PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection
items: https://peerj.com/articles/10727
items: Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
items: Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa
items: Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary
items: The influence of estrogen deficiency on the structural and mechanical properties of rat cortical bone
items: Geographic disparities, determinants, and temporal changes in the prevalence of pre-diabetes in Florida
items: Effectiveness of iron polymaltose complex in treatment and prevention of iron deficiency anemia in children: a systematic review and meta-analysis
items: Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage
items: The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection
type: item
type: AcademicArticle
description: Although liver cirrhosis and hepatocellular carcinoma are major consequences of hepatitis C (HCV), there has been an increasing number of studies examining extrahepatic manifestations, especially those caused by systemic chronic inflammation and metabolic complications that might predispose HCV patients to atherosclerosis and ischemic cerebrovascular disease (CVD). The aim of our study was to assess E-selectin, VCAM-1, ICAM-1 and VEGF-A serum levels in patients with chronic HCV infection and to correlate them with cerebrovascular reactivity. A blood sample was taken from eighteen patients with chronic hepatitis C infection and from the same number of healthy blood donors in the control group. The aim was to analyse markers of endothelial dysfunction and to correlate them with cerebrovascular reactivity expressed as breath-holding index (BHI) determined using transcranial color Doppler. The obtained results revealed significant differences between the groups in all endothelial markers except for the E selectin. While the ICAM-1 and sVCAM-1 were significantly increased in the hepatitis group, VEGF-A was significantly decreased. A significant reduction of 0.5 (95% CI 0.2, 0.8) in the mean BHI was found in the hepatitis group (mean BHI 0.64) compared to controls (mean BHI 1.10). No significant association between the BHI and any of the endothelial markers was found in the control group, while in the hepatitis group, the scatter plot of ICAM-1 vs BHI suggested that the association might be present. In conclusion, the results of this study confirm an association between a chronic HCV infection and altered cerebrovascular reactivity as well as higher levels of markers of endothelial activation (ICAM-1, VCAM-1) as possible indicators of an increased CVD risk.
format: application/pdf
format: text/html
creator: Mirela Pavicic Ivelja
creator: Kresimir Dolic
creator: Leida Tandara
creator: Nikola Perkovic
creator: Antonio Mestrovic
creator: Ivo Ivic
subject: Virology
subject: Infectious Diseases
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10723
publisher: PeerJ Inc.
rights: © 2021 Pavicic Ivelja et al.
abstract: Although liver cirrhosis and hepatocellular carcinoma are major consequences of hepatitis C (HCV), there has been an increasing number of studies examining extrahepatic manifestations, especially those caused by systemic chronic inflammation and metabolic complications that might predispose HCV patients to atherosclerosis and ischemic cerebrovascular disease (CVD). The aim of our study was to assess E-selectin, VCAM-1, ICAM-1 and VEGF-A serum levels in patients with chronic HCV infection and to correlate them with cerebrovascular reactivity. A blood sample was taken from eighteen patients with chronic hepatitis C infection and from the same number of healthy blood donors in the control group. The aim was to analyse markers of endothelial dysfunction and to correlate them with cerebrovascular reactivity expressed as breath-holding index (BHI) determined using transcranial color Doppler. The obtained results revealed significant differences between the groups in all endothelial markers except for the E selectin. While the ICAM-1 and sVCAM-1 were significantly increased in the hepatitis group, VEGF-A was significantly decreased. A significant reduction of 0.5 (95% CI 0.2, 0.8) in the mean BHI was found in the hepatitis group (mean BHI 0.64) compared to controls (mean BHI 1.10). No significant association between the BHI and any of the endothelial markers was found in the control group, while in the hepatitis group, the scatter plot of ICAM-1 vs BHI suggested that the association might be present. In conclusion, the results of this study confirm an association between a chronic HCV infection and altered cerebrovascular reactivity as well as higher levels of markers of endothelial activation (ICAM-1, VCAM-1) as possible indicators of an increased CVD risk.
bibliographic citation: Pavicic Ivelja et al. (2021) Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection. PeerJ 9:e10723 https://doi.org/10.7717/peerj.10723
date submitted: 2020-09-23
date accepted: 2020-12-16
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pavicic Ivelja
  given name: Mirela
author list: Agent
  family name: Dolic
  given name: Kresimir
author list: Agent
  family name: Tandara
  given name: Leida
author list: Agent
  family name: Perkovic
  given name: Nikola
author list: Agent
  family name: Mestrovic
  given name: Antonio
author list: Agent
  family name: Ivic
  given name: Ivo
doi: 10.7717/peerj.10723
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Pavicic Ivelja et al.
attribution name: Pavicic Ivelja et al.

https://peerj.com/articles/10727
type: item
type: AcademicArticle
title: Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters
description: Background Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. Methods We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. Results In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to …
format: application/pdf
format: text/html
creator: Hiroki Murata
creator: Motoyuki Hara
creator: Chinatsu Yonezawa
creator: Teruhisa Komatsu
subject: Aquaculture, Fisheries and Fish Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10727
publisher: PeerJ Inc.
rights: © 2021 Murata et al.
abstract: Background Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. Methods We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. Results In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to …
bibliographic citation: Murata et al. (2021) Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters. PeerJ 9:e10727 https://doi.org/10.7717/peerj.10727
date submitted: 2020-07-16
date accepted: 2020-12-17
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murata
  given name: Hiroki
author list: Agent
  family name: Hara
  given name: Motoyuki
author list: Agent
  family name: Yonezawa
  given name: Chinatsu
author list: Agent
  family name: Komatsu
  given name: Teruhisa
doi: 10.7717/peerj.10727
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Murata et al.
attribution name: Murata et al.

Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
type: item
type: AcademicArticle
description: The Asian giant hornet (AGH, Vespa mandarinia) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion.
format: application/pdf
format: text/html
creator: Claudia Nuñez-Penichet
creator: Luis Osorio-Olvera
creator: Victor H. Gonzalez
creator: Marlon E. Cobos
creator: Laura Jiménez
creator: Devon A. DeRaad
creator: Abdelghafar Alkishe
creator: Rusby G. Contreras-Díaz
creator: Angela Nava-Bolaños
creator: Kaera Utsumi
creator: Uzma Ashraf
creator: Adeola Adeboje
creator: A. Townsend Peterson
creator: Jorge Soberon
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10690
publisher: PeerJ Inc.
rights: © 2021 Nuñez-Penichet et al.
abstract: The Asian giant hornet (AGH, Vespa mandarinia) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion.
bibliographic citation: Nuñez-Penichet et al. (2021) Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America. PeerJ 9:e10690 https://doi.org/10.7717/peerj.10690
date submitted: 2020-08-12
date accepted: 2020-12-11
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nuñez-Penichet
  given name: Claudia
author list: Agent
  family name: Osorio-Olvera
  given name: Luis
author list: Agent
  family name: Gonzalez
  given name: Victor H.
author list: Agent
  family name: Cobos
  given name: Marlon E.
author list: Agent
  family name: Jiménez
  given name: Laura
author list: Agent
  family name: DeRaad
  given name: Devon A.
author list: Agent
  family name: Alkishe
  given name: Abdelghafar
author list: Agent
  family name: Contreras-Díaz
  given name: Rusby G.
author list: Agent
  family name: Nava-Bolaños
  given name: Angela
author list: Agent
  family name: Utsumi
  given name: Kaera
author list: Agent
  family name: Ashraf
  given name: Uzma
author list: Agent
  family name: Adeboje
  given name: Adeola
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Soberon
  given name: Jorge
doi: 10.7717/peerj.10690
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Nuñez-Penichet et al.
attribution name: Nuñez-Penichet et al.

Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa
type: item
type: AcademicArticle
description: Background Understanding the prescription practices and attitudes of veterinarians towards antimicrobial resistance (AMR) is crucial in guiding efforts to curb AMR. This study investigated prescription practices and attitudes towards AMR among veterinarians in the City of Tshwane, South Africa. Methods Out of the 83 veterinarians invited to participate in the study, 54 signed the consent form and completed the questionnaire. Percentages and 95% confidence intervals of all categorical variables were computed. A multinomial logistic model was used to identify predictors of the veterinarians’ view towards antimicrobial use. Results The majority (88%) of respondents indicated that improper use of antimicrobials contributed to selection for AMR. Veterinarians relied on clinical signs and symptoms (88%, 48/54) to decide whether to prescribe antimicrobials or not. However, the choice of antimicrobials depended on the cost of antibiotics (77.2%), route of administration (81.5%), and risk of potential adverse reactions (79.6%; 43/54). Many (61.5%) veterinarians were of the view that often antimicrobials are appropriately prescribed and 88.7% agreed that improper use of antimicrobials contributed to selection for antimicrobial resistant organisms. Compared to females, males were significantly more likely (Relative Risk Ratio (RRR) = 9.0; P = 0.0069) to agree rather than to “neither agree nor disagree” that their colleagues over-prescribed antimicrobials. Conclusions The decisions to prescribe antimicrobials by the veterinarians depended on clinical presentation of the patient, while the choice of antimicrobial depended on cost, route of administration, and risk of potential adverse reactions. Most veterinarians were of the view that antimicrobials were prescribed judiciously.
format: application/pdf
format: text/html
creator: Ronita Samuels
creator: Daniel Nenene Qekwana
creator: James W. Oguttu
creator: Agricola Odoi
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.10144
publisher: PeerJ Inc.
rights: © 2021 Samuels et al.
abstract: Background Understanding the prescription practices and attitudes of veterinarians towards antimicrobial resistance (AMR) is crucial in guiding efforts to curb AMR. This study investigated prescription practices and attitudes towards AMR among veterinarians in the City of Tshwane, South Africa. Methods Out of the 83 veterinarians invited to participate in the study, 54 signed the consent form and completed the questionnaire. Percentages and 95% confidence intervals of all categorical variables were computed. A multinomial logistic model was used to identify predictors of the veterinarians’ view towards antimicrobial use. Results The majority (88%) of respondents indicated that improper use of antimicrobials contributed to selection for AMR. Veterinarians relied on clinical signs and symptoms (88%, 48/54) to decide whether to prescribe antimicrobials or not. However, the choice of antimicrobials depended on the cost of antibiotics (77.2%), route of administration (81.5%), and risk of potential adverse reactions (79.6%; 43/54). Many (61.5%) veterinarians were of the view that often antimicrobials are appropriately prescribed and 88.7% agreed that improper use of antimicrobials contributed to selection for antimicrobial resistant organisms. Compared to females, males were significantly more likely (Relative Risk Ratio (RRR) = 9.0; P = 0.0069) to agree rather than to “neither agree nor disagree” that their colleagues over-prescribed antimicrobials. Conclusions The decisions to prescribe antimicrobials by the veterinarians depended on clinical presentation of the patient, while the choice of antimicrobial depended on cost, route of administration, and risk of potential adverse reactions. Most veterinarians were of the view that antimicrobials were prescribed judiciously.
bibliographic citation: Samuels et al. (2021) Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa. PeerJ 9:e10144 https://doi.org/10.7717/peerj.10144
date submitted: 2020-05-13
date accepted: 2020-09-20
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samuels
  given name: Ronita
author list: Agent
  family name: Qekwana
  given name: Daniel Nenene
author list: Agent
  family name: Oguttu
  given name: James W.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.10144
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Samuels et al.
attribution name: Samuels et al.

Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary
type: item
type: AcademicArticle
description: Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered…
format: application/pdf
format: text/html
creator: Romen Singh Naorem
creator: Jochen Blom
creator: Csaba Fekete
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.10185
publisher: PeerJ Inc.
rights: © 2021 Naorem et al.
abstract: Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered…
bibliographic citation: Naorem et al. (2021) Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PeerJ 9:e10185 https://doi.org/10.7717/peerj.10185
date submitted: 2020-05-21
date accepted: 2020-09-24
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naorem
  given name: Romen Singh
author list: Agent
  family name: Blom
  given name: Jochen
author list: Agent
  family name: Fekete
  given name: Csaba
doi: 10.7717/peerj.10185
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Naorem et al.
attribution name: Naorem et al.

The influence of estrogen deficiency on the structural and mechanical properties of rat cortical bone
type: item
type: AcademicArticle
description: Background Post-menopausal osteoporosis is a common health problem worldwide, most commonly caused by estrogen deficiency. Most of the information regarding the skeletal effects of this disease relates to trabecular bone, while cortical bone is less studied. The purpose of this study was to evaluate the influence of estrogen deficiency on the structure and mechanical properties of cortical bone. Methods Eight ovariectomized (OVH) and eight intact (control) Sprague Dawley rats were used.Structural features of femoral cortical bone were studied by light microscopy, scanning electron microscopy and synchrotron-based microcomputer-tomography and their mechanical properties determined by nano-indentation. Results Cortical bone of both study groups contains two distinct regions: organized circumferential lamellae and disordered bone with highly mineralized cartilaginous islands. Lacunar volume was lower in the OVH group both in the lamellar and disorganized regions (182 ± 75 µm3 vs 232 ± 106 µm3, P < 0.001 and 195 ± 86 µm3 vs. 247 ± 106 µm3, P < 0.001, respectively). Lacunar density was also lower in both bone regions of the OVH group (40 ± 18 ×103 lacunae/mm3 vs. 47 ± 9×103 lacunae/mm3 in the lamellar region, P = 0.003 and 63 ± 18×103lacunae/mm3 vs. 75 ± 13×103 lacunae/mm3 in the disorganized region, P < 0.001). Vascular canal volume was lower in the disorganized region of the bone in the OVH group compared to the same region in the control group (P < 0.001). Indentation moduli were not different between the study groups in both bone regions. Discussion Changes to cortical bone associated with estrogen deficiency in rats require high-resolution methods for detection. Caution is required in the application of these results to humans due to major structural differences between human and rat bone.
format: application/pdf
format: text/html
creator: Anna Shipov
creator: Paul Zaslansky
creator: Heinrich Riesemeier
creator: Gilad Segev
creator: Ayelet Atkins
creator: Noga Kalish-Achrai
creator: Stephen Weiner
creator: Ron Shahar
subject: Anatomy and Physiology
subject: Orthopedics
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.10213
publisher: PeerJ Inc.
rights: © 2021 Shipov et al.
abstract: Background Post-menopausal osteoporosis is a common health problem worldwide, most commonly caused by estrogen deficiency. Most of the information regarding the skeletal effects of this disease relates to trabecular bone, while cortical bone is less studied. The purpose of this study was to evaluate the influence of estrogen deficiency on the structure and mechanical properties of cortical bone. Methods Eight ovariectomized (OVH) and eight intact (control) Sprague Dawley rats were used.Structural features of femoral cortical bone were studied by light microscopy, scanning electron microscopy and synchrotron-based microcomputer-tomography and their mechanical properties determined by nano-indentation. Results Cortical bone of both study groups contains two distinct regions: organized circumferential lamellae and disordered bone with highly mineralized cartilaginous islands. Lacunar volume was lower in the OVH group both in the lamellar and disorganized regions (182 ± 75 µm3 vs 232 ± 106 µm3, P < 0.001 and 195 ± 86 µm3 vs. 247 ± 106 µm3, P < 0.001, respectively). Lacunar density was also lower in both bone regions of the OVH group (40 ± 18 ×103 lacunae/mm3 vs. 47 ± 9×103 lacunae/mm3 in the lamellar region, P = 0.003 and 63 ± 18×103lacunae/mm3 vs. 75 ± 13×103 lacunae/mm3 in the disorganized region, P < 0.001). Vascular canal volume was lower in the disorganized region of the bone in the OVH group compared to the same region in the control group (P < 0.001). Indentation moduli were not different between the study groups in both bone regions. Discussion Changes to cortical bone associated with estrogen deficiency in rats require high-resolution methods for detection. Caution is required in the application of these results to humans due to major structural differences between human and rat bone.
bibliographic citation: Shipov et al. (2021) The influence of estrogen deficiency on the structural and mechanical properties of rat cortical bone. PeerJ 9:e10213 https://doi.org/10.7717/peerj.10213
date submitted: 2020-03-25
date accepted: 2020-09-28
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shipov
  given name: Anna
author list: Agent
  family name: Zaslansky
  given name: Paul
author list: Agent
  family name: Riesemeier
  given name: Heinrich
author list: Agent
  family name: Segev
  given name: Gilad
author list: Agent
  family name: Atkins
  given name: Ayelet
author list: Agent
  family name: Kalish-Achrai
  given name: Noga
author list: Agent
  family name: Weiner
  given name: Stephen
author list: Agent
  family name: Shahar
  given name: Ron
doi: 10.7717/peerj.10213
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Shipov et al.
attribution name: Shipov et al.

Geographic disparities, determinants, and temporal changes in the prevalence of pre-diabetes in Florida
type: item
type: AcademicArticle
description: Background Left unchecked, pre-diabetes progresses to diabetes and its complications that are important health burdens in the United States. There is evidence of geographic disparities in the condition with some areas having a significantly high risks of the condition and its risk factors. Identifying these disparities, their determinants, and changes in burden are useful for guiding control programs and stopping the progression of pre-diabetes to diabetes. Therefore, the objectives of this study were to investigate geographic disparities of pre-diabetes prevalence in Florida, identify predictors of the observed spatial patterns, as well as changes in disease burden between 2013 and 2016. Methods The 2013 and 2016 Behavioral Risk Factor Surveillance System data were obtained from the Florida Department of Health. Counties with significant changes in the prevalence of the condition between 2013 and 2016 were identified using tests for equality of proportions adjusted for multiple comparisons using the Simes method. Flexible scan statistics were used to identify significant high prevalence geographic clusters. Multivariable regression models were used to identify determinants of county-level pre-diabetes prevalence. Results The state-wide age-adjusted prevalence of pre-diabetes increased significantly (p ≤ 0.05) from 8.0% in 2013 to 10.5% in 2016 with 72% (48/67) of the counties reporting statistically significant increases. Significant local geographic hotspots were identified. High prevalence of pre-diabetes tended to occur in counties with high proportions of non-Hispanic black population, low median household income, and low proportion of the population without health insurance coverage. Conclusions Geographic disparities of pre-diabetes continues to exist in Florida with most counties reporting significant increases in prevalence between 2013 and 2016. These findings are critical for guiding health planning, resource allocation and intervention programs.
format: application/pdf
format: text/html
creator: Jennifer Lord
creator: Shamarial Roberson
creator: Agricola Odoi
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.10443
publisher: PeerJ Inc.
rights: © 2021 Lord et al.
abstract: Background Left unchecked, pre-diabetes progresses to diabetes and its complications that are important health burdens in the United States. There is evidence of geographic disparities in the condition with some areas having a significantly high risks of the condition and its risk factors. Identifying these disparities, their determinants, and changes in burden are useful for guiding control programs and stopping the progression of pre-diabetes to diabetes. Therefore, the objectives of this study were to investigate geographic disparities of pre-diabetes prevalence in Florida, identify predictors of the observed spatial patterns, as well as changes in disease burden between 2013 and 2016. Methods The 2013 and 2016 Behavioral Risk Factor Surveillance System data were obtained from the Florida Department of Health. Counties with significant changes in the prevalence of the condition between 2013 and 2016 were identified using tests for equality of proportions adjusted for multiple comparisons using the Simes method. Flexible scan statistics were used to identify significant high prevalence geographic clusters. Multivariable regression models were used to identify determinants of county-level pre-diabetes prevalence. Results The state-wide age-adjusted prevalence of pre-diabetes increased significantly (p ≤ 0.05) from 8.0% in 2013 to 10.5% in 2016 with 72% (48/67) of the counties reporting statistically significant increases. Significant local geographic hotspots were identified. High prevalence of pre-diabetes tended to occur in counties with high proportions of non-Hispanic black population, low median household income, and low proportion of the population without health insurance coverage. Conclusions Geographic disparities of pre-diabetes continues to exist in Florida with most counties reporting significant increases in prevalence between 2013 and 2016. These findings are critical for guiding health planning, resource allocation and intervention programs.
bibliographic citation: Lord et al. (2021) Geographic disparities, determinants, and temporal changes in the prevalence of pre-diabetes in Florida. PeerJ 9:e10443 https://doi.org/10.7717/peerj.10443
date submitted: 2020-05-18
date accepted: 2020-11-07
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lord
  given name: Jennifer
author list: Agent
  family name: Roberson
  given name: Shamarial
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.10443
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Lord et al.
attribution name: Lord et al.

Effectiveness of iron polymaltose complex in treatment and prevention of iron deficiency anemia in children: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Iron deficiency anemia (IDA) is commonly treated with iron formulations. Despite the expanding acceptance of iron polymaltose complex (IPC) among clinicians, there is sparse and contradictory evidence regarding its efficacy in the management of IDA in children. This systematic review and meta-analysis aimed to assess the effectiveness of IPC in the treatment and prevention of IDA in children. Methods We searched the Cochrane Central Register of Controlled Trials, MEDLINE and Epistemonikos for all randomized control trials (RCTs) comparing oral IPC with standard oral iron supplementation for the treatment or prevention of IDA in children. We independently screened the titles and abstracts of identified trials before the full text of relevant trials was evaluated for eligibility. We then independently extracted data on the methods, interventions, outcomes, and risk of bias from the included trials. A random-effects model was used to estimate the risk ratios and mean differences with 95% confidence intervals. Results Eight trials comprising 493 randomized patients were included and analyzed using three comparison groups. The comparison group of which was used to evaluate IPC and ferrous sulphate (FS) for treatment of IDA showed that IPC is less effective in increasing Hb (MD −0.81, 95% CI −1.08 to −0.53; I2 = 48%, P < 0.001; six studies, 368 participants; high certainty of evidence), ferritin (MD −21.24, 95% CI −39.26 to −3.23, random-effects; I2 = 65%, P = 0.020; 3 studies, 183 participants; moderate certainty of evidence) and MCV levels (MD −3.20, 95% CI −5.35 to −1.05; P = 0.003; one study, 103 participants; low certainty of evidence). There was no difference in the occurrence of side effects between IPC and FS group (MD 0.78, 95% CI 0.47 to 1.31; I2 = 4%, P = 0.35; three studies, 274 participants; high certainty of evidence). Conclusions There was moderate to high certainty evidence that FS is superior to IPC with a clinically meaningful difference in im…
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format: text/html
creator: Ritzzaleena Rosli Mohd Rosli
creator: Mohd Noor Norhayati
creator: Shaiful Bahari Ismail
subject: Clinical Trials
subject: Drugs and Devices
subject: Hematology
subject: Nutrition
subject: Pediatrics
description: doi:10.7717/peerj.10527
publisher: PeerJ Inc.
rights: © 2021 Mohd Rosli et al.
abstract: Background Iron deficiency anemia (IDA) is commonly treated with iron formulations. Despite the expanding acceptance of iron polymaltose complex (IPC) among clinicians, there is sparse and contradictory evidence regarding its efficacy in the management of IDA in children. This systematic review and meta-analysis aimed to assess the effectiveness of IPC in the treatment and prevention of IDA in children. Methods We searched the Cochrane Central Register of Controlled Trials, MEDLINE and Epistemonikos for all randomized control trials (RCTs) comparing oral IPC with standard oral iron supplementation for the treatment or prevention of IDA in children. We independently screened the titles and abstracts of identified trials before the full text of relevant trials was evaluated for eligibility. We then independently extracted data on the methods, interventions, outcomes, and risk of bias from the included trials. A random-effects model was used to estimate the risk ratios and mean differences with 95% confidence intervals. Results Eight trials comprising 493 randomized patients were included and analyzed using three comparison groups. The comparison group of which was used to evaluate IPC and ferrous sulphate (FS) for treatment of IDA showed that IPC is less effective in increasing Hb (MD −0.81, 95% CI −1.08 to −0.53; I2 = 48%, P < 0.001; six studies, 368 participants; high certainty of evidence), ferritin (MD −21.24, 95% CI −39.26 to −3.23, random-effects; I2 = 65%, P = 0.020; 3 studies, 183 participants; moderate certainty of evidence) and MCV levels (MD −3.20, 95% CI −5.35 to −1.05; P = 0.003; one study, 103 participants; low certainty of evidence). There was no difference in the occurrence of side effects between IPC and FS group (MD 0.78, 95% CI 0.47 to 1.31; I2 = 4%, P = 0.35; three studies, 274 participants; high certainty of evidence). Conclusions There was moderate to high certainty evidence that FS is superior to IPC with a clinically meaningful difference in im…
bibliographic citation: Mohd Rosli et al. (2021) Effectiveness of iron polymaltose complex in treatment and prevention of iron deficiency anemia in children: a systematic review and meta-analysis. PeerJ 9:e10527 https://doi.org/10.7717/peerj.10527
date submitted: 2020-05-14
date accepted: 2020-11-18
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mohd Rosli
  given name: Ritzzaleena Rosli
author list: Agent
  family name: Norhayati
  given name: Mohd Noor
author list: Agent
  family name: Ismail
  given name: Shaiful Bahari
doi: 10.7717/peerj.10527
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Mohd Rosli et al.
attribution name: Mohd Rosli et al.

Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage
type: item
type: AcademicArticle
description: Background Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in Talaromyces marneffei (TM)-macrophages is still limited. Methods Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the ceRNA network of lncRNA–miRNA–mRNA interaction was constructed in Cytoscape. Similarly, functional enrichment analysis on mRNA in the ceRNA network. Finally, two mRNAs and four lncRNAs in the ceRNA network were randomly selected to verify the expression using qRT-PCR. Results In total, 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. The constructed ceRNA network contains 38 lncRNAs, 10 miRNAs and 45 mRNAs. GO and KEGG analysis of mRNA in the ceRNA network indicated that activated pathways in TM-infected macrophages were related to immunity, inflammation and metabolism. The quantitative validation of the expression of four randomly selected differentially expressed lncRNAs, AC006252.1, AC090197.1, IL6R-AS1, LINC02009 and two mRNAs, CSF1, NR4A3 showed that the expression levels were consistent with those in the RNA-sequencing. Conclusions The ceRNA network related to immunity, inflammation and metabolism plays an important role in TM-macrophage interaction. This study may provide effective and novel insights for further understanding the underlying mechanism of TM infection.
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creator: Yueqi Li
creator: Wudi Wei
creator: Sanqi An
creator: Junjun Jiang
creator: Jinhao He
creator: Hong Zhang
creator: Gang Wang
creator: Jing Han
creator: Bingyu Liang
creator: Li Ye
creator: Hao Liang
subject: Bioinformatics
subject: Genomics
subject: Mycology
description: doi:10.7717/peerj.10529
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in Talaromyces marneffei (TM)-macrophages is still limited. Methods Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the ceRNA network of lncRNA–miRNA–mRNA interaction was constructed in Cytoscape. Similarly, functional enrichment analysis on mRNA in the ceRNA network. Finally, two mRNAs and four lncRNAs in the ceRNA network were randomly selected to verify the expression using qRT-PCR. Results In total, 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. The constructed ceRNA network contains 38 lncRNAs, 10 miRNAs and 45 mRNAs. GO and KEGG analysis of mRNA in the ceRNA network indicated that activated pathways in TM-infected macrophages were related to immunity, inflammation and metabolism. The quantitative validation of the expression of four randomly selected differentially expressed lncRNAs, AC006252.1, AC090197.1, IL6R-AS1, LINC02009 and two mRNAs, CSF1, NR4A3 showed that the expression levels were consistent with those in the RNA-sequencing. Conclusions The ceRNA network related to immunity, inflammation and metabolism plays an important role in TM-macrophage interaction. This study may provide effective and novel insights for further understanding the underlying mechanism of TM infection.
bibliographic citation: Li et al. (2021) Identification and analysis of lncRNA, microRNA and mRNA expression profiles and construction of ceRNA network in Talaromyces marneffei-infected THP-1 macrophage. PeerJ 9:e10529 https://doi.org/10.7717/peerj.10529
date submitted: 2020-07-28
date accepted: 2020-11-18
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yueqi
author list: Agent
  family name: Wei
  given name: Wudi
author list: Agent
  family name: An
  given name: Sanqi
author list: Agent
  family name: Jiang
  given name: Junjun
author list: Agent
  family name: He
  given name: Jinhao
author list: Agent
  family name: Zhang
  given name: Hong
author list: Agent
  family name: Wang
  given name: Gang
author list: Agent
  family name: Han
  given name: Jing
author list: Agent
  family name: Liang
  given name: Bingyu
author list: Agent
  family name: Ye
  given name: Li
author list: Agent
  family name: Liang
  given name: Hao
doi: 10.7717/peerj.10529
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Li et al.
attribution name: Li et al.

The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing
type: item
type: AcademicArticle
description: Background The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts. Methods Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes. Results The complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lin…
format: application/pdf
format: text/html
creator: Igor Filipović
creator: James P. Hereward
creator: Gordana Rašić
creator: Gregor J. Devine
creator: Michael J. Furlong
creator: Kayvan Etebari
subject: Computational Biology
subject: Entomology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.10552
publisher: PeerJ Inc.
rights: © 2021 Filipović et al.
abstract: Background The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts. Methods Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes. Results The complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lin…
bibliographic citation: Filipović et al. (2021) The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing. PeerJ 9:e10552 https://doi.org/10.7717/peerj.10552
date submitted: 2020-08-10
date accepted: 2020-11-21
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Filipović
  given name: Igor
author list: Agent
  family name: Hereward
  given name: James P.
author list: Agent
  family name: Rašić
  given name: Gordana
author list: Agent
  family name: Devine
  given name: Gregor J.
author list: Agent
  family name: Furlong
  given name: Michael J.
author list: Agent
  family name: Etebari
  given name: Kayvan
doi: 10.7717/peerj.10552
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Filipović et al.
attribution name: Filipović et al.

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