PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center
items: Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration
items: In vitro and in vivo hypolipidemic properties of the aqueous extract of Spirulina platensis, cultivated in colored flasks under artificial illumination
items: Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China
items: Expression and phylogeny of multidrug resistance protein 2 and 4 in African white backed vulture (Gyps africanus)
items: Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer
items: Salivary microbial changes during the first 6 months of orthodontic treatment
items: Assessing anxiety, depression and quality of life in patients with peripheral facial palsy: a systematic review
items: Clinical significance of pretreatment prognostic nutritional index and lymphocyte-to-monocyte ratio in patients with advanced p16-negative oropharyngeal cancer—a retrospective study
items: Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil

The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center
type: item
type: AcademicArticle
description: As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue.
format: application/pdf
format: text/html
creator: Yu Guan
creator: Hongfang Wang
creator: Yinan Gong
creator: Jianping Ge
creator: Lei Bao
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.9970
publisher: PeerJ Inc.
rights: © 2020 Guan et al.
abstract: As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue.
bibliographic citation: Guan et al. (2020) The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center. PeerJ 8:e9970 https://doi.org/10.7717/peerj.9970
date submitted: 2020-01-27
date accepted: 2020-08-26
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Yu
author list: Agent
  family name: Wang
  given name: Hongfang
author list: Agent
  family name: Gong
  given name: Yinan
author list: Agent
  family name: Ge
  given name: Jianping
author list: Agent
  family name: Bao
  given name: Lei
doi: 10.7717/peerj.9970
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: ©2020 Guan et al.
attribution name: Guan et al.

Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration
type: item
type: AcademicArticle
description: Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
format: application/pdf
format: text/html
creator: Yohei Yamazaki
creator: Yuichi Sakai
creator: Juanwen Yu
creator: Sayaka Mino
creator: Tomoo Sawabe
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10260
publisher: PeerJ Inc.
rights: © 2020 Yamazaki et al.
abstract: Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
bibliographic citation: Yamazaki et al. (2020) Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration. PeerJ 8:e10260 https://doi.org/10.7717/peerj.10260
date submitted: 2020-03-30
date accepted: 2020-10-06
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamazaki
  given name: Yohei
author list: Agent
  family name: Sakai
  given name: Yuichi
author list: Agent
  family name: Yu
  given name: Juanwen
author list: Agent
  family name: Mino
  given name: Sayaka
author list: Agent
  family name: Sawabe
  given name: Tomoo
doi: 10.7717/peerj.10260
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Yamazaki et al.
attribution name: Yamazaki et al.

In vitro and in vivo hypolipidemic properties of the aqueous extract of Spirulina platensis, cultivated in colored flasks under artificial illumination
type: item
type: AcademicArticle
description: Background Spirulina is blue-green algae that grows mainly in tropical and subtropical lakes and is commonly used due to its nutritional features including high concentrations of protein, vitamins, mineral salts, carotenoids and antioxidants. This study aimed to investigate the anti-hypercholesterolemic potential of aqueous extract of Spirulina platensis cultivated in different colored flasks under artificial illumination; in vitro and in the diet induced hypercholesterolemic Swiss albino mice. Methods Spirulina platensis was cultivated in red, blue, green and colorless Erlenmeyer flasks containing Zarrouk’s medium under aerobic conditions, with incessant illumination by artificial cool white fluorescent with light intensity of 2500 lux (35 µmol photon m−2 s−1). Chlorophyll a and total carotenoid contents were estimated using colorimetric methods, fatty acids composition was determined by GC-Mass, in vitro and in vivo anti-cholesterol assays were used in assessing the anti-hypercholesterolemia potential of obtained Spirulina cells. Results The results showed that the highest cell dry weight, chlorophyl a, and carotenoid of S. platensis were observed in colorless flasks and that the lowest values were recorded with the green colored flasks. Also, the hot water extract of S. platensis obtained from colorless flasks at a concentration of 15 mg/mL after 60 min of incubation exhibited the greatest reduction of cholesterol level. Gas chromatography-mass spectrometry analysis of S. platensis methanolic extract showed 15 bioactive compounds were identified and grouped according to their chemical structures. An experimental model of hypercholesterolemic mice had been examined for impact of S. platensis individually and combined with atorvastatin drug. All S. platensis groups resulted in a remarkable decrease in plasma total cholesterol, triglycerides and low density lipoprotein; and increase in high density lipoprotein. Conclusion The present study concluded that the hot aqu…
format: application/pdf
format: text/html
creator: Mahmoud A. Al-Saman
creator: Nada M. Doleib
creator: Mohamed R. Ibrahim
creator: Mohamed Y. Nasr
creator: Ahmed A. Tayel
creator: Ragaa A. Hamouda
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.10366
publisher: PeerJ Inc.
rights: © 2020 Al-Saman et al.
abstract: Background Spirulina is blue-green algae that grows mainly in tropical and subtropical lakes and is commonly used due to its nutritional features including high concentrations of protein, vitamins, mineral salts, carotenoids and antioxidants. This study aimed to investigate the anti-hypercholesterolemic potential of aqueous extract of Spirulina platensis cultivated in different colored flasks under artificial illumination; in vitro and in the diet induced hypercholesterolemic Swiss albino mice. Methods Spirulina platensis was cultivated in red, blue, green and colorless Erlenmeyer flasks containing Zarrouk’s medium under aerobic conditions, with incessant illumination by artificial cool white fluorescent with light intensity of 2500 lux (35 µmol photon m−2 s−1). Chlorophyll a and total carotenoid contents were estimated using colorimetric methods, fatty acids composition was determined by GC-Mass, in vitro and in vivo anti-cholesterol assays were used in assessing the anti-hypercholesterolemia potential of obtained Spirulina cells. Results The results showed that the highest cell dry weight, chlorophyl a, and carotenoid of S. platensis were observed in colorless flasks and that the lowest values were recorded with the green colored flasks. Also, the hot water extract of S. platensis obtained from colorless flasks at a concentration of 15 mg/mL after 60 min of incubation exhibited the greatest reduction of cholesterol level. Gas chromatography-mass spectrometry analysis of S. platensis methanolic extract showed 15 bioactive compounds were identified and grouped according to their chemical structures. An experimental model of hypercholesterolemic mice had been examined for impact of S. platensis individually and combined with atorvastatin drug. All S. platensis groups resulted in a remarkable decrease in plasma total cholesterol, triglycerides and low density lipoprotein; and increase in high density lipoprotein. Conclusion The present study concluded that the hot aqu…
bibliographic citation: Al-Saman et al. (2020) In vitro and in vivo hypolipidemic properties of the aqueous extract of Spirulina platensis, cultivated in colored flasks under artificial illumination. PeerJ 8:e10366 https://doi.org/10.7717/peerj.10366
date submitted: 2020-05-22
date accepted: 2020-10-24
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Saman
  given name: Mahmoud A.
author list: Agent
  family name: Doleib
  given name: Nada M.
author list: Agent
  family name: Ibrahim
  given name: Mohamed R.
author list: Agent
  family name: Nasr
  given name: Mohamed Y.
author list: Agent
  family name: Tayel
  given name: Ahmed A.
author list: Agent
  family name: Hamouda
  given name: Ragaa A.
doi: 10.7717/peerj.10366
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Al-Saman et al.
attribution name: Al-Saman et al.

Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China
type: item
type: AcademicArticle
description: Background Inappropriate disposal of the plastic mulching debris could create macroplastics (MaPs) and microplastics (MiPs) pollution in agricultural soil. Methods To study the effects of farming systems on accumulation and distribution of agricultural plastic debris, research was carried out on two farming systems in Northwest China. Farming in Wutong Village (S1) is characterized by small plots and low-intensity machine tillage while farming in Shihezi (S2) is characterized by large plots and high-intensity machine tillage. In September 2017, we selected six fields in S1, three fields with 6–8 years of continuous plastic mulching (CM) as well as three fields with over 30 years of intermittent mulching (IM). In S2, we selected five cotton fields with 6, 7, 8, 15 and 18 years of continuous mulching. In both regions, MaPs and MiPs from soil surface to 30 cm depth (0–30 cm) were sampled. Results The results showed that in S1, MaPs mass in fields with 6–8 years CM (i.e., 97.4kg·ha−1) were significantly higher than in fields with 30 years IM (i.e., 53.7 kg·ha−1). MaPs in size category of 10–50 cm2 accounted for 46.9% in fields of CM and 44.5% in fields of IM of total collected MaPs number. In S2, MaPs mass ranged from 43.5 kg·ha−1 to 148 kg·ha−1. MaPs in size category of 2–10 cm2 account for 41.1% of total collected MaPs number while 0.25–2 cm2 accounted for 40.6%. MiPs in S1 were mainly detected in fields with over 30 years of intermittent mulching (up to 2,200 particles·kg−1 soil), whereas in S2 were detected in all fields (up to 900 particles·kg−1 soil). The results indicated farming systems could substantially affect the accumulation and distribution of agricultural plastic debris. Continuous plastic mulching could accumulate higher amount of MaPs than intermittent plastic mulching. High-intensity machine tillage could lead to higher fragmentation of MaPs and more severe MiPs pollution. These results suggest that agricultural plastic regulations are needed.
format: application/pdf
format: text/html
creator: Fanrong Meng
creator: Tinglu Fan
creator: Xiaomei Yang
creator: Michel Riksen
creator: Minggang Xu
creator: Violette Geissen
subject: Agricultural Science
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.10375
publisher: PeerJ Inc.
rights: © 2020 Meng et al.
abstract: Background Inappropriate disposal of the plastic mulching debris could create macroplastics (MaPs) and microplastics (MiPs) pollution in agricultural soil. Methods To study the effects of farming systems on accumulation and distribution of agricultural plastic debris, research was carried out on two farming systems in Northwest China. Farming in Wutong Village (S1) is characterized by small plots and low-intensity machine tillage while farming in Shihezi (S2) is characterized by large plots and high-intensity machine tillage. In September 2017, we selected six fields in S1, three fields with 6–8 years of continuous plastic mulching (CM) as well as three fields with over 30 years of intermittent mulching (IM). In S2, we selected five cotton fields with 6, 7, 8, 15 and 18 years of continuous mulching. In both regions, MaPs and MiPs from soil surface to 30 cm depth (0–30 cm) were sampled. Results The results showed that in S1, MaPs mass in fields with 6–8 years CM (i.e., 97.4kg·ha−1) were significantly higher than in fields with 30 years IM (i.e., 53.7 kg·ha−1). MaPs in size category of 10–50 cm2 accounted for 46.9% in fields of CM and 44.5% in fields of IM of total collected MaPs number. In S2, MaPs mass ranged from 43.5 kg·ha−1 to 148 kg·ha−1. MaPs in size category of 2–10 cm2 account for 41.1% of total collected MaPs number while 0.25–2 cm2 accounted for 40.6%. MiPs in S1 were mainly detected in fields with over 30 years of intermittent mulching (up to 2,200 particles·kg−1 soil), whereas in S2 were detected in all fields (up to 900 particles·kg−1 soil). The results indicated farming systems could substantially affect the accumulation and distribution of agricultural plastic debris. Continuous plastic mulching could accumulate higher amount of MaPs than intermittent plastic mulching. High-intensity machine tillage could lead to higher fragmentation of MaPs and more severe MiPs pollution. These results suggest that agricultural plastic regulations are needed.
bibliographic citation: Meng et al. (2020) Effects of plastic mulching on the accumulation and distribution of macro and micro plastics in soils of two farming systems in Northwest China. PeerJ 8:e10375 https://doi.org/10.7717/peerj.10375
date submitted: 2020-07-16
date accepted: 2020-10-26
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fanrong
author list: Agent
  family name: Fan
  given name: Tinglu
author list: Agent
  family name: Yang
  given name: Xiaomei
author list: Agent
  family name: Riksen
  given name: Michel
author list: Agent
  family name: Xu
  given name: Minggang
author list: Agent
  family name: Geissen
  given name: Violette
doi: 10.7717/peerj.10375
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Meng et al.
attribution name: Meng et al.

Expression and phylogeny of multidrug resistance protein 2 and 4 in African white backed vulture (Gyps africanus)
type: item
type: AcademicArticle
description: Diclofenac toxicity in old world vultures is well described in the literature by both the severity of the toxicity induced and the speed of death. While the mechanism of toxicity remains unknown at present, the necropsy signs of gout suggests primary renal involvement at the level of the uric acid excretory pathways. From information in the chicken and man, uric acid excretion is known to be a complex process that involves a combination of glomerular filtration and active tubular excretion. For the proximal convoluted tubules excretion occurs as a two-step process with the basolateral cell membrane using the organic anion transporters and the apical membrane using the multidrug resistant protein to transport uric acid from the blood into the tubular fluid. With uric acid excretion seemingly inhibited by diclofenac, it becomes important to characterize these transporter mechanism at the species level. With no information being available on the molecular characterization/expression of MRPs of Gyps africanus, for this study we used next generation sequencing, and Sanger sequencing on the renal tissue of African white backed vulture (AWB), as the first step to establish if the MRPs gene are expressed in AWB. In silico analysis was conducted using different software to ascertain the function of the latter genes. The sequencing results revealed that the MRP2 and MRP4 are expressed in AWB vultures. Phylogeny of avian MRPs genes confirms that vultures and eagles are closely related, which could be attributed to having the same ancestral genes and foraging behavior. In silico analysis confirmed the transcribed proteins would transports anionic compounds and glucose.
format: application/pdf
format: text/html
creator: Bono Nethathe
creator: Aron Abera
creator: Vinny Naidoo
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10422
publisher: PeerJ Inc.
rights: © 2020 Nethathe et al.
abstract: Diclofenac toxicity in old world vultures is well described in the literature by both the severity of the toxicity induced and the speed of death. While the mechanism of toxicity remains unknown at present, the necropsy signs of gout suggests primary renal involvement at the level of the uric acid excretory pathways. From information in the chicken and man, uric acid excretion is known to be a complex process that involves a combination of glomerular filtration and active tubular excretion. For the proximal convoluted tubules excretion occurs as a two-step process with the basolateral cell membrane using the organic anion transporters and the apical membrane using the multidrug resistant protein to transport uric acid from the blood into the tubular fluid. With uric acid excretion seemingly inhibited by diclofenac, it becomes important to characterize these transporter mechanism at the species level. With no information being available on the molecular characterization/expression of MRPs of Gyps africanus, for this study we used next generation sequencing, and Sanger sequencing on the renal tissue of African white backed vulture (AWB), as the first step to establish if the MRPs gene are expressed in AWB. In silico analysis was conducted using different software to ascertain the function of the latter genes. The sequencing results revealed that the MRP2 and MRP4 are expressed in AWB vultures. Phylogeny of avian MRPs genes confirms that vultures and eagles are closely related, which could be attributed to having the same ancestral genes and foraging behavior. In silico analysis confirmed the transcribed proteins would transports anionic compounds and glucose.
bibliographic citation: Nethathe et al. (2020) Expression and phylogeny of multidrug resistance protein 2 and 4 in African white backed vulture (Gyps africanus). PeerJ 8:e10422 https://doi.org/10.7717/peerj.10422
date submitted: 2020-07-22
date accepted: 2020-11-02
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nethathe
  given name: Bono
author list: Agent
  family name: Abera
  given name: Aron
author list: Agent
  family name: Naidoo
  given name: Vinny
doi: 10.7717/peerj.10422
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: ©2020 Nethathe et al.
attribution name: Nethathe et al.

Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer
type: item
type: AcademicArticle
description: Background Ovarian cancer (OC) is a highly malignant disease with a poor prognosis and high recurrence rate. At present, there is no accurate strategy to predict the prognosis and recurrence of OC. The aim of this study was to identify gene-based signatures to predict OC prognosis and recurrence. Methods mRNA expression profiles and corresponding clinical information regarding OC were collected from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and LASSO analysis were performed, and Kaplan–Meier curves, time-dependent ROC curves, and nomograms were constructed using R software and GraphPad Prism7. Results We first identified several key signalling pathways that affected ovarian tumorigenesis by GSEA. We then established a nine-gene-based signature for overall survival (OS) and a five-gene-based-signature for relapse-free survival (RFS) using LASSO Cox regression analysis of the TCGA dataset and validated the prognostic value of these signatures in independent GEO datasets. We also confirmed that these signatures were independent risk factors for OS and RFS by multivariate Cox analysis. Time-dependent ROC analysis showed that the AUC values for OS and RFS were 0.640, 0.663, 0.758, and 0.891, and 0.638, 0.722, 0.813, and 0.972 at 1, 3, 5, and 10 years, respectively. The results of the nomogram analysis demonstrated that combining two signatures with the TNM staging system and tumour status yielded better predictive ability. Conclusion In conclusion, the two-gene-based signatures established in this study may serve as novel and independent prognostic indicators for OS and RFS.
format: application/pdf
format: text/html
creator: Xinnan Zhao
creator: Miao He
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.10437
publisher: PeerJ Inc.
rights: © 2020 Zhao and He
abstract: Background Ovarian cancer (OC) is a highly malignant disease with a poor prognosis and high recurrence rate. At present, there is no accurate strategy to predict the prognosis and recurrence of OC. The aim of this study was to identify gene-based signatures to predict OC prognosis and recurrence. Methods mRNA expression profiles and corresponding clinical information regarding OC were collected from The Cancer Genome Atlas (TCGA) database. Gene set enrichment analysis (GSEA) and LASSO analysis were performed, and Kaplan–Meier curves, time-dependent ROC curves, and nomograms were constructed using R software and GraphPad Prism7. Results We first identified several key signalling pathways that affected ovarian tumorigenesis by GSEA. We then established a nine-gene-based signature for overall survival (OS) and a five-gene-based-signature for relapse-free survival (RFS) using LASSO Cox regression analysis of the TCGA dataset and validated the prognostic value of these signatures in independent GEO datasets. We also confirmed that these signatures were independent risk factors for OS and RFS by multivariate Cox analysis. Time-dependent ROC analysis showed that the AUC values for OS and RFS were 0.640, 0.663, 0.758, and 0.891, and 0.638, 0.722, 0.813, and 0.972 at 1, 3, 5, and 10 years, respectively. The results of the nomogram analysis demonstrated that combining two signatures with the TNM staging system and tumour status yielded better predictive ability. Conclusion In conclusion, the two-gene-based signatures established in this study may serve as novel and independent prognostic indicators for OS and RFS.
bibliographic citation: Zhao et al. (2020) Comprehensive pathway-related genes signature for prognosis and recurrence of ovarian cancer. PeerJ 8:e10437 https://doi.org/10.7717/peerj.10437
date submitted: 2020-07-13
date accepted: 2020-11-06
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Xinnan
author list: Agent
  family name: He
  given name: Miao
doi: 10.7717/peerj.10437
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: ©2020 Zhao and He
attribution name: Zhao and He

Salivary microbial changes during the first 6 months of orthodontic treatment
type: item
type: AcademicArticle
description: Background Orthodontic treatment is widely used to treat malocclusion. However, the influence of treatment on the oral microbiome remains unclear. In this study, we investigated salivary microbial changes in patients undergoing orthodontic treatment. Methods In total, 19 orthodontic patients participated in this study. Saliva samples were collected at the following three timepoints: before (T0) and 3 months (T1) and 6 months (T2) after the placement of orthodontic appliances. High-throughput sequencing was performed based on the 16S rRNA gene V4 region. Results The phyla of Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were predominant. Observed Species, Chao1 and ACE, which represent α diversity, were significantly decreased at T1 and subsequently increased at T2. In addition, the β diversity at T1 based on the Bray-Curtis distances differed from T0 and T2. The relative abundances of Prevotella, Porphyromonas and Peptostreptococcus were decreased with treatment, whereas those of Capnocytophaga and Neisseria exhibited the opposite results. In total, 385 of 410 operational taxonomic units were shared at T0, T1 and T2. The co-occurrence networks with hub nodes at T1 were the most complex. Conclusion Orthodontic treatment temporarily affected the saliva microbial community. This dynamic alteration in species did not induce deterioration in oral health. Oral hygiene instructions were necessary and should be emphasized during each visit. Further studies with longer observation periods and more participants are required.
format: application/pdf
format: text/html
creator: Mei Zhao
creator: Min Liu
creator: Wei Chen
creator: Haiping Zhang
creator: Yuxing Bai
creator: Wen Ren
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.10446
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Background Orthodontic treatment is widely used to treat malocclusion. However, the influence of treatment on the oral microbiome remains unclear. In this study, we investigated salivary microbial changes in patients undergoing orthodontic treatment. Methods In total, 19 orthodontic patients participated in this study. Saliva samples were collected at the following three timepoints: before (T0) and 3 months (T1) and 6 months (T2) after the placement of orthodontic appliances. High-throughput sequencing was performed based on the 16S rRNA gene V4 region. Results The phyla of Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Fusobacteria were predominant. Observed Species, Chao1 and ACE, which represent α diversity, were significantly decreased at T1 and subsequently increased at T2. In addition, the β diversity at T1 based on the Bray-Curtis distances differed from T0 and T2. The relative abundances of Prevotella, Porphyromonas and Peptostreptococcus were decreased with treatment, whereas those of Capnocytophaga and Neisseria exhibited the opposite results. In total, 385 of 410 operational taxonomic units were shared at T0, T1 and T2. The co-occurrence networks with hub nodes at T1 were the most complex. Conclusion Orthodontic treatment temporarily affected the saliva microbial community. This dynamic alteration in species did not induce deterioration in oral health. Oral hygiene instructions were necessary and should be emphasized during each visit. Further studies with longer observation periods and more participants are required.
bibliographic citation: Zhao et al. (2020) Salivary microbial changes during the first 6 months of orthodontic treatment. PeerJ 8:e10446 https://doi.org/10.7717/peerj.10446
date submitted: 2020-08-06
date accepted: 2020-11-07
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Mei
author list: Agent
  family name: Liu
  given name: Min
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Haiping
author list: Agent
  family name: Bai
  given name: Yuxing
author list: Agent
  family name: Ren
  given name: Wen
doi: 10.7717/peerj.10446
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Assessing anxiety, depression and quality of life in patients with peripheral facial palsy: a systematic review
type: item
type: AcademicArticle
description: Objective Peripheral facial palsy (PFP) is predominantly a unilateral disorder of the facial nerve, which can lead to psychological disorders that can result in decreased quality of life. The aim of this systematic review was to assess anxiety, depression and quality of life symptoms associated with PFP. Data sources We searched the Medline, PEDro, CINAHL and Google Scholar databases to conduct this systematic review while following Preferred Reporting Items for Systematic Reviews and Meta-Analyses standards. The search was performed by two independent reviewers, and differences between the two reviewers were resolved by consensus. Study Selection The search terms used were derived from the combination of the following MeSH terms: “facial paralysis”, “bell palsy”, “anxiety”, “anxiety disorders”, “depression”, “depressive disorders”, “quality of life” and not MeSH: “facial palsy”, “hemifacial paralysis”, “facial paresis”, “Peripheral Facial Paralysis”, using the combination of different Boolean operators (AND/OR). Data Extraction On November 1st (2019). Data Synthesis In total, 18 cross-sectional articles and two case-control studies were selected. Conclusions The cross-sectional articles showed low methodological quality, while the case-control studies showed acceptable methodological quality. Limited evidence suggests that patients with PFP might have increased levels of anxiety and depressive symptoms. A qualitative analysis also showed limited evidence that quality of life might be diminished in patients with PFP. PROSPERO CRD42020159843.
format: application/pdf
format: text/html
creator: Ferran Cuenca-Martínez
creator: Eva Zapardiel-Sánchez
creator: Enrique Carrasco-González
creator: Roy La Touche
creator: Luis Suso-Martí
subject: Kinesiology
subject: Neurology
subject: Ophthalmology
subject: Orthopedics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.10449
publisher: PeerJ Inc.
rights: © 2020 Cuenca-Martínez et al.
abstract: Objective Peripheral facial palsy (PFP) is predominantly a unilateral disorder of the facial nerve, which can lead to psychological disorders that can result in decreased quality of life. The aim of this systematic review was to assess anxiety, depression and quality of life symptoms associated with PFP. Data sources We searched the Medline, PEDro, CINAHL and Google Scholar databases to conduct this systematic review while following Preferred Reporting Items for Systematic Reviews and Meta-Analyses standards. The search was performed by two independent reviewers, and differences between the two reviewers were resolved by consensus. Study Selection The search terms used were derived from the combination of the following MeSH terms: “facial paralysis”, “bell palsy”, “anxiety”, “anxiety disorders”, “depression”, “depressive disorders”, “quality of life” and not MeSH: “facial palsy”, “hemifacial paralysis”, “facial paresis”, “Peripheral Facial Paralysis”, using the combination of different Boolean operators (AND/OR). Data Extraction On November 1st (2019). Data Synthesis In total, 18 cross-sectional articles and two case-control studies were selected. Conclusions The cross-sectional articles showed low methodological quality, while the case-control studies showed acceptable methodological quality. Limited evidence suggests that patients with PFP might have increased levels of anxiety and depressive symptoms. A qualitative analysis also showed limited evidence that quality of life might be diminished in patients with PFP. PROSPERO CRD42020159843.
bibliographic citation: Cuenca-Martínez et al. (2020) Assessing anxiety, depression and quality of life in patients with peripheral facial palsy: a systematic review. PeerJ 8:e10449 https://doi.org/10.7717/peerj.10449
date submitted: 2020-06-18
date accepted: 2020-11-09
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuenca-Martínez
  given name: Ferran
author list: Agent
  family name: Zapardiel-Sánchez
  given name: Eva
author list: Agent
  family name: Carrasco-González
  given name: Enrique
author list: Agent
  family name: La Touche
  given name: Roy
author list: Agent
  family name: Suso-Martí
  given name: Luis
doi: 10.7717/peerj.10449
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Cuenca-Martínez et al.
attribution name: Cuenca-Martínez et al.

Clinical significance of pretreatment prognostic nutritional index and lymphocyte-to-monocyte ratio in patients with advanced p16-negative oropharyngeal cancer—a retrospective study
type: item
type: AcademicArticle
description: Background Systemic inflammation and nutritional status both play roles in the survival of cancer patients. Therefore, it is important to understand the effects of prognostic nutritional index (PNI) and lymphocyte-to-monocyte ratio (LMR) on the survival of patients with advanced p16-negative oropharyngeal cancer. Methods A total of 142 patients diagnosed with advanced p16-negative oropharyngeal cancer between 2008 and 2015 were enrolled in this study. All patients received primary treatment with definite concurrent chemoradiotherapy (CCRT). Optimal cutoff values for PNI and LMR were determined using receiver operating characteristic curves for survival prediction. Survival rates for different level of PNI and LMR were estimated and compared using Kaplan–Meier method and log-rank test to see if there were significant effects on these end points, including 5-year overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS) rates. The effects of PNI and LMR on survival were assessed using Cox regression model adjusted for other prognostic factors. Results The results showed the optimal cutoff values for PNI and LMR were 50.5 and 4.45, respectively. A high PNI (≧50.5) was significantly improved the 5-year OS. A low LMR (<4.45) was significantly associated with a poor 5-year DFS, DSS, and OS. In multivariate analysis, both PNI and LMR were independent prognosticators for 5-year OS. Conclusions Elevated pretreatment PNI and LMR are both favorable prognosticators in advanced p16-negative oropharyngeal cancer patients undergoing CCRT.
format: application/pdf
format: text/html
creator: Ming-Hsien Tsai
creator: Tai-Lin Huang
creator: Hui-Ching Chuang
creator: Yu-Tsai Lin
creator: Fu-Min Fang
creator: Hui Lu
creator: Chih-Yen Chien
subject: Hematology
subject: Immunology
subject: Nutrition
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.10465
publisher: PeerJ Inc.
rights: © 2020 Tsai et al.
abstract: Background Systemic inflammation and nutritional status both play roles in the survival of cancer patients. Therefore, it is important to understand the effects of prognostic nutritional index (PNI) and lymphocyte-to-monocyte ratio (LMR) on the survival of patients with advanced p16-negative oropharyngeal cancer. Methods A total of 142 patients diagnosed with advanced p16-negative oropharyngeal cancer between 2008 and 2015 were enrolled in this study. All patients received primary treatment with definite concurrent chemoradiotherapy (CCRT). Optimal cutoff values for PNI and LMR were determined using receiver operating characteristic curves for survival prediction. Survival rates for different level of PNI and LMR were estimated and compared using Kaplan–Meier method and log-rank test to see if there were significant effects on these end points, including 5-year overall survival (OS), disease-specific survival (DSS) and disease-free survival (DFS) rates. The effects of PNI and LMR on survival were assessed using Cox regression model adjusted for other prognostic factors. Results The results showed the optimal cutoff values for PNI and LMR were 50.5 and 4.45, respectively. A high PNI (≧50.5) was significantly improved the 5-year OS. A low LMR (<4.45) was significantly associated with a poor 5-year DFS, DSS, and OS. In multivariate analysis, both PNI and LMR were independent prognosticators for 5-year OS. Conclusions Elevated pretreatment PNI and LMR are both favorable prognosticators in advanced p16-negative oropharyngeal cancer patients undergoing CCRT.
bibliographic citation: Tsai et al. (2020) Clinical significance of pretreatment prognostic nutritional index and lymphocyte-to-monocyte ratio in patients with advanced p16-negative oropharyngeal cancer—a retrospective study. PeerJ 8:e10465 https://doi.org/10.7717/peerj.10465
date submitted: 2020-07-22
date accepted: 2020-11-10
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Ming-Hsien
author list: Agent
  family name: Huang
  given name: Tai-Lin
author list: Agent
  family name: Chuang
  given name: Hui-Ching
author list: Agent
  family name: Lin
  given name: Yu-Tsai
author list: Agent
  family name: Fang
  given name: Fu-Min
author list: Agent
  family name: Lu
  given name: Hui
author list: Agent
  family name: Chien
  given name: Chih-Yen
doi: 10.7717/peerj.10465
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Tsai et al.
attribution name: Tsai et al.

Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil
type: item
type: AcademicArticle
description: Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.
format: application/pdf
format: text/html
creator: Pablo Viana Oliveira
creator: Francine Alves Nogueira de Almeida
creator: Magda Delorence Lugon
creator: Karolinni Bianchi Britto
creator: Janyra Oliveira-Costa
creator: Alexandre Rosa Santos
creator: Greiciane Gaburro Paneto
subject: Biodiversity
subject: Biotechnology
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.9680
publisher: PeerJ Inc.
rights: © 2020 Oliveira et al.
abstract: Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.
bibliographic citation: Oliveira et al. (2020) Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil. PeerJ 8:e9680 https://doi.org/10.7717/peerj.9680
date submitted: 2020-04-06
date accepted: 2020-07-17
issued: 2020-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira
  given name: Pablo Viana
author list: Agent
  family name: de Almeida
  given name: Francine Alves Nogueira
author list: Agent
  family name: Lugon
  given name: Magda Delorence
author list: Agent
  family name: Britto
  given name: Karolinni Bianchi
author list: Agent
  family name: Oliveira-Costa
  given name: Janyra
author list: Agent
  family name: Santos
  given name: Alexandre Rosa
author list: Agent
  family name: Paneto
  given name: Greiciane Gaburro
doi: 10.7717/peerj.9680
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-30
copyright: © 2020 Oliveira et al.
attribution name: Oliveira et al.

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