PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
items: https://peerj.com/articles/11822
items: Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs
items: Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers
items: Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach
items: Towards an open and synergistic framework for mapping global land cover
items: Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens
items: The effect of uncorrected ametropia on ocular torsion induced by changes in fixation
items: Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking
items: Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models

iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
type: item
type: AcademicArticle
description: Sumoylation is the post-translational modification that is involved in the adaption of the cells and the functional properties of a large number of proteins. Sumoylation has key importance in subcellular concentration, transcriptional synchronization, chromatin remodeling, response to stress, and regulation of mitosis. Sumoylation is associated with developmental defects in many human diseases such as cancer, Huntington’s, Alzheimer’s, Parkinson’s, Spin cerebellar ataxia 1, and amyotrophic lateral sclerosis. The covalent bonding of Sumoylation is essential to inheriting part of the operative characteristics of some other proteins. For that reason, the prediction of the Sumoylation site has significance in the scientific community. A novel and efficient technique is proposed to predict the Sumoylation sites in proteins by incorporating Chou’s Pseudo Amino Acid Composition (PseAAC) with statistical moments-based features. The outcomes from the proposed system using 10 fold cross-validation testing are 94.51%, 94.24%, 94.79% and 0.8903% accuracy, sensitivity, specificity and MCC, respectively. The performance of the proposed system is so far the best in comparison to the other state-of-the-art methods. The codes for the current study are available on the GitHub repository using the link: https://github.com/csbioinfopk/iSumoK-PseAAC.
format: application/pdf
format: text/html
creator: Yaser Daanial Khan
creator: Nabeel Sabir Khan
creator: Sheraz Naseer
creator: Ahmad Hassan Butt
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.11581
publisher: PeerJ Inc.
rights: © 2021 Khan et al.
abstract: Sumoylation is the post-translational modification that is involved in the adaption of the cells and the functional properties of a large number of proteins. Sumoylation has key importance in subcellular concentration, transcriptional synchronization, chromatin remodeling, response to stress, and regulation of mitosis. Sumoylation is associated with developmental defects in many human diseases such as cancer, Huntington’s, Alzheimer’s, Parkinson’s, Spin cerebellar ataxia 1, and amyotrophic lateral sclerosis. The covalent bonding of Sumoylation is essential to inheriting part of the operative characteristics of some other proteins. For that reason, the prediction of the Sumoylation site has significance in the scientific community. A novel and efficient technique is proposed to predict the Sumoylation sites in proteins by incorporating Chou’s Pseudo Amino Acid Composition (PseAAC) with statistical moments-based features. The outcomes from the proposed system using 10 fold cross-validation testing are 94.51%, 94.24%, 94.79% and 0.8903% accuracy, sensitivity, specificity and MCC, respectively. The performance of the proposed system is so far the best in comparison to the other state-of-the-art methods. The codes for the current study are available on the GitHub repository using the link: https://github.com/csbioinfopk/iSumoK-PseAAC.
bibliographic citation: Khan et al. (2021) iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC. PeerJ 9:e11581 https://doi.org/10.7717/peerj.11581
date submitted: 2021-02-18
date accepted: 2021-05-19
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khan
  given name: Yaser Daanial
author list: Agent
  family name: Khan
  given name: Nabeel Sabir
author list: Agent
  family name: Naseer
  given name: Sheraz
author list: Agent
  family name: Butt
  given name: Ahmad Hassan
doi: 10.7717/peerj.11581
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: © 2021 Khan et al.
attribution name: Khan et al.

https://peerj.com/articles/11822
type: item
type: AcademicArticle
title: Effects of delivery via pressure-adjustable pneumatic gas-powered dart gun of three antimicrobial drugs (ceftiofur crystalline free acid, tildopirosin, and tulathromycin) on drug disposition and meat quality in cattle
description: Background Although Beef Quality Assurance guidelines do not recommend use of darting methods to deliver drugs, cattle in the US may be raised on farms and ranches without restraint facilities, and reports from the field suggest that dart guns are being used to deliver antimicrobial drugs. Few studies report whether this route of administration results in altered drug disposition or carcass quality. Methods Forty steers were blocked by sire and then randomly assigned to treatment with saline, ceftiofur crystalline free acid, tildipirosin, or tulathromycin delivered via dart gun. To assess drug disposition, eight ceftiofur, six tulathromycin, and six tildipirosin-treated calves were selected to measure plasma concentrations of drugs up to 10 days after drug administration. Steers were then fed a balanced ration for approximately 6.5 months and slaughtered. To evaluate carcass quality, tenderness of steaks from darted-side and non-darted sides was evaluated via Warner–Bratzler shear force testing. Due to the prohibition of extralabel routes of administration for ceftiofur in the U.S., animals treated with this drug did not enter the food supply. Results Ceftiofur disposition differed from published reports with lower mean Cmax but similar mean apparent elimination half-life. Tildipirosin disposition differed from published reports with lower Cmax and shorter apparent elimination half-life. Tulathromycin was similar to previous published reports but Cmax and apparent elimination half-life was highly variable. All steaks (from darted and non-darted sides) from cattle treated with ceftiofur and saline were more tender than from cattle treated with tulathromycin or tildipirosin (P = 0.003). There was a trend toward more tenderness in steaks from the non-darted compared to the darted side. Steaks from the darted side for one treatment, tildipirosin, were less tender than the non-darted side. Conclusions Pharmacokinetic parameters of ceftiofur crystalline free acid, tildipi…
format: application/pdf
format: text/html
creator: Thomas B. Hairgrove
creator: Virginia Fajt
creator: Ronald Gill
creator: Rhonda Miller
creator: Michael Miller
creator: Travis Mays
subject: Agricultural Science
subject: Food Science and Technology
subject: Veterinary Medicine
subject: Pharmacology
description: doi:10.7717/peerj.11822
publisher: PeerJ Inc.
rights: © 2021 Hairgrove et al.
abstract: Background Although Beef Quality Assurance guidelines do not recommend use of darting methods to deliver drugs, cattle in the US may be raised on farms and ranches without restraint facilities, and reports from the field suggest that dart guns are being used to deliver antimicrobial drugs. Few studies report whether this route of administration results in altered drug disposition or carcass quality. Methods Forty steers were blocked by sire and then randomly assigned to treatment with saline, ceftiofur crystalline free acid, tildipirosin, or tulathromycin delivered via dart gun. To assess drug disposition, eight ceftiofur, six tulathromycin, and six tildipirosin-treated calves were selected to measure plasma concentrations of drugs up to 10 days after drug administration. Steers were then fed a balanced ration for approximately 6.5 months and slaughtered. To evaluate carcass quality, tenderness of steaks from darted-side and non-darted sides was evaluated via Warner–Bratzler shear force testing. Due to the prohibition of extralabel routes of administration for ceftiofur in the U.S., animals treated with this drug did not enter the food supply. Results Ceftiofur disposition differed from published reports with lower mean Cmax but similar mean apparent elimination half-life. Tildipirosin disposition differed from published reports with lower Cmax and shorter apparent elimination half-life. Tulathromycin was similar to previous published reports but Cmax and apparent elimination half-life was highly variable. All steaks (from darted and non-darted sides) from cattle treated with ceftiofur and saline were more tender than from cattle treated with tulathromycin or tildipirosin (P = 0.003). There was a trend toward more tenderness in steaks from the non-darted compared to the darted side. Steaks from the darted side for one treatment, tildipirosin, were less tender than the non-darted side. Conclusions Pharmacokinetic parameters of ceftiofur crystalline free acid, tildipi…
bibliographic citation: Hairgrove et al. (2021) Effects of delivery via pressure-adjustable pneumatic gas-powered dart gun of three antimicrobial drugs (ceftiofur crystalline free acid, tildopirosin, and tulathromycin) on drug disposition and meat quality in cattle. PeerJ 9:e11822 https://doi.org/10.7717/peerj.11822
date submitted: 2020-02-19
date accepted: 2021-06-29
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hairgrove
  given name: Thomas B.
author list: Agent
  family name: Fajt
  given name: Virginia
author list: Agent
  family name: Gill
  given name: Ronald
author list: Agent
  family name: Miller
  given name: Rhonda
author list: Agent
  family name: Miller
  given name: Michael
author list: Agent
  family name: Mays
  given name: Travis
doi: 10.7717/peerj.11822
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: © 2021 Hairgrove et al.
attribution name: Hairgrove et al.

Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs
type: item
type: AcademicArticle
description: Background The aim of this study was to detect the optimal values for Age, Body Mass Index (BMI) and HOMA-IR of obese patients prior to surgery that results in a maximal decrease of visceral fat mass 6 months after bariatric surgery. Method In this study, 33 experimental set-ups were designed. This study was approved by Baskent University Medical and Health Sciences Research Board (Approval number: KA16/281). The study data consisted of 40 obese patients who lost weight through the bariatric surgery between February 2015 and December 2016. The values of BMI, Age and HOMA for the obese patients who lost weight through the bariatric surgery were evaluated in three categories and at three levels; the response variable was determined as the Change in Epicardial Fat Thickness (ΔEFT). Results As a result of CCD analysis, the optimum ΔEFT = 2.571 was determined when Age = 30.52, BMI = 45.30, and HOMA = 34.62. As a result of the BBD analysis, the optimum ΔEFT = 3.756 was determined, when Age = 38.36, BMI = 63.18, and HOMA = 14.95. The optimum ΔEFT was modeled with Contour and Response Surface plots. Conclusion Based on the two surface response models used in our study, the maximal decrease of visceral fat mass as assessed by measuring echography images of epicardial fat thickness can be obtained by bariatric surgery of persons who are between 31 and 38 year old, have a BMI between 45 and 63 kg/m2 and have a HOMA-IR 34 between 15 and 35. Central Composite Design and a Box-Behnken Design of suitable patient data predicted 35 optimal settings of independent variables for the maximal clinical response of an intervention.
format: application/pdf
format: text/html
creator: Ferhan Elmalı
creator: Mustafa Agâh Tekindal
creator: Cihan Altın
creator: Can Ateş
creator: Varlık Erol
subject: Cardiology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
subject: Statistics
subject: Metabolic Sciences
description: doi:10.7717/peerj.11831
publisher: PeerJ Inc.
rights: © 2021 Elmalıet al.
abstract: Background The aim of this study was to detect the optimal values for Age, Body Mass Index (BMI) and HOMA-IR of obese patients prior to surgery that results in a maximal decrease of visceral fat mass 6 months after bariatric surgery. Method In this study, 33 experimental set-ups were designed. This study was approved by Baskent University Medical and Health Sciences Research Board (Approval number: KA16/281). The study data consisted of 40 obese patients who lost weight through the bariatric surgery between February 2015 and December 2016. The values of BMI, Age and HOMA for the obese patients who lost weight through the bariatric surgery were evaluated in three categories and at three levels; the response variable was determined as the Change in Epicardial Fat Thickness (ΔEFT). Results As a result of CCD analysis, the optimum ΔEFT = 2.571 was determined when Age = 30.52, BMI = 45.30, and HOMA = 34.62. As a result of the BBD analysis, the optimum ΔEFT = 3.756 was determined, when Age = 38.36, BMI = 63.18, and HOMA = 14.95. The optimum ΔEFT was modeled with Contour and Response Surface plots. Conclusion Based on the two surface response models used in our study, the maximal decrease of visceral fat mass as assessed by measuring echography images of epicardial fat thickness can be obtained by bariatric surgery of persons who are between 31 and 38 year old, have a BMI between 45 and 63 kg/m2 and have a HOMA-IR 34 between 15 and 35. Central Composite Design and a Box-Behnken Design of suitable patient data predicted 35 optimal settings of independent variables for the maximal clinical response of an intervention.
bibliographic citation: Elmalı et al. (2021) Optimization of change in epicardial fat thickness for obese patients who lost weight via the bariatric surgery method using central composite and Box-Behnken experimental designs. PeerJ 9:e11831 https://doi.org/10.7717/peerj.11831
date submitted: 2021-01-06
date accepted: 2021-06-30
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elmalı
  given name: Ferhan
author list: Agent
  family name: Tekindal
  given name: Mustafa Agâh
author list: Agent
  family name: Altın
  given name: Cihan
author list: Agent
  family name: Ateş
  given name: Can
author list: Agent
  family name: Erol
  given name: Varlık
doi: 10.7717/peerj.11831
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: ©2021 Elmalıet al.
attribution name: Elmalıet al.

Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers
type: item
type: AcademicArticle
description: Background The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula. Methods Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci. Results Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.
format: application/pdf
format: text/html
creator: Riho Gross
creator: Leona Lovrenčić
creator: Mišel Jelić
creator: Frederic Grandjean
creator: Simona Ðuretanović
creator: Vladica Simić
creator: Oksana Burimski
creator: Lena Bonassin
creator: Marius-Ioan Groza
creator: Ivana Maguire
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11838
publisher: PeerJ Inc.
rights: © 2021 Gross et al.
abstract: Background The noble crayfish (Astacus astacus) is a native European species in decline, with a contracting range and diminishing populations and abundance. Previous studies revealed this species significant genetic diversity in the south-eastern Europe, with populations from the western and the southern part of the Balkan Peninsula being the most divergent. However, sampling of populations from the western part of the Balkans was limited and insufficient for investigating genetic diversity and population divergence for the purpose of conservation planning and management. Thus, the major aim of this study was to fill in this knowledge gap by studying mitochondrial and microsatellite DNA diversity, using 413 noble crayfish from 18 populations from waterbodies in the western part of the Balkan Peninsula. Methods Phylogenetic analysis of studied populations and their mitochondrial diversity were studied using COI and 16S sequences and population genetic structure was described using 15 microsatellite loci. Results Phylogeographic analysis revealed new divergent mitochondrial haplotypes for the populations in the westernmost part of the Balkan Peninsula in the tributaries of the Sava and Drava rivers. Microsatellite data indicated that these populations harbour an important component of genetic diversity within A. astacus. The results suggest that the western part of the Balkans played an important role as microrefugia during the Pleistocene climate fluctuations, allowing the long term persistence of A. astacus populations in this region. These results will also be important to supporting conservation decision making and planning.
bibliographic citation: Gross et al. (2021) Genetic diversity and structure of the noble crayfish populations in the Balkan Peninsula revealed by mitochondrial and microsatellite DNA markers. PeerJ 9:e11838 https://doi.org/10.7717/peerj.11838
date submitted: 2021-05-19
date accepted: 2021-07-01
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gross
  given name: Riho
author list: Agent
  family name: Lovrenčić
  given name: Leona
author list: Agent
  family name: Jelić
  given name: Mišel
author list: Agent
  family name: Grandjean
  given name: Frederic
author list: Agent
  family name: Ðuretanović
  given name: Simona
author list: Agent
  family name: Simić
  given name: Vladica
author list: Agent
  family name: Burimski
  given name: Oksana
author list: Agent
  family name: Bonassin
  given name: Lena
author list: Agent
  family name: Groza
  given name: Marius-Ioan
author list: Agent
  family name: Maguire
  given name: Ivana
doi: 10.7717/peerj.11838
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: ©2021 Gross et al.
attribution name: Gross et al.

Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach
type: item
type: AcademicArticle
description: Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clust…
format: application/pdf
format: text/html
creator: Sarahani Harun
creator: Nor Afiqah-Aleng
creator: Mohammad Bozlul Karim
creator: Md Altaf Ul Amin
creator: Shigehiko Kanaya
creator: Zeti-Azura Mohamed-Hussein
subject: Bioinformatics
subject: Computational Biology
subject: Plant Science
description: doi:10.7717/peerj.11876
publisher: PeerJ Inc.
rights: © 2021 Harun et al.
abstract: Background Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset. Methods We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher’s exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher’s exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters. Results The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clust…
bibliographic citation: Harun et al. (2021) Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach. PeerJ 9:e11876 https://doi.org/10.7717/peerj.11876
date submitted: 2021-05-06
date accepted: 2021-07-06
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harun
  given name: Sarahani
author list: Agent
  family name: Afiqah-Aleng
  given name: Nor
author list: Agent
  family name: Karim
  given name: Mohammad Bozlul
author list: Agent
  family name: Altaf Ul Amin
  given name: Md
author list: Agent
  family name: Kanaya
  given name: Shigehiko
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
doi: 10.7717/peerj.11876
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: © 2021 Harun et al.
attribution name: Harun et al.

Towards an open and synergistic framework for mapping global land cover
type: item
type: AcademicArticle
description: Global land-cover datasets are key sources of information for understanding the complex inter-actions between human activities and global change. They are also among the most critical variables for climate change studies. Over time, the spatial resolution of land cover maps has increased from the kilometer scale to 10-m scale. Single-type historical land cover datasets, including for forests, water, and impervious surfaces, have also been developed in recent years. In this study, we present an open and synergy framework to produce a global land cover dataset that combines supervised land cover classification and aggregation of existing multiple thematic land cover maps with the Google Earth Engine (GEE) cloud computing platform. On the basis of this method of classification and mosaicking, we derived a global land cover dataset for 6 years over a time span of 25 years. The overall accuracies of the six maps were around 75% and the accuracy for change area detection was over 70%. Our product also showed good similarity with the FAO and existing land cover maps.
format: application/pdf
format: text/html
creator: Jiyao Zhao
creator: Le Yu
creator: Han Liu
creator: Huabing Huang
creator: Jie Wang
creator: Peng Gong
subject: Environmental Sciences
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11877
publisher: PeerJ Inc.
rights: © 2021 Zhao et al.
abstract: Global land-cover datasets are key sources of information for understanding the complex inter-actions between human activities and global change. They are also among the most critical variables for climate change studies. Over time, the spatial resolution of land cover maps has increased from the kilometer scale to 10-m scale. Single-type historical land cover datasets, including for forests, water, and impervious surfaces, have also been developed in recent years. In this study, we present an open and synergy framework to produce a global land cover dataset that combines supervised land cover classification and aggregation of existing multiple thematic land cover maps with the Google Earth Engine (GEE) cloud computing platform. On the basis of this method of classification and mosaicking, we derived a global land cover dataset for 6 years over a time span of 25 years. The overall accuracies of the six maps were around 75% and the accuracy for change area detection was over 70%. Our product also showed good similarity with the FAO and existing land cover maps.
bibliographic citation: Zhao et al. (2021) Towards an open and synergistic framework for mapping global land cover. PeerJ 9:e11877 https://doi.org/10.7717/peerj.11877
date submitted: 2021-06-10
date accepted: 2021-07-07
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Jiyao
author list: Agent
  family name: Yu
  given name: Le
author list: Agent
  family name: Liu
  given name: Han
author list: Agent
  family name: Huang
  given name: Huabing
author list: Agent
  family name: Wang
  given name: Jie
author list: Agent
  family name: Gong
  given name: Peng
doi: 10.7717/peerj.11877
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: © 2021 Zhao et al.
attribution name: Zhao et al.

Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens
type: item
type: AcademicArticle
description: Background Natural minerals have many beneficial properties in poultry production, taking into account production as well as hygiene, health, safety, and quality of broiler meat. The aim of the study was to evaluate the effect of aluminosilicates in feed and litter on the growth performance and meat quality in chickens. Aluminosilicates, including halloysite and zeolite, could be a good alternative for synthetics, as a good solution for the environment in line with the current trends. Methods Five-hundred male Ross 308 chickens were managed in 5 groups (10 replicates/group): LITTER: 1, control; 2, 0.95 kg/m2 of halloysite; 3, 0.475 kg/m2 of halloysite and 0.475 zeolite; 4, 0.95 kg/m2 of zeolite; 5, 0.25 kg/m2of halloysite and 0.7 kg/m2 of zeolite. FEED: groups 2–5, halloysite and zeolite addition (25:75 ratio; 0.5–2%). Growth performance (body weight and feed indicators), carcass, and meat quality (pH, colour, water-holding capacity, chemical composition of muscles) were recorded. The experimental setup, where the aluminosilicate additives were applied simultaneously, was proposed and approved by experts after pilot testing and on the basis of extensive literature where feed or litter additives were tested. Results Body weight and its gain were higher in groups 3 and 4 than in 1, and feed intake was higher in 4. The weight of the carcass and some of its components, including muscles and skin with subcutaneous fat, were higher in 2–4. Water loss from leg muscles was lower in 4. The content of protein in muscles was significantly higher in 3. The addition of aluminosilicates in feed and litter had a positive effect on the growth performance and some traits of carcasses and meat quality, especially in group 3. Halloysite and zeolite can be used in feed and litter (especially 0.475 kg/m2 for each mineral in the wheat litter).
format: application/pdf
format: text/html
creator: Mirosław Banaszak
creator: Jakub Biesek
creator: Marek Adamski
subject: Agricultural Science
subject: Food Science and Technology
subject: Zoology
description: doi:10.7717/peerj.11918
publisher: PeerJ Inc.
rights: © 2021 Banaszak et al.
abstract: Background Natural minerals have many beneficial properties in poultry production, taking into account production as well as hygiene, health, safety, and quality of broiler meat. The aim of the study was to evaluate the effect of aluminosilicates in feed and litter on the growth performance and meat quality in chickens. Aluminosilicates, including halloysite and zeolite, could be a good alternative for synthetics, as a good solution for the environment in line with the current trends. Methods Five-hundred male Ross 308 chickens were managed in 5 groups (10 replicates/group): LITTER: 1, control; 2, 0.95 kg/m2 of halloysite; 3, 0.475 kg/m2 of halloysite and 0.475 zeolite; 4, 0.95 kg/m2 of zeolite; 5, 0.25 kg/m2of halloysite and 0.7 kg/m2 of zeolite. FEED: groups 2–5, halloysite and zeolite addition (25:75 ratio; 0.5–2%). Growth performance (body weight and feed indicators), carcass, and meat quality (pH, colour, water-holding capacity, chemical composition of muscles) were recorded. The experimental setup, where the aluminosilicate additives were applied simultaneously, was proposed and approved by experts after pilot testing and on the basis of extensive literature where feed or litter additives were tested. Results Body weight and its gain were higher in groups 3 and 4 than in 1, and feed intake was higher in 4. The weight of the carcass and some of its components, including muscles and skin with subcutaneous fat, were higher in 2–4. Water loss from leg muscles was lower in 4. The content of protein in muscles was significantly higher in 3. The addition of aluminosilicates in feed and litter had a positive effect on the growth performance and some traits of carcasses and meat quality, especially in group 3. Halloysite and zeolite can be used in feed and litter (especially 0.475 kg/m2 for each mineral in the wheat litter).
bibliographic citation: Banaszak et al. (2021) Wheat litter and feed with aluminosilicates for improved growth and meat quality in broiler chickens. PeerJ 9:e11918 https://doi.org/10.7717/peerj.11918
date submitted: 2021-04-01
date accepted: 2021-07-15
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Banaszak
  given name: Mirosław
author list: Agent
  family name: Biesek
  given name: Jakub
author list: Agent
  family name: Adamski
  given name: Marek
doi: 10.7717/peerj.11918
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: ©2021 Banaszak et al.
attribution name: Banaszak et al.

The effect of uncorrected ametropia on ocular torsion induced by changes in fixation
type: item
type: AcademicArticle
description: Background and Objective Ocular torsion, the eye movements to rotating around the line of sight, has not been well investigated regarding the influence of refractive errors. The purpose of this study was to investigate the effect of uncorrected ametropia on ocular torsion induced by fixation distances. Methods Seventy-two subjects were classified according to the type of their refractive error, and ocular torsion of the uncorrected eye was compared based on changes induced by different fixation distances. Ocular torsion was measured using a slit-lamp biomicroscope equipped with an ophthalmic camera and a half-silvered mirror. Results In all groups, excyclotorsion values increased as the fixation distance decreased, but the myopia and astigmatism groups had larger amounts of ocular torsion than the emmetropia group. In addition, as the amount of uncorrected myopia and astigmatism increased, the amount of ocular torsion increased. Conclusion Since the amount of ocular torsion caused by a change to a shorter fixation distance was larger when the refractive error was uncorrected, we suggest that ametropia should be fully corrected in patients frequently exposed to ocular torsion due to changes in fixation distance.
format: application/pdf
format: text/html
creator: Kwang-Keun Oh
creator: Byeong-Yeon Moon
creator: Hyun Gug Cho
creator: Sang-Yeob Kim
creator: Dong-Sik Yu
subject: Neurology
subject: Ophthalmology
description: doi:10.7717/peerj.11932
publisher: PeerJ Inc.
rights: © 2021 Oh et al.
abstract: Background and Objective Ocular torsion, the eye movements to rotating around the line of sight, has not been well investigated regarding the influence of refractive errors. The purpose of this study was to investigate the effect of uncorrected ametropia on ocular torsion induced by fixation distances. Methods Seventy-two subjects were classified according to the type of their refractive error, and ocular torsion of the uncorrected eye was compared based on changes induced by different fixation distances. Ocular torsion was measured using a slit-lamp biomicroscope equipped with an ophthalmic camera and a half-silvered mirror. Results In all groups, excyclotorsion values increased as the fixation distance decreased, but the myopia and astigmatism groups had larger amounts of ocular torsion than the emmetropia group. In addition, as the amount of uncorrected myopia and astigmatism increased, the amount of ocular torsion increased. Conclusion Since the amount of ocular torsion caused by a change to a shorter fixation distance was larger when the refractive error was uncorrected, we suggest that ametropia should be fully corrected in patients frequently exposed to ocular torsion due to changes in fixation distance.
bibliographic citation: Oh et al. (2021) The effect of uncorrected ametropia on ocular torsion induced by changes in fixation. PeerJ 9:e11932 https://doi.org/10.7717/peerj.11932
date submitted: 2021-03-26
date accepted: 2021-07-18
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oh
  given name: Kwang-Keun
author list: Agent
  family name: Moon
  given name: Byeong-Yeon
author list: Agent
  family name: Cho
  given name: Hyun Gug
author list: Agent
  family name: Kim
  given name: Sang-Yeob
author list: Agent
  family name: Yu
  given name: Dong-Sik
doi: 10.7717/peerj.11932
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: © 2021 Oh et al.
attribution name: Oh et al.

Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking
type: item
type: AcademicArticle
description: Loss of a lower limb below the knee, i.e., transtibial limb loss, and subsequently walking with a prosthesis, is generally thought to increase the metabolic cost of walking vs. able-bodied controls. However, high-functioning individuals with limb loss such as military service members often walk with the same metabolic cost as controls. Here we used a 3-D computer model and optimal control simulation approach to test the hypothesis that transtibial limb loss in and of itself causes an increase in metabolic cost of walking. We first generated N = 36 simulations of walking at 1.45 m/s using a “pre-limb loss” model, with two intact biological legs, that minimized deviations from able-bodied experimental walking mechanics with minimum muscular effort. We then repeated these simulations using a “post-limb loss” model, with the right leg’s ankle muscles and joints replaced with a simple model of a passive transtibial prosthesis. No other changes were made to the post-limb loss model’s remaining muscles or musculoskeletal parameters compared to the pre-limb loss case. Post-limb loss, the gait deviations on average increased by only 0.17 standard deviations from the experimental means, and metabolic cost did not increase (3.58 ± 0.10 J/m/kg pre-limb loss vs. 3.59 ± 0.12 J/m/kg post-limb loss, p = 0.65). The results suggest that transtibial limb loss does not directly lead to an increase in metabolic cost, even when deviations from able-bodied gait mechanics are minimized. High metabolic costs observed in individuals with transtibial limb loss may be due to secondary changes in strength or general fitness after limb loss, modifiable prosthesis issues, or to prioritization of factors that affect locomotor control other than gait deviations and muscular effort.
format: application/pdf
format: text/html
creator: Ross H. Miller
creator: Elizabeth Russell Esposito
subject: Bioengineering
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.11960
publisher: PeerJ Inc.
rights: © 2021 Miller and Russell Esposito
abstract: Loss of a lower limb below the knee, i.e., transtibial limb loss, and subsequently walking with a prosthesis, is generally thought to increase the metabolic cost of walking vs. able-bodied controls. However, high-functioning individuals with limb loss such as military service members often walk with the same metabolic cost as controls. Here we used a 3-D computer model and optimal control simulation approach to test the hypothesis that transtibial limb loss in and of itself causes an increase in metabolic cost of walking. We first generated N = 36 simulations of walking at 1.45 m/s using a “pre-limb loss” model, with two intact biological legs, that minimized deviations from able-bodied experimental walking mechanics with minimum muscular effort. We then repeated these simulations using a “post-limb loss” model, with the right leg’s ankle muscles and joints replaced with a simple model of a passive transtibial prosthesis. No other changes were made to the post-limb loss model’s remaining muscles or musculoskeletal parameters compared to the pre-limb loss case. Post-limb loss, the gait deviations on average increased by only 0.17 standard deviations from the experimental means, and metabolic cost did not increase (3.58 ± 0.10 J/m/kg pre-limb loss vs. 3.59 ± 0.12 J/m/kg post-limb loss, p = 0.65). The results suggest that transtibial limb loss does not directly lead to an increase in metabolic cost, even when deviations from able-bodied gait mechanics are minimized. High metabolic costs observed in individuals with transtibial limb loss may be due to secondary changes in strength or general fitness after limb loss, modifiable prosthesis issues, or to prioritization of factors that affect locomotor control other than gait deviations and muscular effort.
bibliographic citation: Miller et al. (2021) Transtibial limb loss does not increase metabolic cost in three-dimensional computer simulations of human walking. PeerJ 9:e11960 https://doi.org/10.7717/peerj.11960
date submitted: 2021-04-01
date accepted: 2021-07-21
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miller
  given name: Ross H.
author list: Agent
  family name: Russell Esposito
  given name: Elizabeth
doi: 10.7717/peerj.11960
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: ©2021 Miller and Russell Esposito
attribution name: Miller and Russell Esposito

Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models
type: item
type: AcademicArticle
description: Background Accurate diagnosis of major depressive disorder (MDD) remains difficult, and one of the key challenges in diagnosing MDD is the lack of reliable diagnostic biomarkers. The objective of this study was to explore gene networks and identify potential biomarkers for MDD. Methods In the present study, we performed a comprehensive analysis of the mRNA expression profiles using blood samples of four patients with MDD and four controls by RNA sequencing. Differentially expressed genes (DEGs) were screened, and functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. All DEGs were inputted to the STRING database to build a PPI network, and the top 10 hub genes were screened using the cytoHubba plugin of the Cytoscape software. The relative expression of 10 key genes was identified by quantitative real-time polymerase chain reaction (qRT-PCR) of blood samples from 50 MDD patients and 50 controls. Plasma levels of SQSTM1 and TNFα were measured using an enzyme-linked immunosorbent assay in blood samples of 44 MDD patients and 44 controls. A sucrose preference test was used to evaluate depression-like behavior in chronic unpredictable mild stress (CUMS) model rats. Immunofluorescence assay and western blotting were performed to study the expression of proteins in the brain samples of CUMS model rats Results We identified 247 DEGs that were closely associated with MDD. Gene ontology analyses suggested that the DEGs were mainly enriched in negative regulation of transcription by RNA polymerase II promoter, cytoplasm, and protein binding. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the DEGs were significantly enriched in the MAPK signaling pathway. Ten hub genes were screened through the PPI network, and qRT-PCR assay revealed that one and six genes were downregulated and upregulated, respectively; however, SMARCA2, PPP3CB, and RAB5C were not detected. Pathw…
format: application/pdf
format: text/html
creator: Jun He
creator: Zhenkui Ren
creator: Wansong Xia
creator: Cao Zhou
creator: Bin Bi
creator: Wenfeng Yu
creator: Li Zuo
subject: Molecular Biology
subject: Cognitive Disorders
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11694
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Background Accurate diagnosis of major depressive disorder (MDD) remains difficult, and one of the key challenges in diagnosing MDD is the lack of reliable diagnostic biomarkers. The objective of this study was to explore gene networks and identify potential biomarkers for MDD. Methods In the present study, we performed a comprehensive analysis of the mRNA expression profiles using blood samples of four patients with MDD and four controls by RNA sequencing. Differentially expressed genes (DEGs) were screened, and functional and pathway enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery. All DEGs were inputted to the STRING database to build a PPI network, and the top 10 hub genes were screened using the cytoHubba plugin of the Cytoscape software. The relative expression of 10 key genes was identified by quantitative real-time polymerase chain reaction (qRT-PCR) of blood samples from 50 MDD patients and 50 controls. Plasma levels of SQSTM1 and TNFα were measured using an enzyme-linked immunosorbent assay in blood samples of 44 MDD patients and 44 controls. A sucrose preference test was used to evaluate depression-like behavior in chronic unpredictable mild stress (CUMS) model rats. Immunofluorescence assay and western blotting were performed to study the expression of proteins in the brain samples of CUMS model rats Results We identified 247 DEGs that were closely associated with MDD. Gene ontology analyses suggested that the DEGs were mainly enriched in negative regulation of transcription by RNA polymerase II promoter, cytoplasm, and protein binding. Moreover, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that the DEGs were significantly enriched in the MAPK signaling pathway. Ten hub genes were screened through the PPI network, and qRT-PCR assay revealed that one and six genes were downregulated and upregulated, respectively; however, SMARCA2, PPP3CB, and RAB5C were not detected. Pathw…
bibliographic citation: He et al. (2021) Identification of key genes and crucial pathways for major depressive disorder using peripheral blood samples and chronic unpredictable mild stress rat models. PeerJ 9:e11694 https://doi.org/10.7717/peerj.11694
date submitted: 2021-01-11
date accepted: 2021-06-08
issued: 2021-08-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: He
  given name: Jun
author list: Agent
  family name: Ren
  given name: Zhenkui
author list: Agent
  family name: Xia
  given name: Wansong
author list: Agent
  family name: Zhou
  given name: Cao
author list: Agent
  family name: Bi
  given name: Bin
author list: Agent
  family name: Yu
  given name: Wenfeng
author list: Agent
  family name: Zuo
  given name: Li
doi: 10.7717/peerj.11694
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-03
copyright: ©2021 He et al.
attribution name: He et al.

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