PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture
items: Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China
items: Karst grassland forage quality and its determinants in Guizhou Province of Southwest China
items: Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study
items: New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking
items: Autistic traits are associated with individual differences in finger tapping: an online study
items: Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers
items: Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane
items: Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India
items: Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces

Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture
type: item
type: AcademicArticle
description: Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected …
format: application/pdf
format: text/html
creator: Nolwenn Callac
creator: Carolane Giraud
creator: Viviane Boulo
creator: Nelly Wabete
creator: Dominique Pham
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15201
publisher: PeerJ Inc.
rights: © 2023 Callac et al.
abstract: Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected …
bibliographic citation: Callac et al. (2023) Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture. PeerJ 11:e15201 https://doi.org/10.7717/peerj.15201
date submitted: 2022-10-04
date accepted: 2023-03-17
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Callac
  given name: Nolwenn
author list: Agent
  family name: Giraud
  given name: Carolane
author list: Agent
  family name: Boulo
  given name: Viviane
author list: Agent
  family name: Wabete
  given name: Nelly
author list: Agent
  family name: Pham
  given name: Dominique
doi: 10.7717/peerj.15201
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Callac et al.
attribution name: Callac et al.

Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China
type: item
type: AcademicArticle
description: Background The prevalence of Helicobacter pylori (H. pylori) keeps rising while the eradication rate continues to decline due to the increasing antibiotic resistance. Regional variations of antimicrobial resistance to H. pylori have been recommended by guidelines in recent years. This study aims to investigate the antibiotic resistance rate of H. pylori and its association with infected subjects’ characteristics in Liaoning Province, an area in north China. Methods Gastric tissues from 178 H. pylori positive participants without previous antibiotic use within four weeks were collected for H. pylori culture. Antibiotic susceptibility to furazolidone (AOZ), tetracycline (TC), levofloxacin (LFX), metronidazole (MET), clarithromycin (CLA), and amoxicillin (AMX) were examined with the agar dilution method. Associations between H. pylori resistance and patient characteristics were further analysed. Results No resistance was observed in AOZ or TC. For LFX, MET, CLA, and AMX, the overall resistance rates were 41.10%, 79.14%, 71.78%, and 22.09% respectively. There were significant differences between resistance to CLA and MALToma (P = 0.021), and between resistance to MET and age (P < 0.001). Conclusions The primary resistant rates of LEX, MET, CLA, and AMX were relatively high in Liaoning. Treatment effectiveness improvement could be achieved by prior antimicrobial susceptibility tests before antibiotic prescription.
format: application/pdf
format: text/html
creator: Yanmeng Wang
creator: Yiling Li
creator: Yuehua Gong
creator: Yuzhen Dong
creator: Jing Sun
creator: Moye Chen
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.15268
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background The prevalence of Helicobacter pylori (H. pylori) keeps rising while the eradication rate continues to decline due to the increasing antibiotic resistance. Regional variations of antimicrobial resistance to H. pylori have been recommended by guidelines in recent years. This study aims to investigate the antibiotic resistance rate of H. pylori and its association with infected subjects’ characteristics in Liaoning Province, an area in north China. Methods Gastric tissues from 178 H. pylori positive participants without previous antibiotic use within four weeks were collected for H. pylori culture. Antibiotic susceptibility to furazolidone (AOZ), tetracycline (TC), levofloxacin (LFX), metronidazole (MET), clarithromycin (CLA), and amoxicillin (AMX) were examined with the agar dilution method. Associations between H. pylori resistance and patient characteristics were further analysed. Results No resistance was observed in AOZ or TC. For LFX, MET, CLA, and AMX, the overall resistance rates were 41.10%, 79.14%, 71.78%, and 22.09% respectively. There were significant differences between resistance to CLA and MALToma (P = 0.021), and between resistance to MET and age (P < 0.001). Conclusions The primary resistant rates of LEX, MET, CLA, and AMX were relatively high in Liaoning. Treatment effectiveness improvement could be achieved by prior antimicrobial susceptibility tests before antibiotic prescription.
bibliographic citation: Wang et al. (2023) Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China. PeerJ 11:e15268 https://doi.org/10.7717/peerj.15268
date submitted: 2022-12-05
date accepted: 2023-03-29
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yanmeng
author list: Agent
  family name: Li
  given name: Yiling
author list: Agent
  family name: Gong
  given name: Yuehua
author list: Agent
  family name: Dong
  given name: Yuzhen
author list: Agent
  family name: Sun
  given name: Jing
author list: Agent
  family name: Chen
  given name: Moye
doi: 10.7717/peerj.15268
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Karst grassland forage quality and its determinants in Guizhou Province of Southwest China
type: item
type: AcademicArticle
description: Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.
format: application/pdf
format: text/html
creator: Dengming He
creator: Baocheng Jin
creator: Xuechun Zhao
creator: Hua Cheng
creator: Chao Chen
creator: Huanhuan Wang
creator: Jinping Zhang
creator: Yaoyao Zhang
creator: Qin Yang
creator: Kun Liu
creator: Min Han
creator: Zhongcai Li
creator: Jing Peng
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.15323
publisher: PeerJ Inc.
rights: © 2023 He et al.
abstract: Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.
bibliographic citation: He et al. (2023) Karst grassland forage quality and its determinants in Guizhou Province of Southwest China. PeerJ 11:e15323 https://doi.org/10.7717/peerj.15323
date submitted: 2022-08-01
date accepted: 2023-04-10
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Dengming
author list: Agent
  family name: Jin
  given name: Baocheng
author list: Agent
  family name: Zhao
  given name: Xuechun
author list: Agent
  family name: Cheng
  given name: Hua
author list: Agent
  family name: Chen
  given name: Chao
author list: Agent
  family name: Wang
  given name: Huanhuan
author list: Agent
  family name: Zhang
  given name: Jinping
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Yang
  given name: Qin
author list: Agent
  family name: Liu
  given name: Kun
author list: Agent
  family name: Han
  given name: Min
author list: Agent
  family name: Li
  given name: Zhongcai
author list: Agent
  family name: Peng
  given name: Jing
doi: 10.7717/peerj.15323
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 He et al.
attribution name: He et al.

Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study
type: item
type: AcademicArticle
description: Background The role of thyroid hormones is crucial in the response to stress and critical illness, which has been reported to be closely associated with a poor prognosis in patients admitted to the intensive care unit (ICU). This study aimed to explore the relationship between thyroid hormone and prognosis in septic shock patients. Methods A total of 186 patients with septic shock were enrolled in the analytical study between December 2014 and September 2022. The baseline variables and thyroid hormone were collected. The patients were divided into survivor group and non-survivor group according to whether they died during the ICU hospitalization. Among 186 patients with septic shock, 123 (66.13%) were in the survivor group and 63 (33.87%) were in the non-survivor group. Results There were significant differences in the indictors of free triiodothyronine (FT3) (p = 0.000), triiodothyronine (T3) (p = 0.000), T3/FT3 (p = 0.000), acute physiology and chronic health evaluation II score (APACHE II) (p = 0.000), sequential organ failure assessment score (SOFA) (p = 0.000), pulse rate (p = 0.020), creatinine (p = 0.008), PaO2/FiO2 (p = 0.000), length of stay (p = 0.000) and hospitalization expenses (p = 0.000) in ICU between the two groups. FT3 [odds ratio (OR): 1.062, 95% confidence interval(CI): (0.021, 0.447), p = 0.003], T3 (OR: 0.291, 95% CI: 0.172-0.975, p = 0.037) and T3/FT3 (OR: 0.985, 95% CI:0.974-0.996, p = 0.006) were independent risk factors of the short-term prognosis of septic shock patients after adjustment. The areas under the receiver operating characteristic curves for T3 was associated with ICU mortality (AUC = 0.796, p < 0.05) and was higher than that for FT3 (AUC = 0.670, p < 0.05) and T3/FT3 (AUC = 0.712, p < 0.05). A Kaplan-Meier curve showed that patients with T3 greater than 0.48 nmol/L had a significantly higher survival rate than the patients with T3 less than 0.48 nmol/L. Conclusions The decrease in serum level of T3 in patients with septic shock…
format: application/pdf
format: text/html
creator: Caizhi Sun
creator: Lei Bao
creator: Lei Guo
creator: Jingjing Wei
creator: Yang Song
creator: Hua Shen
creator: Haidong Qin
subject: Diabetes and Endocrinology
subject: Emergency and Critical Care
subject: Metabolic Sciences
description: doi:10.7717/peerj.15335
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: Background The role of thyroid hormones is crucial in the response to stress and critical illness, which has been reported to be closely associated with a poor prognosis in patients admitted to the intensive care unit (ICU). This study aimed to explore the relationship between thyroid hormone and prognosis in septic shock patients. Methods A total of 186 patients with septic shock were enrolled in the analytical study between December 2014 and September 2022. The baseline variables and thyroid hormone were collected. The patients were divided into survivor group and non-survivor group according to whether they died during the ICU hospitalization. Among 186 patients with septic shock, 123 (66.13%) were in the survivor group and 63 (33.87%) were in the non-survivor group. Results There were significant differences in the indictors of free triiodothyronine (FT3) (p = 0.000), triiodothyronine (T3) (p = 0.000), T3/FT3 (p = 0.000), acute physiology and chronic health evaluation II score (APACHE II) (p = 0.000), sequential organ failure assessment score (SOFA) (p = 0.000), pulse rate (p = 0.020), creatinine (p = 0.008), PaO2/FiO2 (p = 0.000), length of stay (p = 0.000) and hospitalization expenses (p = 0.000) in ICU between the two groups. FT3 [odds ratio (OR): 1.062, 95% confidence interval(CI): (0.021, 0.447), p = 0.003], T3 (OR: 0.291, 95% CI: 0.172-0.975, p = 0.037) and T3/FT3 (OR: 0.985, 95% CI:0.974-0.996, p = 0.006) were independent risk factors of the short-term prognosis of septic shock patients after adjustment. The areas under the receiver operating characteristic curves for T3 was associated with ICU mortality (AUC = 0.796, p < 0.05) and was higher than that for FT3 (AUC = 0.670, p < 0.05) and T3/FT3 (AUC = 0.712, p < 0.05). A Kaplan-Meier curve showed that patients with T3 greater than 0.48 nmol/L had a significantly higher survival rate than the patients with T3 less than 0.48 nmol/L. Conclusions The decrease in serum level of T3 in patients with septic shock…
bibliographic citation: Sun et al. (2023) Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study. PeerJ 11:e15335 https://doi.org/10.7717/peerj.15335
date submitted: 2022-12-07
date accepted: 2023-04-11
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Caizhi
author list: Agent
  family name: Bao
  given name: Lei
author list: Agent
  family name: Guo
  given name: Lei
author list: Agent
  family name: Wei
  given name: Jingjing
author list: Agent
  family name: Song
  given name: Yang
author list: Agent
  family name: Shen
  given name: Hua
author list: Agent
  family name: Qin
  given name: Haidong
doi: 10.7717/peerj.15335
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: ©2023 Sun et al.
attribution name: Sun et al.

New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking
type: item
type: AcademicArticle
description: Background The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm−t, were measured. Results The maximum and minimum angles between the m. semimembranosus and the tibia (θsm−t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm−t transition was smoo…
format: application/pdf
format: text/html
creator: Fumihiro Mizuno
creator: Naoki Kohno
subject: Animal Behavior
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.15379
publisher: PeerJ Inc.
rights: © 2023 Mizuno and Kohno
abstract: Background The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm−t, were measured. Results The maximum and minimum angles between the m. semimembranosus and the tibia (θsm−t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm−t transition was smoo…
bibliographic citation: Mizuno et al. (2023) New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking. PeerJ 11:e15379 https://doi.org/10.7717/peerj.15379
date submitted: 2022-08-26
date accepted: 2023-04-18
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mizuno
  given name: Fumihiro
author list: Agent
  family name: Kohno
  given name: Naoki
doi: 10.7717/peerj.15379
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: © 2023 Mizuno and Kohno
attribution name: Mizuno and Kohno

Autistic traits are associated with individual differences in finger tapping: an online study
type: item
type: AcademicArticle
description: In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population.
format: application/pdf
format: text/html
creator: Alycia Messing
creator: Deborah Apthorp
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15406
publisher: PeerJ Inc.
rights: © 2023 Messing and Apthorp
abstract: In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population.
bibliographic citation: Messing et al. (2023) Autistic traits are associated with individual differences in finger tapping: an online study. PeerJ 11:e15406 https://doi.org/10.7717/peerj.15406
date submitted: 2022-12-16
date accepted: 2023-04-21
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Messing
  given name: Alycia
author list: Agent
  family name: Apthorp
  given name: Deborah
doi: 10.7717/peerj.15406
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: © 2023 Messing and Apthorp
attribution name: Messing and Apthorp

Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC. Methods We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan–Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01. Results After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10−5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis. Conclusion Our study suggests that the identification and incorporation of mini-driver genes in addition to k…
format: application/pdf
format: text/html
creator: Anthony Vladimir Campos Segura
creator: Mariana Belén Velásquez Sotomayor
creator: Ana Isabel Flor Gutiérrez Román
creator: César Alexander Ortiz Rojas
creator: Alexis Germán Murillo Carrasco
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.15410
publisher: PeerJ Inc.
rights: © 2023 Campos Segura et al.
abstract: Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC. Methods We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan–Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01. Results After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10−5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis. Conclusion Our study suggests that the identification and incorporation of mini-driver genes in addition to k…
bibliographic citation: Campos Segura et al. (2023) Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers. PeerJ 11:e15410 https://doi.org/10.7717/peerj.15410
date submitted: 2022-12-14
date accepted: 2023-04-23
issued: 2023-05-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campos Segura
  given name: Anthony Vladimir
author list: Agent
  family name: Velásquez Sotomayor
  given name: Mariana Belén
author list: Agent
  family name: Gutiérrez Román
  given name: Ana Isabel Flor
author list: Agent
  family name: Ortiz Rojas
  given name: César Alexander
author list: Agent
  family name: Murillo Carrasco
  given name: Alexis Germán
doi: 10.7717/peerj.15410
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-16
copyright: © 2023 Campos Segura et al.
attribution name: Campos Segura et al.

Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane
type: item
type: AcademicArticle
description: De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
format: application/pdf
format: text/html
creator: Henrique Moura Dias
creator: Andreia Prata Vieira
creator: Erika Maria de Jesus
creator: Nathalia de Setta
creator: Gesiele Barros
creator: Marie-Anne Van Sluys
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.14973
publisher: PeerJ Inc.
rights: © 2023 Moura Dias et al.
abstract: De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
bibliographic citation: Moura Dias et al. (2023) Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 11:e14973 https://doi.org/10.7717/peerj.14973
date submitted: 2022-07-14
date accepted: 2023-02-07
issued: 2023-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moura Dias
  given name: Henrique
author list: Agent
  family name: Vieira
  given name: Andreia Prata
author list: Agent
  family name: de Jesus
  given name: Erika Maria
author list: Agent
  family name: de Setta
  given name: Nathalia
author list: Agent
  family name: Barros
  given name: Gesiele
author list: Agent
  family name: Van Sluys
  given name: Marie-Anne
doi: 10.7717/peerj.14973
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-15
copyright: © 2023 Moura Dias et al.
attribution name: Moura Dias et al.

Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India
type: item
type: AcademicArticle
description: Background Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal diseases affecting an approximate 25% of the world’s population. Some common etiological factors are genetics, nutritional deficiencies, stress and immune dysfunction. There is currently no specific medication to treat the condition but RAS tends to heal by itself within a week or two. We aimed to explore about the prevalence and related risk factors of recurrent aphthous ulcers among college students aged 18–30 years who had been affected within the preceding six months prior to the study duration. Methods A questionnaire survey was conducted among 681 students from four colleges in Mangalore, Karnataka, India after obtaining the approval for the same from the respective colleges. Consenting participants returned a survey containing various questions. The collected data was then analyzed using descriptive statistics. The study was approved by the Institutional Ethics Committee. Results Of the 681 participants, 322 (47.2%) were affected with RAS in the past six months which included 131 (40.6%) males and 191 (59.3%) females. Single mouth ulcers were the most common presentation seen among the study participants (74.2%). Factors showing statistically significant association were: family history of RAS (P < 0.001), known diabetics (P < 0.001), history of smoking (P < 0.001), oral trauma (P < 0.001), history of wearing braces/dentures (P < 0.001) as well as those using toothpastes containing sodium lauryl sulphate (P < 0.001), stress and lack of sleep (P < 0.001). The most common form of medication used were topical agents (43.1%) (P < 0.001). Conclusions There was a statistically significant association between the occurrence of RAS and family history of RAS, diabetes, smoking, history of braces/dentures, oral trauma, sodium lauryl sulphate toothpastes, lack of sleep, stress, menstruation, consumption of particular foods and beverages. Further research is needed in this field to trul…
format: application/pdf
format: text/html
creator: Matthew Antony Manoj
creator: Animesh Jain
creator: Saanchia Andria Madtha
creator: Tina Mary Cherian
subject: Dermatology
subject: Epidemiology
subject: Otorhinolaryngology
subject: Public Health
description: doi:10.7717/peerj.14998
publisher: PeerJ Inc.
rights: © 2023 Manoj et al.
abstract: Background Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal diseases affecting an approximate 25% of the world’s population. Some common etiological factors are genetics, nutritional deficiencies, stress and immune dysfunction. There is currently no specific medication to treat the condition but RAS tends to heal by itself within a week or two. We aimed to explore about the prevalence and related risk factors of recurrent aphthous ulcers among college students aged 18–30 years who had been affected within the preceding six months prior to the study duration. Methods A questionnaire survey was conducted among 681 students from four colleges in Mangalore, Karnataka, India after obtaining the approval for the same from the respective colleges. Consenting participants returned a survey containing various questions. The collected data was then analyzed using descriptive statistics. The study was approved by the Institutional Ethics Committee. Results Of the 681 participants, 322 (47.2%) were affected with RAS in the past six months which included 131 (40.6%) males and 191 (59.3%) females. Single mouth ulcers were the most common presentation seen among the study participants (74.2%). Factors showing statistically significant association were: family history of RAS (P < 0.001), known diabetics (P < 0.001), history of smoking (P < 0.001), oral trauma (P < 0.001), history of wearing braces/dentures (P < 0.001) as well as those using toothpastes containing sodium lauryl sulphate (P < 0.001), stress and lack of sleep (P < 0.001). The most common form of medication used were topical agents (43.1%) (P < 0.001). Conclusions There was a statistically significant association between the occurrence of RAS and family history of RAS, diabetes, smoking, history of braces/dentures, oral trauma, sodium lauryl sulphate toothpastes, lack of sleep, stress, menstruation, consumption of particular foods and beverages. Further research is needed in this field to trul…
bibliographic citation: Manoj et al. (2023) Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India. PeerJ 11:e14998 https://doi.org/10.7717/peerj.14998
date submitted: 2022-04-27
date accepted: 2023-02-13
issued: 2023-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manoj
  given name: Matthew Antony
author list: Agent
  family name: Jain
  given name: Animesh
author list: Agent
  family name: Madtha
  given name: Saanchia Andria
author list: Agent
  family name: Cherian
  given name: Tina Mary
doi: 10.7717/peerj.14998
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-15
copyright: ©2023 Manoj et al.
attribution name: Manoj et al.

Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces
type: item
type: AcademicArticle
description: Background Antibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant’s gut. Methods A total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gentR (aac(6′)/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation. Results One hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation m…
format: application/pdf
format: text/html
creator: Tolulope Elizabeth Fadeyi
creator: Omolanke Temitope Oyedemi
creator: Olushina Olawale Awe
creator: Funmilola Ayeni
subject: Microbiology
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Pediatrics
subject: Medical Genetics
description: doi:10.7717/peerj.15015
publisher: PeerJ Inc.
rights: © 2023 Fadeyi et al.
abstract: Background Antibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant’s gut. Methods A total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gentR (aac(6′)/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation. Results One hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation m…
bibliographic citation: Fadeyi et al. (2023) Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces. PeerJ 11:e15015 https://doi.org/10.7717/peerj.15015
date submitted: 2022-09-24
date accepted: 2023-02-16
issued: 2023-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fadeyi
  given name: Tolulope Elizabeth
author list: Agent
  family name: Oyedemi
  given name: Omolanke Temitope
author list: Agent
  family name: Awe
  given name: Olushina Olawale
author list: Agent
  family name: Ayeni
  given name: Funmilola
doi: 10.7717/peerj.15015
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-15
copyright: © 2023 Fadeyi et al.
attribution name: Fadeyi et al.

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