PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices
items: OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
items: Healthy eating promoting in a Brazilian sports-oriented school: a pilot study
items: Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement
items: A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies
items: Effect of adjuvant radioactive iodine therapy on survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma)
items: Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells
items: Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing
items: Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)
items: Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum

The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices
type: item
type: AcademicArticle
description: Background Wrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices. Methods A total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension. Results All of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other fou…
format: application/pdf
format: text/html
creator: Yongfang Li
creator: Yuyan Liu
creator: Jing He
creator: Ping Ma
creator: Luyang Yu
creator: Guifan Sun
subject: Epidemiology
subject: Global Health
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.7599
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Wrist circumference (WrC) is an easily obtained measure in estimating the body frame and regional fat distribution, and has increasingly used as an obesity index. The aim of our study is to estimate the association of WrC with elevated blood pressure (BP) among northeastern Chinese community-dwelling residents, and compare the strength of this association to other anthropometric obesity indices. Methods A total of 2,331 adult participants (761 male participants, and 1,570 female participants) were included. WrC and other five generally used obesity indices, including body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR) and neck circumference (NC) were measured. Hypertension was defined as systolic blood pressure (SBP)/diastolic blood pressure (DBP) ≥140/90 mmHg or anti-hypertensive medication use. Multivariable linear and logistic regression models were performed to identify associations of BP and hypertension with per standard deviation (SD) increase of obesity indices. Areas under receiver operative characteristic curves (AUC) were calculated to compare the predicting capacity of WrC and other obesity indices on hypertension. Results All of the six obesity indices were positively associated with both SBP and DBP after adjustment for age and gender (P-values of associations of SBP with obesity indices were 0.043 for WrC, and <0.001 for other five indices; P-values of associations of DBP with obesity indices were 0.011 for WrC, 0.031 for WHR, and <0.001 for other four indices), while the association between SBP and WrC showed no statistically significant after further adjusted for life-style and metabolic risk factors (P-value was 0.062). The increases of both SBP and DBP per SD increase of BMI were the largest. The positive associations of five obesity indices but WHR with hypertension were observed after adjustment for all risk factors (P-values were 0.024 for WrC, 0.064 for WHR and <0.001 for other fou…
bibliographic citation: Li et al. (2019) The association of wrist circumference with hypertension in northeastern Chinese residents in comparison with other anthropometric obesity indices. PeerJ 7:e7599 https://doi.org/10.7717/peerj.7599
date submitted: 2019-05-29
date accepted: 2019-07-31
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yongfang
author list: Agent
  family name: Liu
  given name: Yuyan
author list: Agent
  family name: He
  given name: Jing
author list: Agent
  family name: Ma
  given name: Ping
author list: Agent
  family name: Yu
  given name: Luyang
author list: Agent
  family name: Sun
  given name: Guifan
doi: 10.7717/peerj.7599
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Li et al.
attribution name: Li et al.

OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling
type: item
type: AcademicArticle
description: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.
format: application/pdf
format: text/html
creator: Ming-Hsin Tsai
creator: Yen-Yi Liu
creator: Chih-Chieh Chen
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.7600
publisher: PeerJ Inc.
rights: © 2019 Tsai et al.
abstract: With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a tool called OutbreakFinder that can accept a distance matrix in csv format; alignment files from Lyve-SET, Parsnp, and ClustalOmega; and a tree file in Newick format as inputs to compute a cluster-labeled two-dimensional plot based on multidimensional-scaling dimension reduction coupled with affinity propagation clustering. OutbreakFinder can be downloaded for free at https://github.com/skypes/Newton-method-MDS.
bibliographic citation: Tsai et al. (2019) OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling. PeerJ 7:e7600 https://doi.org/10.7717/peerj.7600
date submitted: 2019-04-16
date accepted: 2019-08-01
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Ming-Hsin
author list: Agent
  family name: Liu
  given name: Yen-Yi
author list: Agent
  family name: Chen
  given name: Chih-Chieh
doi: 10.7717/peerj.7600
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: © 2019 Tsai et al.
attribution name: Tsai et al.

Healthy eating promoting in a Brazilian sports-oriented school: a pilot study
type: item
type: AcademicArticle
description: Background Adolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation. Methods Our pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57). Results In 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating. Conclusion Our results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency …
format: application/pdf
format: text/html
creator: Fábia Albernaz Massarani
creator: Marta Citelli
creator: Daniela Silva Canella
creator: Josely Correa Koury
subject: Global Health
subject: Kinesiology
subject: Nutrition
subject: Public Health
subject: Science and Medical Education
description: doi:10.7717/peerj.7601
publisher: PeerJ Inc.
rights: © 2019 Massarani et al.
abstract: Background Adolescents, particularly athletes, have high exposure to ultra-processed foods, which could be harmful to their health and physical performance. School environments are capable of improving eating patterns. Our study is aimed at capturing changes in students’ food consumption three years after they enrolled at an experimental school, considered a model of health promotion in Rio de Janeiro city. We also aimed to depict the promising nature of the healthy eating promotion program implemented in the school and share the learnings from its implementation. Methods Our pilot study was a follow-up on the implementation of a school garden, experimental kitchen activities, and health promotion classes. We evaluated 83 adolescent athletes’ food consumption twice during the study: at its beginning (2013) and end (2016), by administering a food frequency questionnaire (FFQ) that inquired about the frequency of foods consumed in the past week. To evaluate how effectively the activities were established, integrated, and sustained in schools, the Garden Resources, Education, and Environment Nexus (GREEN) tool was used, and the school’s adherence to the school garden program was classified as high (scored 47 points out of 57). Results In 2013, 89 adolescents (mean ± SD 11.9 ± 0.4 years, 54% male) participated in the study, of which 83 continued until 2016 (14.8 ± 0.5 years, 55% male). In 2013, the mean frequency of raw salad and fruits consumption was 1.4 (CI [1.0–1.9]) and 4.3 (CI [3.8–4.9]) days per week, respectively. Three years later, the frequency of raw salad and fruits consumption was 2.2 (CI [1.6–2.7]) and 5.0 (4.5–5.5), respectively. Considering that five meals were offered at school (five days/week), it may be possible to assume that the program raised awareness on the importance of healthy eating. Conclusion Our results suggest that such integrated healthy eating promotion programs may improve adolescent athletes’ eating habits, by increasing the frequency …
bibliographic citation: Massarani et al. (2019) Healthy eating promoting in a Brazilian sports-oriented school: a pilot study. PeerJ 7:e7601 https://doi.org/10.7717/peerj.7601
date submitted: 2018-12-13
date accepted: 2019-08-01
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Massarani
  given name: Fábia Albernaz
author list: Agent
  family name: Citelli
  given name: Marta
author list: Agent
  family name: Canella
  given name: Daniela Silva
author list: Agent
  family name: Koury
  given name: Josely Correa
doi: 10.7717/peerj.7601
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Massarani et al.
attribution name: Massarani et al.

Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement
type: item
type: AcademicArticle
description: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
format: application/pdf
format: text/html
creator: Hao Zhang
creator: Juan Cheng
creator: Zijian Li
creator: Yaming Xi
subject: Molecular Biology
subject: Hematology
subject: Oncology
subject: Pediatrics
description: doi:10.7717/peerj.7628
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Infant acute lymphoblastic leukemia (ALL) with the mixed lineage leukemia (MLL) gene rearrangement (MLL-R) is considered a distinct leukemia from childhood or non-MLL-R infant ALL. To detect key genes and elucidate the molecular mechanisms of MLL-R infant ALL, microarray expression data were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between MLL-R and non-MLL-R infant ALL were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out. Then, we constructed a protein-protein interaction (PPI) network and identified the hub genes. Finally, drug-gene interactions were mined. A total of 139 cases of MLL-R infant ALL including 77 (55.4%) fusions with AF4, 38 (27.3%) with ENL, 14 (10.1%) with AF9, and 10 (7.2%) other gene fusions were characterized. A total of 236 up-regulated and 84 down-regulated DEGs were identified. The up-regulated DEGs were mainly involved in homophilic cell adhesion, negative regulation of apoptotic process and cellular response to drug GO terms, while down-regulated DEGs were mainly enriched in extracellular matrix organization, protein kinase C signaling and neuron projection extension GO terms. The up-regulated DEGs were enriched in seven KEGG pathways, mainly involving transcriptional regulation and signaling pathways, and down-regulated DEGs were involved in three main KEGG pathways including Alzheimer’s disease, TGF-beta signaling pathway, and hematopoietic cell lineage. The PPI network included 297 nodes and 410 edges, with MYC, ALB, CD44, PTPRC and TNF identified as hub genes. Twenty-three drug-gene interactions including four up-regulated hub genes and 24 drugs were constructed by Drug Gene Interaction database (DGIdb). In conclusion, MYC, ALB, CD44, PTPRC and TNF may be potential bio-markers for the diagnosis and therapy of MLL-R infant ALL.
bibliographic citation: Zhang et al. (2019) Identification of hub genes and molecular mechanisms in infant acute lymphoblastic leukemia with MLL gene rearrangement. PeerJ 7:e7628 https://doi.org/10.7717/peerj.7628
date submitted: 2019-04-16
date accepted: 2019-08-06
issued: 2019-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Cheng
  given name: Juan
author list: Agent
  family name: Li
  given name: Zijian
author list: Agent
  family name: Xi
  given name: Yaming
doi: 10.7717/peerj.7628
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-28
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies
type: item
type: AcademicArticle
description: Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with…
format: application/pdf
format: text/html
creator: Leidys Murillo-Ramos
creator: Gunnar Brehm
creator: Pasi Sihvonen
creator: Axel Hausmann
creator: Sille Holm
creator: Hamid Reza Ghanavi
creator: Erki Õunap
creator: Andro Truuverk
creator: Hermann Staude
creator: Egbert Friedrich
creator: Toomas Tammaru
creator: Niklas Wahlberg
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7386
publisher: PeerJ Inc.
rights: © 2019 Murillo-Ramos et al.
abstract: Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with…
bibliographic citation: Murillo-Ramos et al. (2019) A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies. PeerJ 7:e7386 https://doi.org/10.7717/peerj.7386
date submitted: 2019-02-06
date accepted: 2019-07-01
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murillo-Ramos
  given name: Leidys
author list: Agent
  family name: Brehm
  given name: Gunnar
author list: Agent
  family name: Sihvonen
  given name: Pasi
author list: Agent
  family name: Hausmann
  given name: Axel
author list: Agent
  family name: Holm
  given name: Sille
author list: Agent
  family name: Reza Ghanavi
  given name: Hamid
author list: Agent
  family name: Õunap
  given name: Erki
author list: Agent
  family name: Truuverk
  given name: Andro
author list: Agent
  family name: Staude
  given name: Hermann
author list: Agent
  family name: Friedrich
  given name: Egbert
author list: Agent
  family name: Tammaru
  given name: Toomas
author list: Agent
  family name: Wahlberg
  given name: Niklas
doi: 10.7717/peerj.7386
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: © 2019 Murillo-Ramos et al.
attribution name: Murillo-Ramos et al.

Effect of adjuvant radioactive iodine therapy on survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma)
type: item
type: AcademicArticle
description: Purpose Radioactive iodine (RAI) is widely used for adjuvant therapy after thyroidectomy, while its value for thyroid cancer has been controversial recently. The primary objectives of this study were to clarify the influence of Radioactive iodine (RAI) on the survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma, HCC). Methods Patients diagnosed with oxyphilic thyroid carcinoma from 2004 to 2015 were extracted from the Surveillance, Epidemiology, and End Results Program database. The Kaplan-Meier method was used to compare overall survival (OS) and cancer-specific survival (CSS) among patients who had adjuvant RAI use or not. Univariate and multivariate Cox proportional hazard models were performed for survival analysis, and subsequently visualized by nomogram. Results In all, 2,799 patients were identified, of which 1529 patients had adjuvant RAI use while 1,270 patients had not. Based on multivariate Cox analysis, the RAI therapy confers an improved OS for HCC patients (HR = 0.57, 95% CI [0.44–0.72], P < 0.001), whereas it has no significant benefit in the survival analysis regarding CSS (HR = 0.79, 95% CI [[0.47–1.34], P = 0.382). In a subgroup analysis, the same survival benefit of RAI treatment on OS, but not CSS was observed among patients stratified by AJCC stage and tumor extension. Nevertheless, patients with regional lymph node metastasis benefited from RAI therapy both in OS and CSS (P < 0.001, respectively). Furthermore, nomograms used for predicting long term survival of HCC patients exhibited a better prediction power for OS compared with traditional tumor, nodal and metastatic (TNM) stage made by American Joint Committee on Cancer (AJCC) (C-index = 0.833 of the nomogram model vs. 0.696 of the AJCC system). Conclusions This study suggests that RAI therapy is significantly associated with improved OS in patients with Hürthle cell carcinoma. However, there was no association between treatment with radioiodine and CSS, possibly due …
format: application/pdf
format: text/html
creator: Qiong Yang
creator: Zhongsheng Zhao
creator: Guansheng Zhong
creator: Aixiang Jin
creator: Kun Yu
subject: Oncology
description: doi:10.7717/peerj.7458
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Purpose Radioactive iodine (RAI) is widely used for adjuvant therapy after thyroidectomy, while its value for thyroid cancer has been controversial recently. The primary objectives of this study were to clarify the influence of Radioactive iodine (RAI) on the survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma, HCC). Methods Patients diagnosed with oxyphilic thyroid carcinoma from 2004 to 2015 were extracted from the Surveillance, Epidemiology, and End Results Program database. The Kaplan-Meier method was used to compare overall survival (OS) and cancer-specific survival (CSS) among patients who had adjuvant RAI use or not. Univariate and multivariate Cox proportional hazard models were performed for survival analysis, and subsequently visualized by nomogram. Results In all, 2,799 patients were identified, of which 1529 patients had adjuvant RAI use while 1,270 patients had not. Based on multivariate Cox analysis, the RAI therapy confers an improved OS for HCC patients (HR = 0.57, 95% CI [0.44–0.72], P < 0.001), whereas it has no significant benefit in the survival analysis regarding CSS (HR = 0.79, 95% CI [[0.47–1.34], P = 0.382). In a subgroup analysis, the same survival benefit of RAI treatment on OS, but not CSS was observed among patients stratified by AJCC stage and tumor extension. Nevertheless, patients with regional lymph node metastasis benefited from RAI therapy both in OS and CSS (P < 0.001, respectively). Furthermore, nomograms used for predicting long term survival of HCC patients exhibited a better prediction power for OS compared with traditional tumor, nodal and metastatic (TNM) stage made by American Joint Committee on Cancer (AJCC) (C-index = 0.833 of the nomogram model vs. 0.696 of the AJCC system). Conclusions This study suggests that RAI therapy is significantly associated with improved OS in patients with Hürthle cell carcinoma. However, there was no association between treatment with radioiodine and CSS, possibly due …
bibliographic citation: Yang et al. (2019) Effect of adjuvant radioactive iodine therapy on survival in rare oxyphilic subtype of thyroid cancer (Hürthle cell carcinoma). PeerJ 7:e7458 https://doi.org/10.7717/peerj.7458
date submitted: 2019-04-16
date accepted: 2019-07-10
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Qiong
author list: Agent
  family name: Zhao
  given name: Zhongsheng
author list: Agent
  family name: Zhong
  given name: Guansheng
author list: Agent
  family name: Jin
  given name: Aixiang
author list: Agent
  family name: Yu
  given name: Kun
doi: 10.7717/peerj.7458
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells
type: item
type: AcademicArticle
description: Background Aluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity. Methods MTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes. Results Al inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings. Conclusion The metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism.
format: application/pdf
format: text/html
creator: Leilei Yu
creator: Jiangping Wu
creator: Qixiao Zhai
creator: Fengwei Tian
creator: Jianxin Zhao
creator: Hao Zhang
creator: Wei Chen
subject: Food Science and Technology
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.7524
publisher: PeerJ Inc.
rights: © 2019 Yu et al.
abstract: Background Aluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity. Methods MTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes. Results Al inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings. Conclusion The metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism.
bibliographic citation: Yu et al. (2019) Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells. PeerJ 7:e7524 https://doi.org/10.7717/peerj.7524
date submitted: 2019-04-18
date accepted: 2019-07-21
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Leilei
author list: Agent
  family name: Wu
  given name: Jiangping
author list: Agent
  family name: Zhai
  given name: Qixiao
author list: Agent
  family name: Tian
  given name: Fengwei
author list: Agent
  family name: Zhao
  given name: Jianxin
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Chen
  given name: Wei
doi: 10.7717/peerj.7524
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: © 2019 Yu et al.
attribution name: Yu et al.

Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing
type: item
type: AcademicArticle
description: Background The degradation of nucleotides and their enzymes had been widely used to evaluate fish freshness. Immediately after fish death, adenosine triphosphate (ATP) degrades into inosine-5-monophosphate (IMP) via adenosine-5-diphosphate (ADP) and adenosine-5-monophosphate (AMP). IMP degradation continues to produce inosine (ino) and hypoxanthine (Hx) and further deteriorates the fish by producing xanthine and uric acid. The dephosphorylation of IMP to Ino is carried out by the enzyme 5′-nucleotidase (5′-NT), whereas the degradation of Ino to Hx is carried out by the enzyme nucleoside phosphorylase (NP). This study assesses the application of high pressure processing (HPP) in two species of fishes; haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) as a means to extend the shelf-life by slowing down the rate of nucleotides degradation. Methods Haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) fillets were subjected to HPP at 200, 250 and 300 MPa for 1 and 3 min before being stored for 14 days. In addition, 5′-NT and NP enzyme activities were determined on both fish species that were subjected to 100–600 MPa for 1 and 3 min. Results Adenosine triphosphate, ADP and AMP in both haddock and herring were lower at higher pressure levels. Inosine (Ino) increased (p < 0.05) after treatment at higher pressures in both species. Hx in herring decreased significantly (p < 0.05) at higher pressures but not in haddock. K values are the ratio of Ino and Hx to all nucleotides. K values in haddock were not significantly (p > 0.05) affected by the pressure treatment. H values are ratio of Hx to the sum of IMP, Ino and Hx. H values in haddock were significantly decreased (p < 0.05) with increasing pressure level. F values are ratio of IMP to the sum of IMP, Ino and Hx. F values showed no significant effects (p > 0.05) after pressure treatment. Furthermore, K values in control herring were significantly higher (p < 0.05) than those of the pressure-treated…
format: application/pdf
format: text/html
creator: Nurul Ulfah Karim
creator: James Terence Kennedy
creator: Mark Linton
creator: Margaret Patterson
creator: Sally Watson
creator: Norman Gault
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Food Science and Technology
subject: Nutrition
description: doi:10.7717/peerj.7527
publisher: PeerJ Inc.
rights: © 2019 Karim et al.
abstract: Background The degradation of nucleotides and their enzymes had been widely used to evaluate fish freshness. Immediately after fish death, adenosine triphosphate (ATP) degrades into inosine-5-monophosphate (IMP) via adenosine-5-diphosphate (ADP) and adenosine-5-monophosphate (AMP). IMP degradation continues to produce inosine (ino) and hypoxanthine (Hx) and further deteriorates the fish by producing xanthine and uric acid. The dephosphorylation of IMP to Ino is carried out by the enzyme 5′-nucleotidase (5′-NT), whereas the degradation of Ino to Hx is carried out by the enzyme nucleoside phosphorylase (NP). This study assesses the application of high pressure processing (HPP) in two species of fishes; haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) as a means to extend the shelf-life by slowing down the rate of nucleotides degradation. Methods Haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) fillets were subjected to HPP at 200, 250 and 300 MPa for 1 and 3 min before being stored for 14 days. In addition, 5′-NT and NP enzyme activities were determined on both fish species that were subjected to 100–600 MPa for 1 and 3 min. Results Adenosine triphosphate, ADP and AMP in both haddock and herring were lower at higher pressure levels. Inosine (Ino) increased (p < 0.05) after treatment at higher pressures in both species. Hx in herring decreased significantly (p < 0.05) at higher pressures but not in haddock. K values are the ratio of Ino and Hx to all nucleotides. K values in haddock were not significantly (p > 0.05) affected by the pressure treatment. H values are ratio of Hx to the sum of IMP, Ino and Hx. H values in haddock were significantly decreased (p < 0.05) with increasing pressure level. F values are ratio of IMP to the sum of IMP, Ino and Hx. F values showed no significant effects (p > 0.05) after pressure treatment. Furthermore, K values in control herring were significantly higher (p < 0.05) than those of the pressure-treated…
bibliographic citation: Karim et al. (2019) Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing. PeerJ 7:e7527 https://doi.org/10.7717/peerj.7527
date submitted: 2018-11-07
date accepted: 2019-07-22
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karim
  given name: Nurul Ulfah
author list: Agent
  family name: Kennedy
  given name: James Terence
author list: Agent
  family name: Linton
  given name: Mark
author list: Agent
  family name: Patterson
  given name: Margaret
author list: Agent
  family name: Watson
  given name: Sally
author list: Agent
  family name: Gault
  given name: Norman
doi: 10.7717/peerj.7527
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: © 2019 Karim et al.
attribution name: Karim et al.

Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)
type: item
type: AcademicArticle
description: Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.
format: application/pdf
format: text/html
creator: Carl J. Yeoman
creator: Laura M. Brutscher
creator: Özcan C. Esen
creator: Furkan Ibaoglu
creator: Curtis Fowler
creator: A. Murat Eren
creator: Kevin Wanner
creator: David K. Weaver
subject: Agricultural Science
subject: Entomology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.7548
publisher: PeerJ Inc.
rights: © 2019 Yeoman et al.
abstract: Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.
bibliographic citation: Yeoman et al. (2019) Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus). PeerJ 7:e7548 https://doi.org/10.7717/peerj.7548
date submitted: 2019-02-21
date accepted: 2019-07-25
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeoman
  given name: Carl J.
author list: Agent
  family name: Brutscher
  given name: Laura M.
author list: Agent
  family name: Esen
  given name: Özcan C.
author list: Agent
  family name: Ibaoglu
  given name: Furkan
author list: Agent
  family name: Fowler
  given name: Curtis
author list: Agent
  family name: Eren
  given name: A. Murat
author list: Agent
  family name: Wanner
  given name: Kevin
author list: Agent
  family name: Weaver
  given name: David K.
doi: 10.7717/peerj.7548
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: ©2019 Yeoman et al.
attribution name: Yeoman et al.

Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum
type: item
type: AcademicArticle
description: This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.
format: application/pdf
format: text/html
creator: Md Javed Foysal
creator: Thi Thu Thuy Nguyen
creator: Md Reaz Chaklader
creator: Muhammad A.B. Siddik
creator: Chin-Yen Tay
creator: Ravi Fotedar
creator: Sanjay Kumar Gupta
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.7553
publisher: PeerJ Inc.
rights: © 2019 Foysal et al.
abstract: This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.
bibliographic citation: Foysal et al. (2019) Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum. PeerJ 7:e7553 https://doi.org/10.7717/peerj.7553
date submitted: 2019-02-05
date accepted: 2019-07-25
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Foysal
  given name: Md Javed
author list: Agent
  family name: Nguyen
  given name: Thi Thu Thuy
author list: Agent
  family name: Chaklader
  given name: Md Reaz
author list: Agent
  family name: Siddik
  given name: Muhammad A.B.
author list: Agent
  family name: Tay
  given name: Chin-Yen
author list: Agent
  family name: Fotedar
  given name: Ravi
author list: Agent
  family name: Gupta
  given name: Sanjay Kumar
doi: 10.7717/peerj.7553
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: ©2019 Foysal et al.
attribution name: Foysal et al.

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