed by adopting two control techniques, combining cultural methods and pesticides in a hybrid approach. To control the adverse effects in the long term and to be able to evaluate the extensive use of pesticides on the environment and nearby ecosystems, the novel decision model assumes the use of pesticides only in an emergency situation. We, therefore, formulate a rice-pest-control model by rigorously modelling a rice-pest system and including the decision model and control techniques. The model is then extended to become an optimal control system with an objective function that minimizes the annual losses of rice by controlling insect pest infestations and simultaneously reduce the adverse impacts of pesticides on the environment and nearby ecosystems. This rice-pest-control model is verified by analysis, obtains the necessary conditions for optimality, and confirms our main results numerically. The rice-pest system is verified by stability analysis at equilibrium points and shows transcritical bifurcations indicative of acceptable thresholds for insect pests to demonstrate the pest control strategy.
format: application/pdf
format: text/html
creator: Sajib Mandal
creator: Sebastian Oberst
creator: Md. Haider Ali Biswas
creator: Md. Sirajul Islam
subject: Agricultural Science
subject: Entomology
subject: Mathematical Biology
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.16083
publisher: PeerJ Inc.
rights: © 2023 Mandal et al.
abstract: A decision model is developed by adopting two control techniques, combining cultural methods and pesticides in a hybrid approach. To control the adverse effects in the long term and to be able to evaluate the extensive use of pesticides on the environment and nearby ecosystems, the novel decision model assumes the use of pesticides only in an emergency situation. We, therefore, formulate a rice-pest-control model by rigorously modelling a rice-pest system and including the decision model and control techniques. The model is then extended to become an optimal control system with an objective function that minimizes the annual losses of rice by controlling insect pest infestations and simultaneously reduce the adverse impacts of pesticides on the environment and nearby ecosystems. This rice-pest-control model is verified by analysis, obtains the necessary conditions for optimality, and confirms our main results numerically. The rice-pest system is verified by stability analysis at equilibrium points and shows transcritical bifurcations indicative of acceptable thresholds for insect pests to demonstrate the pest control strategy.
bibliographic citation: Mandal et al. (2023) Dynamic analysis and control of a rice-pest system under transcritical bifurcations. PeerJ 11:e16083 https://doi.org/10.7717/peerj.16083
date submitted: 2022-09-26
date accepted: 2023-08-21
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mandal
  given name: Sajib
author list: Agent
  family name: Oberst
  given name: Sebastian
author list: Agent
  family name: Biswas
  given name: Md. Haider Ali
author list: Agent
  family name: Islam
  given name: Md. Sirajul
doi: 10.7717/peerj.16083
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: ©2023 Mandal et al.
attribution name: Mandal et al.

Validation of the HeLD-14 functional oral health literacy instrument in a general population
type: item
type: AcademicArticle
description: Background Oral health literacy (OHL) is recognized as an important determinant of oral outcomes. Measuring OHL with a valid and reliable instrument that accurately captures the functional nature of this construct across cultures is needed. The short version of the Health Literacy in Dentistry scale (HeLD-14) shows promise as an appropriate instrument due to its inclusion of comprehensive domains hypothesized to comprise OHL. While studies validating the instrument in several languages have occurred, the number of dimensions in the various analyses range from one to seven. Validation of the HeLD-14 in a general English-speaking population is also lacking. The purpose of this study was to explore and confirm the dimensionality of the HeLD-14 in a general US English-speaking population. Methods The psychometric properties of HeLD-14 were evaluated in a sample of 631 participants attending the Minnesota State Fair. Construct validity was assessed using exploratory factor analysis (EFA) followed by confirmatory factor analysis (CFA) on the data set split into two groups. Internal consistency reliability was assessed using the Cronbach’s alpha coefficient. Concurrent validity was established between the HeLD-14 and the Oral Health Inventory Profile (OHIP-5) using Pearson’s correlation. Results EFA found, and CFA reinforced, a unidimensional structure of the HeLD-14. Cronbach’s alpha was acceptable at 0.92. Fit assessment also supported a unidimensional structure, comparative fit index = 0.992, Tucker-Lewis index = 0.991, root mean square error of approximation = 0.065, and standardized root mean square residual = 0.074. Concurrent validity analyses showed that the HeLD-14 correlated with the OHIP-5. Conclusions The HeLD-14 is a unidimensional reliable and valid instrument for measuring the oral health literacy in the general US English-speaking adult population.
format: application/pdf
format: text/html
creator: Priscilla Flynn
creator: Aparna Ingleshwar
creator: Xing Chen
creator: Leah Feuerstahler
creator: Yvette Reibel
creator: Mike T. John
subject: Dentistry
subject: Evidence Based Medicine
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.16106
publisher: PeerJ Inc.
rights: © 2023 Flynn et al.
abstract: Background Oral health literacy (OHL) is recognized as an important determinant of oral outcomes. Measuring OHL with a valid and reliable instrument that accurately captures the functional nature of this construct across cultures is needed. The short version of the Health Literacy in Dentistry scale (HeLD-14) shows promise as an appropriate instrument due to its inclusion of comprehensive domains hypothesized to comprise OHL. While studies validating the instrument in several languages have occurred, the number of dimensions in the various analyses range from one to seven. Validation of the HeLD-14 in a general English-speaking population is also lacking. The purpose of this study was to explore and confirm the dimensionality of the HeLD-14 in a general US English-speaking population. Methods The psychometric properties of HeLD-14 were evaluated in a sample of 631 participants attending the Minnesota State Fair. Construct validity was assessed using exploratory factor analysis (EFA) followed by confirmatory factor analysis (CFA) on the data set split into two groups. Internal consistency reliability was assessed using the Cronbach’s alpha coefficient. Concurrent validity was established between the HeLD-14 and the Oral Health Inventory Profile (OHIP-5) using Pearson’s correlation. Results EFA found, and CFA reinforced, a unidimensional structure of the HeLD-14. Cronbach’s alpha was acceptable at 0.92. Fit assessment also supported a unidimensional structure, comparative fit index = 0.992, Tucker-Lewis index = 0.991, root mean square error of approximation = 0.065, and standardized root mean square residual = 0.074. Concurrent validity analyses showed that the HeLD-14 correlated with the OHIP-5. Conclusions The HeLD-14 is a unidimensional reliable and valid instrument for measuring the oral health literacy in the general US English-speaking adult population.
bibliographic citation: Flynn et al. (2023) Validation of the HeLD-14 functional oral health literacy instrument in a general population. PeerJ 11:e16106 https://doi.org/10.7717/peerj.16106
date submitted: 2023-07-05
date accepted: 2023-08-25
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flynn
  given name: Priscilla
author list: Agent
  family name: Ingleshwar
  given name: Aparna
author list: Agent
  family name: Chen
  given name: Xing
author list: Agent
  family name: Feuerstahler
  given name: Leah
author list: Agent
  family name: Reibel
  given name: Yvette
author list: Agent
  family name: John
  given name: Mike T.
doi: 10.7717/peerj.16106
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: ©2023 Flynn et al.
attribution name: Flynn et al.

Sociodemographic distributions and molecular characterization of colonized Enterococcus faecium isolates from locality hospitals in Khartoum, Sudan
type: item
type: AcademicArticle
description: Background Enterococcus faecium is an opportunistic pathogen of humans with diverse hosts, encompassing animals as well as human beings. In the past twenty years, there has been a rise in the instances of nosocomial infections that are linked to antibiotic-resistant Enterococcus faecium. The acquisition of diverse antimicrobial resistance factors has driven the global development of robust and convergent adaptive mechanisms within the healthcare environment. The presence of microorganisms in hospitalized and non-hospitalized patient populations has been significantly aided by the facilitation of various perturbations within their respective microbiomes. Objective This study aimed to determine the antimicrobial profile, demographic and clinical characteristics, along with the detection of virulence encoding genes, and to find out the clonal genetic relationship among colonized E. faecium strains. Methodology A hospital-based cross-sectional study was carried out between October 2018 and March 2020 at four Khartoum locality hospitals in Sudan. The study comprised a total of 108 strains of E. faecium isolated from patients admitted to four locality hospitals in Khartoum. A self-structured questionnaire was used to gather information on sociodemographic traits. Data were analyzed using chi-square test. In all cases, P value ≤ 0.05 with a corresponding 95% confidence interval was considered statistically significant. Moreover, enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) was utilized to assess the prevalence of clonal relationships, and the gel was analyzed using CLIQS software. Results In this study, the isolation rate of colonized E. faecium strains was 108/170 (63.5%). The colonization of E. faecium and its association with various sociodemographic and clinical features was examined. 73 (67.6%) of patients had multidrug-resistant (MDR), and 22 (20.4%) had extensively drug-resistant (XDR), 73 (67.6%) of patients engaged in self-m…
format: application/pdf
format: text/html
creator: Loai Abdelati Siddig
creator: Magdi Bayoumi
creator: Nasreldin Elhadi
subject: Biotechnology
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.16169
publisher: PeerJ Inc.
rights: © 2023 Siddig et al.
abstract: Background Enterococcus faecium is an opportunistic pathogen of humans with diverse hosts, encompassing animals as well as human beings. In the past twenty years, there has been a rise in the instances of nosocomial infections that are linked to antibiotic-resistant Enterococcus faecium. The acquisition of diverse antimicrobial resistance factors has driven the global development of robust and convergent adaptive mechanisms within the healthcare environment. The presence of microorganisms in hospitalized and non-hospitalized patient populations has been significantly aided by the facilitation of various perturbations within their respective microbiomes. Objective This study aimed to determine the antimicrobial profile, demographic and clinical characteristics, along with the detection of virulence encoding genes, and to find out the clonal genetic relationship among colonized E. faecium strains. Methodology A hospital-based cross-sectional study was carried out between October 2018 and March 2020 at four Khartoum locality hospitals in Sudan. The study comprised a total of 108 strains of E. faecium isolated from patients admitted to four locality hospitals in Khartoum. A self-structured questionnaire was used to gather information on sociodemographic traits. Data were analyzed using chi-square test. In all cases, P value ≤ 0.05 with a corresponding 95% confidence interval was considered statistically significant. Moreover, enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) was utilized to assess the prevalence of clonal relationships, and the gel was analyzed using CLIQS software. Results In this study, the isolation rate of colonized E. faecium strains was 108/170 (63.5%). The colonization of E. faecium and its association with various sociodemographic and clinical features was examined. 73 (67.6%) of patients had multidrug-resistant (MDR), and 22 (20.4%) had extensively drug-resistant (XDR), 73 (67.6%) of patients engaged in self-m…
bibliographic citation: Siddig et al. (2023) Sociodemographic distributions and molecular characterization of colonized Enterococcus faecium isolates from locality hospitals in Khartoum, Sudan. PeerJ 11:e16169 https://doi.org/10.7717/peerj.16169
date submitted: 2023-02-24
date accepted: 2023-09-03
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siddig
  given name: Loai Abdelati
author list: Agent
  family name: Bayoumi
  given name: Magdi
author list: Agent
  family name: Elhadi
  given name: Nasreldin
doi: 10.7717/peerj.16169
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: ©2023 Siddig et al.
attribution name: Siddig et al.

Identification of ACHE as the hub gene targeting solasonine associated with non-small cell lung cancer (NSCLC) using integrated bioinformatics analysis
type: item
type: AcademicArticle
description: Background Solasonine, as a major biological component of Solanum nigrum L., has demonstrated anticancer effects against several malignancies. However, little is understood regarding its biological target and mechanism in non-small cell lung cancer (NSCLC). Methods We conducted an analysis on transcriptomic data to identify differentially expressed genes (DEGs), and employed an artificial intelligence (AI) strategy to predict the target protein for solasonine. Subsequently, genetic dependency analysis and molecular docking were performed, with Acetylcholinesterase (ACHE) selected as a pivotal marker for solasonine. We then employed a range of bioinformatic approaches to explore the relationship between ACHE and solasonine. Furthermore, we investigated the impact of solasonine on A549 cells, a human lung cancer cell line. Cell inhibition of A549 cells following solasonine treatment was analyzed using the CCK8 assay. Additionally, we assessed the protein expression of ACHE, as well as markers associated with apoptosis and inflammation, using western blotting. To investigate their functions, we employed a plasmid-based ACHE overexpression system. Finally, we performed dynamics simulations to simulate the interaction mode between solasonine and ACHE. Results The results of the genetic dependency analysis revealed that ACHE could be identified as the pivotal target with the highest docking affinity. The cell experiments yielded significant findings, as evidenced by the negative regulatory effect of solasonine treatment on tumor cells, as demonstrated by the CCK8 assay. Western blotting analysis revealed that solasonine treatment resulted in the downregulation of the Bcl-2/Bax ratio and upregulation of cleaved caspase-3 protein expression levels. Moreover, we observed that ACHE overexpression promoted the expression of the Bcl-2/Bax ratio and decreased cleaved caspase-3 expression in the OE-ACHE group. Notably, solasonine treatment rescued the Bcl-2/Bax ratio and cleaved …
format: application/pdf
format: text/html
creator: Tong Liu
creator: Boke Zhang
creator: Yating Gao
creator: Xingxing Zhang
creator: Jiabing Tong
creator: Zegeng Li
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.16195
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background Solasonine, as a major biological component of Solanum nigrum L., has demonstrated anticancer effects against several malignancies. However, little is understood regarding its biological target and mechanism in non-small cell lung cancer (NSCLC). Methods We conducted an analysis on transcriptomic data to identify differentially expressed genes (DEGs), and employed an artificial intelligence (AI) strategy to predict the target protein for solasonine. Subsequently, genetic dependency analysis and molecular docking were performed, with Acetylcholinesterase (ACHE) selected as a pivotal marker for solasonine. We then employed a range of bioinformatic approaches to explore the relationship between ACHE and solasonine. Furthermore, we investigated the impact of solasonine on A549 cells, a human lung cancer cell line. Cell inhibition of A549 cells following solasonine treatment was analyzed using the CCK8 assay. Additionally, we assessed the protein expression of ACHE, as well as markers associated with apoptosis and inflammation, using western blotting. To investigate their functions, we employed a plasmid-based ACHE overexpression system. Finally, we performed dynamics simulations to simulate the interaction mode between solasonine and ACHE. Results The results of the genetic dependency analysis revealed that ACHE could be identified as the pivotal target with the highest docking affinity. The cell experiments yielded significant findings, as evidenced by the negative regulatory effect of solasonine treatment on tumor cells, as demonstrated by the CCK8 assay. Western blotting analysis revealed that solasonine treatment resulted in the downregulation of the Bcl-2/Bax ratio and upregulation of cleaved caspase-3 protein expression levels. Moreover, we observed that ACHE overexpression promoted the expression of the Bcl-2/Bax ratio and decreased cleaved caspase-3 expression in the OE-ACHE group. Notably, solasonine treatment rescued the Bcl-2/Bax ratio and cleaved …
bibliographic citation: Liu et al. (2023) Identification of ACHE as the hub gene targeting solasonine associated with non-small cell lung cancer (NSCLC) using integrated bioinformatics analysis. PeerJ 11:e16195 https://doi.org/10.7717/peerj.16195
date submitted: 2023-01-12
date accepted: 2023-09-06
issued: 2023-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Tong
author list: Agent
  family name: Zhang
  given name: Boke
author list: Agent
  family name: Gao
  given name: Yating
author list: Agent
  family name: Zhang
  given name: Xingxing
author list: Agent
  family name: Tong
  given name: Jiabing
author list: Agent
  family name: Li
  given name: Zegeng
doi: 10.7717/peerj.16195
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-10
copyright: © 2023 Liu et al.
attribution name: Liu et al.

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