PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia
items: Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice
items: The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings
items: Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment
items: Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer
items: Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program
items: The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis
items: A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs
items: Predictors of work-related musculoskeletal symptoms in shoulders among nursing assistants working in nursing homes
items: Intact tactile anisotropy despite altered hand perception in complex regional pain syndrome: rethinking the role of the primary sensory cortex in tactile and perceptual dysfunction

The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia
type: item
type: AcademicArticle
description: In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs.
format: application/pdf
format: text/html
creator: Marcia M. English
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
description: doi:10.7717/peerj.11357
publisher: PeerJ Inc.
rights: © 2021 English
abstract: In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs.
bibliographic citation: English (2021) The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia. PeerJ 9:e11357 https://doi.org/10.7717/peerj.11357
date submitted: 2020-07-20
date accepted: 2021-04-05
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: English
  given name: Marcia M.
doi: 10.7717/peerj.11357
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: © 2021 English
attribution name: English

Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice
type: item
type: AcademicArticle
description: Rice protein has attracted considerable attention recently due to its physiological effects. This study extracted the proteins from paddy rice (PR) and germinated paddy rice (GPR) using three methods i.e., alkaline, sodium dodecyl sulfate (SDS) reagent and enzymatic extractions. The extracted proteins or protein fractions were assessed for their properties using various techniques. Data were analyzed by 2′3 factorial design experiment. It was found that germination and extraction methods significantly affected the concentration of protein fractions when analyzed by Bradford assay. Average protein fraction concentration of the GPR was lower than that of PR. SDS-PAGE patterns of protein fractions obtained from PR and GPR using any extraction method displayed similar protein profiles. Three major protein bands at about 13 kDa (prolamin), 22–23 kDa (basic glutelin) and 37–39 kDa (acidic glutelin) with small amount of 57 kDa proglutelin were observed. For amino acid profile, germination increased the content of most amino acids, resulting in the higher content of amino acids in GPR, excepted for some amino acids. When processed with in vitro digestion, protein fractions from GPR exhibited a higher level of digestibility than those from PR as evidenced by the less intensity of the protein bands obtained from SDS-PAGE. Alkaline and SDS reagent extractions provided more digestible protein fractions than enzymatic extraction. Extraction methods also influenced phase transition of protein fractions as investigated by a DSC. Alkaline extraction resulted in protein fractions with higher phase transition temperature than the other methods. For antioxidant capacity, extraction methods as well as germination significantly affected antioxidant capacity of the protein fractions. Enzymatic extraction provided protein fractions with the best antioxidant capacity.
format: application/pdf
format: text/html
creator: Wirot Likittrakulwong
creator: Pisit Poolprasert
creator: Khongsak Srikaeo
subject: Agricultural Science
subject: Food Science and Technology
description: doi:10.7717/peerj.11365
publisher: PeerJ Inc.
rights: © 2021 Likittrakulwong et al.
abstract: Rice protein has attracted considerable attention recently due to its physiological effects. This study extracted the proteins from paddy rice (PR) and germinated paddy rice (GPR) using three methods i.e., alkaline, sodium dodecyl sulfate (SDS) reagent and enzymatic extractions. The extracted proteins or protein fractions were assessed for their properties using various techniques. Data were analyzed by 2′3 factorial design experiment. It was found that germination and extraction methods significantly affected the concentration of protein fractions when analyzed by Bradford assay. Average protein fraction concentration of the GPR was lower than that of PR. SDS-PAGE patterns of protein fractions obtained from PR and GPR using any extraction method displayed similar protein profiles. Three major protein bands at about 13 kDa (prolamin), 22–23 kDa (basic glutelin) and 37–39 kDa (acidic glutelin) with small amount of 57 kDa proglutelin were observed. For amino acid profile, germination increased the content of most amino acids, resulting in the higher content of amino acids in GPR, excepted for some amino acids. When processed with in vitro digestion, protein fractions from GPR exhibited a higher level of digestibility than those from PR as evidenced by the less intensity of the protein bands obtained from SDS-PAGE. Alkaline and SDS reagent extractions provided more digestible protein fractions than enzymatic extraction. Extraction methods also influenced phase transition of protein fractions as investigated by a DSC. Alkaline extraction resulted in protein fractions with higher phase transition temperature than the other methods. For antioxidant capacity, extraction methods as well as germination significantly affected antioxidant capacity of the protein fractions. Enzymatic extraction provided protein fractions with the best antioxidant capacity.
bibliographic citation: Likittrakulwong et al. (2021) Effects of extraction methods on protein properties obtained from paddy rice and germinated paddy rice. PeerJ 9:e11365 https://doi.org/10.7717/peerj.11365
date submitted: 2021-01-15
date accepted: 2021-04-07
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Likittrakulwong
  given name: Wirot
author list: Agent
  family name: Poolprasert
  given name: Pisit
author list: Agent
  family name: Srikaeo
  given name: Khongsak
doi: 10.7717/peerj.11365
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Likittrakulwong et al.
attribution name: Likittrakulwong et al.

The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings
type: item
type: AcademicArticle
description: The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.
format: application/pdf
format: text/html
creator: Hongzhan Liu
creator: Chaoqiong Li
creator: Lin Qiao
creator: Lizong Hu
creator: Xueqin Wang
creator: Junsheng Wang
creator: Xianle Ruan
creator: Guangyu Yang
creator: Guihong Yin
creator: Chunping Wang
creator: Zhongke Sun
creator: Keshi Ma
creator: Lili Li
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11371
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.
bibliographic citation: Liu et al. (2021) The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings. PeerJ 9:e11371 https://doi.org/10.7717/peerj.11371
date submitted: 2020-10-04
date accepted: 2021-04-07
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongzhan
author list: Agent
  family name: Li
  given name: Chaoqiong
author list: Agent
  family name: Qiao
  given name: Lin
author list: Agent
  family name: Hu
  given name: Lizong
author list: Agent
  family name: Wang
  given name: Xueqin
author list: Agent
  family name: Wang
  given name: Junsheng
author list: Agent
  family name: Ruan
  given name: Xianle
author list: Agent
  family name: Yang
  given name: Guangyu
author list: Agent
  family name: Yin
  given name: Guihong
author list: Agent
  family name: Wang
  given name: Chunping
author list: Agent
  family name: Sun
  given name: Zhongke
author list: Agent
  family name: Ma
  given name: Keshi
author list: Agent
  family name: Li
  given name: Lili
doi: 10.7717/peerj.11371
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment
type: item
type: AcademicArticle
description: Background Ovarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgently Methods Gene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival. Results Eighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival. Conclusion Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment.
format: application/pdf
format: text/html
creator: Youzheng Xu
creator: Yixin Xu
creator: Chun Wang
creator: Baoguo Xia
creator: Qingling Mu
creator: Shaohong Luan
creator: Jun Fan
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.11375
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: Background Ovarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgently Methods Gene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival. Results Eighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival. Conclusion Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment.
bibliographic citation: Xu et al. (2021) Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment. PeerJ 9:e11375 https://doi.org/10.7717/peerj.11375
date submitted: 2019-03-27
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Youzheng
author list: Agent
  family name: Xu
  given name: Yixin
author list: Agent
  family name: Wang
  given name: Chun
author list: Agent
  family name: Xia
  given name: Baoguo
author list: Agent
  family name: Mu
  given name: Qingling
author list: Agent
  family name: Luan
  given name: Shaohong
author list: Agent
  family name: Fan
  given name: Jun
doi: 10.7717/peerj.11375
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer
type: item
type: AcademicArticle
description: Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using…
format: application/pdf
format: text/html
creator: Chongyang Ren
creator: Xiaojiang Tang
creator: Haitao Lan
subject: Bioinformatics
subject: Oncology
subject: Translational Medicine
subject: Women’s Health
description: doi:10.7717/peerj.11377
publisher: PeerJ Inc.
rights: © 2021 Ren et al.
abstract: Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using…
bibliographic citation: Ren et al. (2021) Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PeerJ 9:e11377 https://doi.org/10.7717/peerj.11377
date submitted: 2020-09-16
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Chongyang
author list: Agent
  family name: Tang
  given name: Xiaojiang
author list: Agent
  family name: Lan
  given name: Haitao
doi: 10.7717/peerj.11377
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Ren et al.
attribution name: Ren et al.

Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program
type: item
type: AcademicArticle
description: The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.
format: application/pdf
format: text/html
creator: Jennifer F. Moore
creator: William E. Pine III
subject: Aquaculture, Fisheries and Fish Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.11378
publisher: PeerJ Inc.
rights: © 2021 Moore and Pine III
abstract: The objective of many fish and wildlife restoration programs is to utilize management actions to change the state of a system. Because restoration programs are often expensive, iteratively assessing whether the restoration is having the desired outcome is a critical aspect of learning how to inform ongoing and sampling designs to evaluate proposed restoration programs. We provide an example of how we are using data resampling as part of an adaptive restoration process to test the effectiveness of a restoration action and associated monitoring program to restore the degraded Lone Cabbage oyster reef in Suwannee Sound, Florida in the northeast Gulf of Mexico. We use a resampling framework through simulations to inform the progress of the restoration efforts by examining the direction and magnitude of the differences in live oyster counts between restored and unrestored (wild) reefs over time. In addition, we evaluated the effort (number of sites sampled) needed to determine the effect of restoration to understand how many surveys should be conducted in subsequent sampling seasons. These efforts allow us to provide timely insight into the effectiveness of both our monitoring efforts and restoration strategy which is of critical importance not only to the restoration of Lone Cabbage Reef but to larger restoration efforts within the Gulf of Mexico as part of the consolidated Deepwater Horizon settlements and funded restoration efforts.
bibliographic citation: Moore et al. (2021) Bootstrap methods can help evaluate monitoring program performance to inform restoration as part of an adaptive management program. PeerJ 9:e11378 https://doi.org/10.7717/peerj.11378
date submitted: 2021-01-08
date accepted: 2021-04-08
issued: 2021-05-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moore
  given name: Jennifer F.
author list: Agent
  family name: Pine III
  given name: William E.
doi: 10.7717/peerj.11378
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-04
copyright: ©2021 Moore and Pine III
attribution name: Moore and Pine III

The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis
type: item
type: AcademicArticle
description: Researches on gut microbiota in autism have mostly focused on children, but the dynamic changes of gut microbiota from weaning to adulthood were still not clear because of the difficulty of diagnosing autism. In this study, autistic-like rats indued by valproate (VPA) were tracked from weaning (end of breastfeeding; four weeks old) to sexual maturation (food; eight weeks old). Autistic-like rats were found to show obvious developmental disorders. During weaning, autistic-like rats only exhibited obvious repetitive stereotyped behaviors, but the autistic-like behaviors were fully apparent upon sexual maturation. Significant differences were observed between the gut microbiota of autistic-like and healthy rats across both age groups. The correlation analysis results revealed that the correlation between behaviors and some microbiota, especially Helicobacter, did not vary with age or diet. The total amount of short-chain fatty acids (SCFAs) decreased, butyric acid metabolism decreased, and propionic acid metabolism increased in the feces of autistic-like rats. The correlation between autistic-like behaviors and the butyric acid and propionic acid levels did not vary with diet or age. Inositol phosphate metabolism, amino acid metabolism, and lipopolysaccharide biosynthesis were significantly associated with autistic-like behaviors. Our results showed that although the microbiota and SCFAs related to autism were affected by age and diet, some remained consistent irrespective of age and diet, and they could be considered two of the factors related to autistic-like behaviors development.
format: application/pdf
format: text/html
creator: Qingmin Kong
creator: Peijun Tian
creator: Jianxin Zhao
creator: Hao Zhang
creator: Gang Wang
creator: Wei Chen
subject: Animal Behavior
subject: Biodiversity
subject: Developmental Biology
subject: Microbiology
subject: Neuroscience
description: doi:10.7717/peerj.11103
publisher: PeerJ Inc.
rights: © 2021 Kong et al.
abstract: Researches on gut microbiota in autism have mostly focused on children, but the dynamic changes of gut microbiota from weaning to adulthood were still not clear because of the difficulty of diagnosing autism. In this study, autistic-like rats indued by valproate (VPA) were tracked from weaning (end of breastfeeding; four weeks old) to sexual maturation (food; eight weeks old). Autistic-like rats were found to show obvious developmental disorders. During weaning, autistic-like rats only exhibited obvious repetitive stereotyped behaviors, but the autistic-like behaviors were fully apparent upon sexual maturation. Significant differences were observed between the gut microbiota of autistic-like and healthy rats across both age groups. The correlation analysis results revealed that the correlation between behaviors and some microbiota, especially Helicobacter, did not vary with age or diet. The total amount of short-chain fatty acids (SCFAs) decreased, butyric acid metabolism decreased, and propionic acid metabolism increased in the feces of autistic-like rats. The correlation between autistic-like behaviors and the butyric acid and propionic acid levels did not vary with diet or age. Inositol phosphate metabolism, amino acid metabolism, and lipopolysaccharide biosynthesis were significantly associated with autistic-like behaviors. Our results showed that although the microbiota and SCFAs related to autism were affected by age and diet, some remained consistent irrespective of age and diet, and they could be considered two of the factors related to autistic-like behaviors development.
bibliographic citation: Kong et al. (2021) The autistic-like behaviors development during weaning and sexual maturation in VPA-induced autistic-like rats is accompanied by gut microbiota dysbiosis. PeerJ 9:e11103 https://doi.org/10.7717/peerj.11103
date submitted: 2020-08-05
date accepted: 2021-02-22
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Qingmin
author list: Agent
  family name: Tian
  given name: Peijun
author list: Agent
  family name: Zhao
  given name: Jianxin
author list: Agent
  family name: Zhang
  given name: Hao
author list: Agent
  family name: Wang
  given name: Gang
author list: Agent
  family name: Chen
  given name: Wei
doi: 10.7717/peerj.11103
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Kong et al.
attribution name: Kong et al.

A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs
type: item
type: AcademicArticle
description: The historical clade “Protorosauria” represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. “Protorosaurs” are characterized by their long necks, which are epitomized in the genus Tanystropheus and in Dinocephalosaurus orientalis. Recent phylogenetic analyses have indicated that “Protorosauria” is a polyphyletic clade, but the exact relationships of the various “protorosaur” taxa within the archosauromorph lineage is currently uncertain. Several taxa, although represented by relatively complete material, have previously not been assessed phylogenetically. We present a new phylogenetic hypothesis that comprises a wide range of archosauromorphs, including the most exhaustive sample of “protorosaurs” to date and several “protorosaur” taxa from the eastern Tethys margin that have not been included in any previous analysis. The polyphyly of “Protorosauria” is confirmed and therefore we suggest the usage of this term should be abandoned. Tanystropheidae is recovered as a monophyletic group and the Chinese taxa Dinocephalosaurus orientalis and Pectodens zhenyuensis form a new archosauromorph clade, Dinocephalosauridae, which is closely related to Tanystropheidae. The well-known crocopod and former “protorosaur” Prolacerta broomi is considerably less closely related to Archosauriformes than was previously considered.
format: application/pdf
format: text/html
creator: Stephan N.F. Spiekman
creator: Nicholas C. Fraser
creator: Torsten M. Scheyer
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11143
publisher: PeerJ Inc.
rights: © 2021 Spiekman et al.
abstract: The historical clade “Protorosauria” represents an important group of archosauromorph reptiles that had a wide geographic distribution between the Late Permian and Late Triassic. “Protorosaurs” are characterized by their long necks, which are epitomized in the genus Tanystropheus and in Dinocephalosaurus orientalis. Recent phylogenetic analyses have indicated that “Protorosauria” is a polyphyletic clade, but the exact relationships of the various “protorosaur” taxa within the archosauromorph lineage is currently uncertain. Several taxa, although represented by relatively complete material, have previously not been assessed phylogenetically. We present a new phylogenetic hypothesis that comprises a wide range of archosauromorphs, including the most exhaustive sample of “protorosaurs” to date and several “protorosaur” taxa from the eastern Tethys margin that have not been included in any previous analysis. The polyphyly of “Protorosauria” is confirmed and therefore we suggest the usage of this term should be abandoned. Tanystropheidae is recovered as a monophyletic group and the Chinese taxa Dinocephalosaurus orientalis and Pectodens zhenyuensis form a new archosauromorph clade, Dinocephalosauridae, which is closely related to Tanystropheidae. The well-known crocopod and former “protorosaur” Prolacerta broomi is considerably less closely related to Archosauriformes than was previously considered.
bibliographic citation: Spiekman et al. (2021) A new phylogenetic hypothesis of Tanystropheidae (Diapsida, Archosauromorpha) and other “protorosaurs”, and its implications for the early evolution of stem archosaurs. PeerJ 9:e11143 https://doi.org/10.7717/peerj.11143
date submitted: 2020-09-01
date accepted: 2021-03-02
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spiekman
  given name: Stephan N.F.
author list: Agent
  family name: Fraser
  given name: Nicholas C.
author list: Agent
  family name: Scheyer
  given name: Torsten M.
doi: 10.7717/peerj.11143
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: © 2021 Spiekman et al.
attribution name: Spiekman et al.

Predictors of work-related musculoskeletal symptoms in shoulders among nursing assistants working in nursing homes
type: item
type: AcademicArticle
description: Nursing assistants (NAs) working in nursing homes (NHs) are at higher risk for work-related musculoskeletal symptoms (WRMSs) than their counterparts working in other health care settings. Worldwide, NAs have ranked shoulders in the top three body parts at risk of WRMSs. However, factors associated with their shoulder WRMSs are currently unknown. The aim of this study was to identify these associated risk factors among NAs working in NHs. 440 NAs from 47 nursing homes (with 60–90% response rate from each nursing home), recruited by convenience sampling, participated in this cross-sectional study in 2014–2015. A validated and reliable questionnaire was used for data collection. Information on demographic, job content questionnaire (JCQ), perceived physical exertion (PE), workstyle, ergonomic and manual handling knowledge and other work-related factors was collected using a self-administered questionnaire. 53% of the participants reported experiencing with WRMSs in their shoulders. Nine associated factors of shoulder WRMSs were identified using bivariate analysis. With the adjustment of age and gender using multivariable logistic regression, body mass index (OR = .931, 95% CI [.874–.991]), job title of health workers (OR = 2.72, 95% CI [1.18–6.25]) and workstyle-working through pain (OR = 1.06, 95% CI [1.01–1.11]) remained as predictors. Effort should be directed at integrating “workstyle intervention” into lifestyle physical activity training for NAs.
format: application/pdf
format: text/html
creator: Kin Cheung
creator: Ka Yan Ma
creator: Hin Hei Cheung
creator: Chun Ho Lee
creator: In Mink Mavis Chan
creator: Sin Ting Cheung
creator: Wing Yee Chung
creator: Sun Sun Yeung
creator: Wing Chi Lo
subject: Epidemiology
subject: Nursing
subject: Public Health
description: doi:10.7717/peerj.11152
publisher: PeerJ Inc.
rights: © 2021 Cheung et al.
abstract: Nursing assistants (NAs) working in nursing homes (NHs) are at higher risk for work-related musculoskeletal symptoms (WRMSs) than their counterparts working in other health care settings. Worldwide, NAs have ranked shoulders in the top three body parts at risk of WRMSs. However, factors associated with their shoulder WRMSs are currently unknown. The aim of this study was to identify these associated risk factors among NAs working in NHs. 440 NAs from 47 nursing homes (with 60–90% response rate from each nursing home), recruited by convenience sampling, participated in this cross-sectional study in 2014–2015. A validated and reliable questionnaire was used for data collection. Information on demographic, job content questionnaire (JCQ), perceived physical exertion (PE), workstyle, ergonomic and manual handling knowledge and other work-related factors was collected using a self-administered questionnaire. 53% of the participants reported experiencing with WRMSs in their shoulders. Nine associated factors of shoulder WRMSs were identified using bivariate analysis. With the adjustment of age and gender using multivariable logistic regression, body mass index (OR = .931, 95% CI [.874–.991]), job title of health workers (OR = 2.72, 95% CI [1.18–6.25]) and workstyle-working through pain (OR = 1.06, 95% CI [1.01–1.11]) remained as predictors. Effort should be directed at integrating “workstyle intervention” into lifestyle physical activity training for NAs.
bibliographic citation: Cheung et al. (2021) Predictors of work-related musculoskeletal symptoms in shoulders among nursing assistants working in nursing homes. PeerJ 9:e11152 https://doi.org/10.7717/peerj.11152
date submitted: 2020-10-15
date accepted: 2021-03-03
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheung
  given name: Kin
author list: Agent
  family name: Ma
  given name: Ka Yan
author list: Agent
  family name: Cheung
  given name: Hin Hei
author list: Agent
  family name: Lee
  given name: Chun Ho
author list: Agent
  family name: Chan
  given name: In Mink Mavis
author list: Agent
  family name: Cheung
  given name: Sin Ting
author list: Agent
  family name: Chung
  given name: Wing Yee
author list: Agent
  family name: Yeung
  given name: Sun Sun
author list: Agent
  family name: Lo
  given name: Wing Chi
doi: 10.7717/peerj.11152
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Cheung et al.
attribution name: Cheung et al.

Intact tactile anisotropy despite altered hand perception in complex regional pain syndrome: rethinking the role of the primary sensory cortex in tactile and perceptual dysfunction
type: item
type: AcademicArticle
description: Complex Regional Pain Syndrome (CRPS) is characterised by pain, autonomic, sensory and motor abnormalities. It is associated with changes in the primary somatosensory cortex (S1 representation), reductions in tactile sensitivity (tested by two-point discrimination), and alterations in perceived hand size or shape (hand perception). The frequent co-occurrence of these three phenomena has led to the assumption that S1 changes underlie tactile sensitivity and perceptual disturbances. However, studies underpinning such a presumed relationship use tactile sensitivity paradigms that involve the processing of both non-spatial and spatial cues. Here, we used a task that evaluates anisotropy (i.e., orientation-dependency; a feature of peripheral and S1 representation) to interrogate spatial processing of tactile input in CRPS and its relation to hand perception. People with upper limb CRPS (n = 14) and controls with (n = 15) or without pain (n = 19) judged tactile distances between stimuli-pairs applied across and along the back of either hand to provide measures of tactile anisotropy. Hand perception was evaluated using a visual scaling task and questionnaires. Data were analysed with generalised estimating equations. Contrary to our hypotheses, tactile anisotropy was bilaterally preserved in CRPS, and the magnitude of anisotropic perception bias was comparable between groups. Hand perception was distorted in CRPS but not related to the magnitude of anisotropy or bias. Our results suggest against impairments in spatial processing of tactile input, and by implication S1 representation, as the cause of distorted hand perception in CRPS. Further work is warranted to elucidate the mechanisms of somatosensory dysfunction and distorted hand perception in CRPS.
format: application/pdf
format: text/html
creator: Annika Reinersmann
creator: Ian W. Skinner
creator: Thomas Lücke
creator: Nicola Massy-Westropp
creator: Henrik Rudolf
creator: G. Lorimer Moseley
creator: Tasha R. Stanton
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11156
publisher: PeerJ Inc.
rights: © 2021 Reinersmann et al.
abstract: Complex Regional Pain Syndrome (CRPS) is characterised by pain, autonomic, sensory and motor abnormalities. It is associated with changes in the primary somatosensory cortex (S1 representation), reductions in tactile sensitivity (tested by two-point discrimination), and alterations in perceived hand size or shape (hand perception). The frequent co-occurrence of these three phenomena has led to the assumption that S1 changes underlie tactile sensitivity and perceptual disturbances. However, studies underpinning such a presumed relationship use tactile sensitivity paradigms that involve the processing of both non-spatial and spatial cues. Here, we used a task that evaluates anisotropy (i.e., orientation-dependency; a feature of peripheral and S1 representation) to interrogate spatial processing of tactile input in CRPS and its relation to hand perception. People with upper limb CRPS (n = 14) and controls with (n = 15) or without pain (n = 19) judged tactile distances between stimuli-pairs applied across and along the back of either hand to provide measures of tactile anisotropy. Hand perception was evaluated using a visual scaling task and questionnaires. Data were analysed with generalised estimating equations. Contrary to our hypotheses, tactile anisotropy was bilaterally preserved in CRPS, and the magnitude of anisotropic perception bias was comparable between groups. Hand perception was distorted in CRPS but not related to the magnitude of anisotropy or bias. Our results suggest against impairments in spatial processing of tactile input, and by implication S1 representation, as the cause of distorted hand perception in CRPS. Further work is warranted to elucidate the mechanisms of somatosensory dysfunction and distorted hand perception in CRPS.
bibliographic citation: Reinersmann et al. (2021) Intact tactile anisotropy despite altered hand perception in complex regional pain syndrome: rethinking the role of the primary sensory cortex in tactile and perceptual dysfunction. PeerJ 9:e11156 https://doi.org/10.7717/peerj.11156
date submitted: 2019-07-01
date accepted: 2021-03-04
issued: 2021-05-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reinersmann
  given name: Annika
author list: Agent
  family name: Skinner
  given name: Ian W.
author list: Agent
  family name: Lücke
  given name: Thomas
author list: Agent
  family name: Massy-Westropp
  given name: Nicola
author list: Agent
  family name: Rudolf
  given name: Henrik
author list: Agent
  family name: Moseley
  given name: G. Lorimer
author list: Agent
  family name: Stanton
  given name: Tasha R.
doi: 10.7717/peerj.11156
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-03
copyright: ©2021 Reinersmann et al.
attribution name: Reinersmann et al.

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