PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan
items: Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model
items: Eating for numbing: a community-based study of trauma exposure, emotion dysregulation, dissociation, body dissatisfaction and eating disorder symptoms
items: Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery
items: Global warming and neurological practice: systematic review
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

Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan
type: item
type: AcademicArticle
description: Background Over 3 million people lost their lives across the globe due to the COVID-19 related pandemic. The unprecedented restrictions on mobility have imposed in the form of isolation, quarantines, and lockdowns to curb the profound effects of the pandemic and retain physical health. This study examined the relationship between various pain levels, demographic variables and patient satisfaction with COVID-19 during isolation. Methods The primary data in this study were collected from isolated patients during their isolation and treatment in a public hospital. We obtained information from patients with COVID-19 (N = 100) about their demographic characteristics, varying levels of pain, and satisfaction with the services provided during the isolation period. We computed the descriptive statistics to explain the profile of participants, ANOVA was used to find out the difference between various groups on patient satisfaction, and structural equation modeling was performed to examine the link between pain levels, demographic factors, and patient satisfaction. This analysis was performed with STATA and SmartPLS-3. Results The findings of this study ascertained that respondent’s education (Beta, β = 2.961, p = 0.003), assets such as possession of a house (β = 4.563, p = 0.000), perception of income adequacy during the lockdown (=2.299, p = 0.022), and negligence in prevention (β = 1.975, p = 0.049) significantly affects patient satisfaction during the isolation period. Moreover, satisfaction with life, physicians and medicine, income adequacy, and fear of the participants was significantly linked to the pain level (Model F-stat = 86.323, p = 0.0001). Patients who were satisfied with their treatment had significantly lower odds of having pain (OR 0.023, 95% CI [0.001–0.0452]). Patients who had enough income to meet their basic necessities were found to have significantly lower odds of having pain (OR 0.155, 95% CI [0.032–0.740]. Discussion and Conclusion We conclude that a…
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format: text/html
creator: Wajiha Haq
creator: Siddrah Irfan
creator: Syed Hassan Raza
creator: Waqar Ahmed
creator: Mian Alam
creator: Samia Wasif
creator: Muhammad Wasif Malik
creator: Saeed Ahmad
subject: Anesthesiology and Pain Management
subject: Global Health
subject: Infectious Diseases
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11859
publisher: PeerJ Inc.
rights: © 2021 Haq et al.
abstract: Background Over 3 million people lost their lives across the globe due to the COVID-19 related pandemic. The unprecedented restrictions on mobility have imposed in the form of isolation, quarantines, and lockdowns to curb the profound effects of the pandemic and retain physical health. This study examined the relationship between various pain levels, demographic variables and patient satisfaction with COVID-19 during isolation. Methods The primary data in this study were collected from isolated patients during their isolation and treatment in a public hospital. We obtained information from patients with COVID-19 (N = 100) about their demographic characteristics, varying levels of pain, and satisfaction with the services provided during the isolation period. We computed the descriptive statistics to explain the profile of participants, ANOVA was used to find out the difference between various groups on patient satisfaction, and structural equation modeling was performed to examine the link between pain levels, demographic factors, and patient satisfaction. This analysis was performed with STATA and SmartPLS-3. Results The findings of this study ascertained that respondent’s education (Beta, β = 2.961, p = 0.003), assets such as possession of a house (β = 4.563, p = 0.000), perception of income adequacy during the lockdown (=2.299, p = 0.022), and negligence in prevention (β = 1.975, p = 0.049) significantly affects patient satisfaction during the isolation period. Moreover, satisfaction with life, physicians and medicine, income adequacy, and fear of the participants was significantly linked to the pain level (Model F-stat = 86.323, p = 0.0001). Patients who were satisfied with their treatment had significantly lower odds of having pain (OR 0.023, 95% CI [0.001–0.0452]). Patients who had enough income to meet their basic necessities were found to have significantly lower odds of having pain (OR 0.155, 95% CI [0.032–0.740]. Discussion and Conclusion We conclude that a…
bibliographic citation: Haq et al. (2021) Pain and satisfaction: the case of isolated COVID-19 patients of Pakistan. PeerJ 9:e11859 https://doi.org/10.7717/peerj.11859
date submitted: 2021-02-08
date accepted: 2021-07-05
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Haq
  given name: Wajiha
author list: Agent
  family name: Irfan
  given name: Siddrah
author list: Agent
  family name: Raza
  given name: Syed Hassan
author list: Agent
  family name: Ahmed
  given name: Waqar
author list: Agent
  family name: Alam
  given name: Mian
author list: Agent
  family name: Wasif
  given name: Samia
author list: Agent
  family name: Malik
  given name: Muhammad Wasif
author list: Agent
  family name: Ahmad
  given name: Saeed
doi: 10.7717/peerj.11859
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Haq et al.
attribution name: Haq et al.

Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model
type: item
type: AcademicArticle
description: Intraoperative identification of parathyroid glands is a tough task for surgeons performing thyroid or parathyroid surgery, because the small size, color and shape of these glands hinder their discrimination from other cervical tissues. In 2011, Paras described the autofluorescence of parathyroid glands, a property that could facilitate their intraoperative identification. Parathyroid glands submitted to a 785 nm laser beam emit fluorescence in the near infrared range, with a peak at 822 nm. As the intrinsic properties of secretory tissues may be affected by the exposure to the near infrared light, a situation that could preclude their intraoperative utilization, the authors compared the structural and ultra-structural patterns of rat’s thyroid and parathyroid glands submitted to irradiation replicating the conditions that allow their intraoperative identification, with those of non irradiated animals. Twenty-four Wistar rats were divided into six groups: animals of Groups 1, 3 and 5 were submitted under general anesthesia to direct irradiation of the cervical area with a 780 nm LED light for 3 minutes through a cervical incision, and animals of Groups 2, 4 and 6 were submitted to cervical dissection without irradiation. Animals of were euthanized immediately (Groups 1 and 2), at Day 30 (Groups 3 and 4) at and at Day 60 (Groups 5 and 6) and thyroid and parathyroid glands were removed: one lobe was prepared for conventional pathological examination and the other lobe for electron microscopy observed by three experienced pathological experts. Twenty-four samples were prepared for conventional histology and there were no alterations reported in any group. Due to technical problems, only 21 samples were observed by electron microscopy and there were no differences in the ultrastructure of parathyroid and thyroid glands, namely the nuclear pattern, mitochondria, endoplasmic reticulum or secretory granules, in any of the groups. These results confirm the innocuity of near…
format: application/pdf
format: text/html
creator: Carlos Serra
creator: Luis Silveira
subject: Biochemistry
subject: Drugs and Devices
subject: Surgery and Surgical Specialties
subject: Histology
description: doi:10.7717/peerj.11891
publisher: PeerJ Inc.
rights: © 2021 Serra and Silveira
abstract: Intraoperative identification of parathyroid glands is a tough task for surgeons performing thyroid or parathyroid surgery, because the small size, color and shape of these glands hinder their discrimination from other cervical tissues. In 2011, Paras described the autofluorescence of parathyroid glands, a property that could facilitate their intraoperative identification. Parathyroid glands submitted to a 785 nm laser beam emit fluorescence in the near infrared range, with a peak at 822 nm. As the intrinsic properties of secretory tissues may be affected by the exposure to the near infrared light, a situation that could preclude their intraoperative utilization, the authors compared the structural and ultra-structural patterns of rat’s thyroid and parathyroid glands submitted to irradiation replicating the conditions that allow their intraoperative identification, with those of non irradiated animals. Twenty-four Wistar rats were divided into six groups: animals of Groups 1, 3 and 5 were submitted under general anesthesia to direct irradiation of the cervical area with a 780 nm LED light for 3 minutes through a cervical incision, and animals of Groups 2, 4 and 6 were submitted to cervical dissection without irradiation. Animals of were euthanized immediately (Groups 1 and 2), at Day 30 (Groups 3 and 4) at and at Day 60 (Groups 5 and 6) and thyroid and parathyroid glands were removed: one lobe was prepared for conventional pathological examination and the other lobe for electron microscopy observed by three experienced pathological experts. Twenty-four samples were prepared for conventional histology and there were no alterations reported in any group. Due to technical problems, only 21 samples were observed by electron microscopy and there were no differences in the ultrastructure of parathyroid and thyroid glands, namely the nuclear pattern, mitochondria, endoplasmic reticulum or secretory granules, in any of the groups. These results confirm the innocuity of near…
bibliographic citation: Serra et al. (2021) Evaluation of structural and ultrastructural changes in thyroid and parathyroid glands after near infrared irradiation: study on an animal model. PeerJ 9:e11891 https://doi.org/10.7717/peerj.11891
date submitted: 2021-04-15
date accepted: 2021-07-10
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Serra
  given name: Carlos
author list: Agent
  family name: Silveira
  given name: Luis
doi: 10.7717/peerj.11891
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Serra and Silveira
attribution name: Serra and Silveira

Eating for numbing: a community-based study of trauma exposure, emotion dysregulation, dissociation, body dissatisfaction and eating disorder symptoms
type: item
type: AcademicArticle
description: Objective The current study tests the relationship between eating disorder (ED) symptoms and trauma exposure. The mechanisms via which trauma is related to ED symptoms have not been sufficiently examined. This study examines the complex role of dissociation and emotional dysregulation in the context of trauma, BMI, ED symptoms and body dissatisfaction (BD). We hypothesized that dissociation and emotional dysregulation would mediate the relationship between trauma exposure and ED symptoms/BD. We further hypothesized that BMI would play a moderating role in this association. Method A community sample of 229 (16.2% male) participants, with a mean age of 29.08 ± 10.68 reported online on traumatic events (Life Events Checklist), dissociation (Dissociative Experiences Scale-II), emotional dysregulation (Difficulties in Emotional Regulation Scale), ED symptoms (Eating Disorders Examination-Questionnaire) and BD (Figure Rating Scale). Results Participants reported experiencing a mean of 2.87 ± 2.27 traumatic events, with a relatively high percentage (~86%) reporting at least one. The most commonly reported traumatic events were transportation accidents and physical assault. Although frequency of traumatic events did not directly predict ED symptoms, BMI, dissociation, emotional dysregulation and BD did. An SEM model showed that traumatic events predicted ED symptoms indirectly through dissociation, emotional dysregulation and BMI. Dissociation and emotional dysregulation predicted ED symptoms directly. BMI also moderated the association between traumatic events and both ED symptoms and BD. Conclusions Therapists treating patients with high BMI or obesity should be aware of these relationships and investigate the possibility that trauma and/or PTSD may underlie the presenting disordered eating or eating disorder.
format: application/pdf
format: text/html
creator: Lilac Lev-ari
creator: Ada H. Zohar
creator: Rachel Bachner-Melman
subject: Nutrition
subject: Psychiatry and Psychology
subject: Metabolic Sciences
description: doi:10.7717/peerj.11899
publisher: PeerJ Inc.
rights: © 2021 Lev-ari et al.
abstract: Objective The current study tests the relationship between eating disorder (ED) symptoms and trauma exposure. The mechanisms via which trauma is related to ED symptoms have not been sufficiently examined. This study examines the complex role of dissociation and emotional dysregulation in the context of trauma, BMI, ED symptoms and body dissatisfaction (BD). We hypothesized that dissociation and emotional dysregulation would mediate the relationship between trauma exposure and ED symptoms/BD. We further hypothesized that BMI would play a moderating role in this association. Method A community sample of 229 (16.2% male) participants, with a mean age of 29.08 ± 10.68 reported online on traumatic events (Life Events Checklist), dissociation (Dissociative Experiences Scale-II), emotional dysregulation (Difficulties in Emotional Regulation Scale), ED symptoms (Eating Disorders Examination-Questionnaire) and BD (Figure Rating Scale). Results Participants reported experiencing a mean of 2.87 ± 2.27 traumatic events, with a relatively high percentage (~86%) reporting at least one. The most commonly reported traumatic events were transportation accidents and physical assault. Although frequency of traumatic events did not directly predict ED symptoms, BMI, dissociation, emotional dysregulation and BD did. An SEM model showed that traumatic events predicted ED symptoms indirectly through dissociation, emotional dysregulation and BMI. Dissociation and emotional dysregulation predicted ED symptoms directly. BMI also moderated the association between traumatic events and both ED symptoms and BD. Conclusions Therapists treating patients with high BMI or obesity should be aware of these relationships and investigate the possibility that trauma and/or PTSD may underlie the presenting disordered eating or eating disorder.
bibliographic citation: Lev-ari et al. (2021) Eating for numbing: a community-based study of trauma exposure, emotion dysregulation, dissociation, body dissatisfaction and eating disorder symptoms. PeerJ 9:e11899 https://doi.org/10.7717/peerj.11899
date submitted: 2021-03-03
date accepted: 2021-07-13
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lev-ari
  given name: Lilac
author list: Agent
  family name: Zohar
  given name: Ada H.
author list: Agent
  family name: Bachner-Melman
  given name: Rachel
doi: 10.7717/peerj.11899
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: © 2021 Lev-ari et al.
attribution name: Lev-ari et al.

Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery
type: item
type: AcademicArticle
description: Background The widespread use of low-dose chest CT screening has improved the detection of early lung adenocarcinoma. Radical surgery is the best treatment strategy for patients with early lung adenocarcinoma; however, some patients present with postoperative recurrence and poor prognosis. Through this study, we hope to establish a model that can identify patients that are prone to recurrence and have poor prognosis after surgery for early lung adenocarcinoma. Materials and Methods We screened prognostic and relapse-related genes using The Cancer Genome Atlas (TCGA) database and the GSE50081 dataset from the Gene Expression Omnibus (GEO) database. The GSE30219 dataset was used to further screen target genes and construct a risk prognosis signature. Time-dependent ROC analysis, calibration degree analysis, and DCA were used to evaluate the reliability of the model. We validated the TCGA dataset, GSE50081, and GSE30219 internally. External validation was conducted in the GSE31210 dataset. Results A novel four-gene signature (INPP5B, FOSL2, CDCA3, RASAL2) was established to predict relapse-related survival outcomes in patients with early lung adenocarcinoma after surgery. The discovery of these genes may reveal the molecular mechanism of recurrence and poor prognosis of early lung adenocarcinoma. In addition, ROC analysis, calibration analysis and DCA were used to verify the genetic signature internally and externally. Our results showed that our gene signature had a good predictive ability for recurrence and prognosis. Conclusions We established a four-gene signature and predictive model to predict the recurrence and corresponding survival rates in patients with early lung adenocarcinoma after surgery. These may be helpful for reforumulating post-operative consolidation treatment strategies.
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creator: Peng Han
creator: Jiaqi Yue
creator: Kangle Kong
creator: Shan Hu
creator: Peng Cao
creator: Yu Deng
creator: Fan Li
creator: Bo Zhao
subject: Bioinformatics
subject: Genomics
subject: Oncology
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.11923
publisher: PeerJ Inc.
rights: © 2021 Han et al.
abstract: Background The widespread use of low-dose chest CT screening has improved the detection of early lung adenocarcinoma. Radical surgery is the best treatment strategy for patients with early lung adenocarcinoma; however, some patients present with postoperative recurrence and poor prognosis. Through this study, we hope to establish a model that can identify patients that are prone to recurrence and have poor prognosis after surgery for early lung adenocarcinoma. Materials and Methods We screened prognostic and relapse-related genes using The Cancer Genome Atlas (TCGA) database and the GSE50081 dataset from the Gene Expression Omnibus (GEO) database. The GSE30219 dataset was used to further screen target genes and construct a risk prognosis signature. Time-dependent ROC analysis, calibration degree analysis, and DCA were used to evaluate the reliability of the model. We validated the TCGA dataset, GSE50081, and GSE30219 internally. External validation was conducted in the GSE31210 dataset. Results A novel four-gene signature (INPP5B, FOSL2, CDCA3, RASAL2) was established to predict relapse-related survival outcomes in patients with early lung adenocarcinoma after surgery. The discovery of these genes may reveal the molecular mechanism of recurrence and poor prognosis of early lung adenocarcinoma. In addition, ROC analysis, calibration analysis and DCA were used to verify the genetic signature internally and externally. Our results showed that our gene signature had a good predictive ability for recurrence and prognosis. Conclusions We established a four-gene signature and predictive model to predict the recurrence and corresponding survival rates in patients with early lung adenocarcinoma after surgery. These may be helpful for reforumulating post-operative consolidation treatment strategies.
bibliographic citation: Han et al. (2021) Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery. PeerJ 9:e11923 https://doi.org/10.7717/peerj.11923
date submitted: 2021-03-12
date accepted: 2021-07-16
issued: 2021-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Peng
author list: Agent
  family name: Yue
  given name: Jiaqi
author list: Agent
  family name: Kong
  given name: Kangle
author list: Agent
  family name: Hu
  given name: Shan
author list: Agent
  family name: Cao
  given name: Peng
author list: Agent
  family name: Deng
  given name: Yu
author list: Agent
  family name: Li
  given name: Fan
author list: Agent
  family name: Zhao
  given name: Bo
doi: 10.7717/peerj.11923
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-05
copyright: ©2021 Han et al.
attribution name: Han et al.

Global warming and neurological practice: systematic review
type: item
type: AcademicArticle
description: Background Climate change, including global warming, will cause poorer global health and rising numbers of environmental refugees. As neurological disorders account for a major share of morbidity and mortality worldwide, global warming is also destined to alter neurological practice; however, to what extent and by which mechanisms is unknown. We aimed to collect information about the effects of ambient temperatures and human migration on the epidemiology and clinical manifestations of neurological disorders. Methods We searched PubMed and Scopus from 01/2000 to 12/2020 for human studies addressing the influence of ambient temperatures and human migration on Alzheimer’s and non-Alzheimer’s dementia, epilepsy, headache/migraine, multiple sclerosis, Parkinson’s disease, stroke, and tick-borne encephalitis (a model disease for neuroinfections). The protocol was pre-registered with PROSPERO (2020 CRD42020147543). Results Ninety-three studies met inclusion criteria, 84 of which reported on ambient temperatures and nine on migration. Overall, most temperature studies suggested a relationship between increasing temperatures and higher mortality and/or morbidity, whereas results were more ambiguous for migration studies. However, we were unable to identify a single adequately designed study addressing how global warming and human migration will change neurological practice. Still, extracted data indicated multiple ways by which these aspects might alter neurological morbidity and mortality soon. Conclusion Significant heterogeneity exists across studies with respect to methodology, outcome measures, confounders and study design, including lack of data from low-income countries, but the evidence so far suggests that climate change will affect the practice of all major neurological disorders in the near future. Adequately designed studies to address this issue are urgently needed, requiring concerted efforts from the entire neurological community.
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format: text/html
creator: Moshgan Amiri
creator: Costanza Peinkhofer
creator: Marwan H. Othman
creator: Teodoro De Vecchi
creator: Vardan Nersesjan
creator: Daniel Kondziella
subject: Neurology
subject: Public Health
subject: Climate Change Biology
description: doi:10.7717/peerj.11941
publisher: PeerJ Inc.
rights: © 2021 Amiri et al.
abstract: Background Climate change, including global warming, will cause poorer global health and rising numbers of environmental refugees. As neurological disorders account for a major share of morbidity and mortality worldwide, global warming is also destined to alter neurological practice; however, to what extent and by which mechanisms is unknown. We aimed to collect information about the effects of ambient temperatures and human migration on the epidemiology and clinical manifestations of neurological disorders. Methods We searched PubMed and Scopus from 01/2000 to 12/2020 for human studies addressing the influence of ambient temperatures and human migration on Alzheimer’s and non-Alzheimer’s dementia, epilepsy, headache/migraine, multiple sclerosis, Parkinson’s disease, stroke, and tick-borne encephalitis (a model disease for neuroinfections). The protocol was pre-registered with PROSPERO (2020 CRD42020147543). Results Ninety-three studies met inclusion criteria, 84 of which reported on ambient temperatures and nine on migration. Overall, most temperature studies suggested a relationship between increasing temperatures and higher mortality and/or morbidity, whereas results were more ambiguous for migration studies. However, we were unable to identify a single adequately designed study addressing how global warming and human migration will change neurological practice. Still, extracted data indicated multiple ways by which these aspects might alter neurological morbidity and mortality soon. Conclusion Significant heterogeneity exists across studies with respect to methodology, outcome measures, confounders and study design, including lack of data from low-income countries, but the evidence so far suggests that climate change will affect the practice of all major neurological disorders in the near future. Adequately designed studies to address this issue are urgently needed, requiring concerted efforts from the entire neurological community.
bibliographic citation: Amiri et al. (2021) Global warming and neurological practice: systematic review. PeerJ 9:e11941 https://doi.org/10.7717/peerj.11941
date submitted: 2021-04-28
date accepted: 2021-07-19
issued: 2021-08-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amiri
  given name: Moshgan
author list: Agent
  family name: Peinkhofer
  given name: Costanza
author list: Agent
  family name: Othman
  given name: Marwan H.
author list: Agent
  family name: De Vecchi
  given name: Teodoro
author list: Agent
  family name: Nersesjan
  given name: Vardan
author list: Agent
  family name: Kondziella
  given name: Daniel
doi: 10.7717/peerj.11941
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-04
copyright: ©2021 Amiri et al.
attribution name: Amiri et al.

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.

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