PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America
items: The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
items: Hemin attenuates response of primary rat adipocytes to adrenergic stimulation
items: Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China
items: Extending density surface models to include multiple and double-observer survey data
items: Level of anxiety among healthcare providers during COVID-19 pandemic in Saudi Arabia: cross-sectional study
items: https://peerj.com/articles/11940
items: Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya
items: To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
items: https://peerj.com/articles/12062

Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America
type: item
type: AcademicArticle
description: Background There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from five travelers who returned to Taiwan from the United States of America (USA) between March and April 2020. Methods Haplotype network analysis was performed using genome-wide single-nucleotide variations to trace potential infection routes. To determine the genetic variations and evolutionary trajectory of the isolates, the genomes of isolates were compared to those of global virus strains from GISAID. Pharyngeal specimens were confirmed to be SARS-CoV-2-positive by RT-PCR. Direct whole-genome sequencing was performed, and viral assemblies were subsequently uploaded to GISAID. Comparative genome sequence and single-nucleotide variation analyses were performed. Results The D614G mutation was identified in imported cases, which separated into two clusters related to viruses originally detected in the USA. Our findings highlight the risk of spreading SARS-CoV-2 variants through air travel and the need for continued genomic tracing for the epidemiological investigation and surveillance of SARS-CoV-2 using viral genomic data. Conclusions Continuous genomic surveillance is warranted to trace virus circulation and evolution in different global settings during future outbreaks.
format: application/pdf
format: text/html
creator: Ming-Jr Jian
creator: Hsing-Yi Chung
creator: Chih-Kai Chang
creator: Shan-Shan Hsieh
creator: Jung-Chung Lin
creator: Kuo-Ming Yeh
creator: Chien-Wen Chen
creator: Feng-Yee Chang
creator: Kuo-Sheng Hung
creator: Ming-Tsan Liu
creator: Ji-Rong Yang
creator: Tein-Yao Chang
creator: Sheng-Hui Tang
creator: Cherng-Lih Perng
creator: Hung-Sheng Shang
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.11991
publisher: PeerJ Inc.
rights: © 2021 Jian et al.
abstract: Background There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from five travelers who returned to Taiwan from the United States of America (USA) between March and April 2020. Methods Haplotype network analysis was performed using genome-wide single-nucleotide variations to trace potential infection routes. To determine the genetic variations and evolutionary trajectory of the isolates, the genomes of isolates were compared to those of global virus strains from GISAID. Pharyngeal specimens were confirmed to be SARS-CoV-2-positive by RT-PCR. Direct whole-genome sequencing was performed, and viral assemblies were subsequently uploaded to GISAID. Comparative genome sequence and single-nucleotide variation analyses were performed. Results The D614G mutation was identified in imported cases, which separated into two clusters related to viruses originally detected in the USA. Our findings highlight the risk of spreading SARS-CoV-2 variants through air travel and the need for continued genomic tracing for the epidemiological investigation and surveillance of SARS-CoV-2 using viral genomic data. Conclusions Continuous genomic surveillance is warranted to trace virus circulation and evolution in different global settings during future outbreaks.
bibliographic citation: Jian et al. (2021) Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. PeerJ 9:e11991 https://doi.org/10.7717/peerj.11991
date submitted: 2021-04-07
date accepted: 2021-07-27
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jian
  given name: Ming-Jr
author list: Agent
  family name: Chung
  given name: Hsing-Yi
author list: Agent
  family name: Chang
  given name: Chih-Kai
author list: Agent
  family name: Hsieh
  given name: Shan-Shan
author list: Agent
  family name: Lin
  given name: Jung-Chung
author list: Agent
  family name: Yeh
  given name: Kuo-Ming
author list: Agent
  family name: Chen
  given name: Chien-Wen
author list: Agent
  family name: Chang
  given name: Feng-Yee
author list: Agent
  family name: Hung
  given name: Kuo-Sheng
author list: Agent
  family name: Liu
  given name: Ming-Tsan
author list: Agent
  family name: Yang
  given name: Ji-Rong
author list: Agent
  family name: Chang
  given name: Tein-Yao
author list: Agent
  family name: Tang
  given name: Sheng-Hui
author list: Agent
  family name: Perng
  given name: Cherng-Lih
author list: Agent
  family name: Shang
  given name: Hung-Sheng
doi: 10.7717/peerj.11991
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02
copyright: ©2021 Jian et al.
attribution name: Jian et al.

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya
type: item
type: AcademicArticle
description: Background There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans. Methods Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3–V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database. Results cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by…
format: application/pdf
format: text/html
creator: Rehema Liyai
creator: Gathii Kimita
creator: Clement Masakhwe
creator: David Abuom
creator: Beth Mutai
creator: David Miruka Onyango
creator: John Waitumbi
subject: Bioinformatics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.12067
publisher: PeerJ Inc.
rights: © 2021 Liyai et al.
abstract: Background There is a global increase in reports of emerging diseases, some of which have emerged as spillover events from wild animals. The spleen is a major phagocytic organ and can therefore be probed for systemic microbiome. This study assessed bacterial diversity in the spleen of wild caught small mammals so as to evaluate their utility as surveillance tools for monitoring bacteria in an ecosystem shared with humans. Methods Fifty-four small mammals (rodents and shrews) were trapped from different sites in Marigat, Baringo County, Kenya. To characterize their bacteriome, DNA was extracted from their spleens and the V3–V4 regions of the 16S rRNA amplified and then sequenced on Illumina MiSeq. A non-target control sample was used to track laboratory contaminants. Sequence data was analyzed with Mothur v1.35, and taxomy determined using the SILVA database. The Shannon diversity index was used to estimate bacterial diversity in each animal and then aggregated to genus level before computing the means. Animal species within the rodents and shrews were identified by amplification of mitochondrial cytochrome b (cytb) gene followed by Sanger sequencing. CLC workbench was used to assemble the cytb gene sequences, after which their phylogenetic placements were determined by querying them against the GenBank nucleotide database. Results cytb gene sequences were generated for 49/54 mammalian samples: 38 rodents (Rodentia) and 11 shrews (Eulipotyphyla). Within the order Rodentia, 21 Acomys, eight Mastomys, six Arvicanthis and three Rattus were identified. In the order Eulipotyphyla, 11 Crucidura were identified. Bacteria characterization revealed 17 phyla that grouped into 182 genera. Of the phyla, Proteobacteria was the most abundant (67.9%). Other phyla included Actinobacteria (16.5%), Firmicutes (5.5%), Chlamydiae (3.8%), Chloroflexi (2.6%) and Bacteroidetes (1.3%) among others. Of the potentially pathogenic bacteria, Bartonella was the most abundant (45.6%), followed by…
bibliographic citation: Liyai et al. (2021) The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. PeerJ 9:e12067 https://doi.org/10.7717/peerj.12067
date submitted: 2020-12-13
date accepted: 2021-08-05
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Liyai
  given name: Rehema
author list: Agent
  family name: Kimita
  given name: Gathii
author list: Agent
  family name: Masakhwe
  given name: Clement
author list: Agent
  family name: Abuom
  given name: David
author list: Agent
  family name: Mutai
  given name: Beth
author list: Agent
  family name: Onyango
  given name: David Miruka
author list: Agent
  family name: Waitumbi
  given name: John
doi: 10.7717/peerj.12067
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02
copyright: ©2021 Liyai et al.
attribution name: Liyai et al.

Hemin attenuates response of primary rat adipocytes to adrenergic stimulation
type: item
type: AcademicArticle
description: Hemin is an activator of heme oxygenase-1 (HO-1), an enzyme catalyzing heme degradation. Up-regulation of HO-1 is observed in response to various pathological conditions. Moreover, pharmacological activation of HO-1 is associated with numerous beneficial effects in the organism. Hemin was shown to exert, among other, anti-diabetic and anti-obesity properties. These effects are strongly linked with adipose tissue. However, the direct influence of hemin on metabolism of the fat cells have not been explored. The present study aimed to determine the short-term effects of hemin on metabolism of the primary rat adipocytes. We focused on processes directly related to lipid accumulation, such as lipogenesis and lipolysis. For this purpose, the isolated cells were subjected for 2 h to 40 µM hemin, and effects of this compound on insulin-stimulated glucose conversion to lipids, lactate release, lipolysis induced by various stimuli, and also on the antilipolytic action of insulin were determined. It was shown that hemin did not affect insulin-induced lipogenesis and lactate release. However, hemin significantly decreased lipolysis stimulated by epinephrine. The inhibitory effect of hemin on epinephrine-induced lipolysis was not abolished in the presence of SnMP, an inhibitor of HO-1, which suggests hemin action irrespective of this enzyme. Similar inhibitory effects on epinephrine-induced lipolysis were observed in the presence of 3 and 12 mM glucose. Moreover, hemin was shown to reduce epinephrine-induced lipolysis also when glucose was replaced by alanine or by succinate. Apart from changes in epinephrine action, it was found that the lipolytic response of the adipocytes to isoproterenol was also diminished by hemin. However, hemin failed to affect lipolysis stimulated by dibutyryl-cAMP (a direct activator of protein kinase A), forskolin (an activator of adenylate cyclase), and also by DPCPX (an adenosine A1 receptor antagonist). Additionally, epinephrine-induced lipolysis w…
format: application/pdf
format: text/html
creator: Tomasz Szkudelski
creator: Karina Frąckowiak
creator: Katarzyna Szkudelska
subject: Biochemistry
subject: Cell Biology
subject: Metabolic Sciences
description: doi:10.7717/peerj.12092
publisher: PeerJ Inc.
rights: © 2021 Szkudelski et al.
abstract: Hemin is an activator of heme oxygenase-1 (HO-1), an enzyme catalyzing heme degradation. Up-regulation of HO-1 is observed in response to various pathological conditions. Moreover, pharmacological activation of HO-1 is associated with numerous beneficial effects in the organism. Hemin was shown to exert, among other, anti-diabetic and anti-obesity properties. These effects are strongly linked with adipose tissue. However, the direct influence of hemin on metabolism of the fat cells have not been explored. The present study aimed to determine the short-term effects of hemin on metabolism of the primary rat adipocytes. We focused on processes directly related to lipid accumulation, such as lipogenesis and lipolysis. For this purpose, the isolated cells were subjected for 2 h to 40 µM hemin, and effects of this compound on insulin-stimulated glucose conversion to lipids, lactate release, lipolysis induced by various stimuli, and also on the antilipolytic action of insulin were determined. It was shown that hemin did not affect insulin-induced lipogenesis and lactate release. However, hemin significantly decreased lipolysis stimulated by epinephrine. The inhibitory effect of hemin on epinephrine-induced lipolysis was not abolished in the presence of SnMP, an inhibitor of HO-1, which suggests hemin action irrespective of this enzyme. Similar inhibitory effects on epinephrine-induced lipolysis were observed in the presence of 3 and 12 mM glucose. Moreover, hemin was shown to reduce epinephrine-induced lipolysis also when glucose was replaced by alanine or by succinate. Apart from changes in epinephrine action, it was found that the lipolytic response of the adipocytes to isoproterenol was also diminished by hemin. However, hemin failed to affect lipolysis stimulated by dibutyryl-cAMP (a direct activator of protein kinase A), forskolin (an activator of adenylate cyclase), and also by DPCPX (an adenosine A1 receptor antagonist). Additionally, epinephrine-induced lipolysis w…
bibliographic citation: Szkudelski et al. (2021) Hemin attenuates response of primary rat adipocytes to adrenergic stimulation. PeerJ 9:e12092 https://doi.org/10.7717/peerj.12092
date submitted: 2021-03-26
date accepted: 2021-08-09
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szkudelski
  given name: Tomasz
author list: Agent
  family name: Frąckowiak
  given name: Karina
author list: Agent
  family name: Szkudelska
  given name: Katarzyna
doi: 10.7717/peerj.12092
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02
copyright: ©2021 Szkudelski et al.
attribution name: Szkudelski et al.

Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China
type: item
type: AcademicArticle
description: Small waterbodies are a unique aquatic ecosystem with an increasing recognition for their important role in maintaining regional biodiversity and delivering ecosystem services. However, small waterbodies in Northwest Yunnan, one of the most concerned global biodiversity hot-spots, remain largely unknown. Here, we investigated the community structure of crustacean zooplankton and their relationships with limnological, morphometric and spatial variables in the highland small waterbodies in Northwest Yunnan in both the dry (October 2015) and rainy (June 2016) seasons. A total of 38 species of crustacean zooplankton were identified in our study, which is significantly higher than many other reported waterbodies in the Yunnan–Guizhou plateau as well as in the Yangtze River basin. This suggests that the highland small waterbodies are critical in maintaining regional zooplankton diversity in Northwest Yunnan. Meanwhile, we found limnological variables could explain most variation of crustacean zooplankton community, comparing to the morphometric and spatial variables in both the rainy and dry seasons. Our study revealed the diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan and highlighted the importance of small waterbodies in maintaining regional biodiversity.
format: application/pdf
format: text/html
creator: Xing Chen
creator: Qinghua Cai
creator: Lu Tan
creator: Shuoran Liu
creator: Wen Xiao
creator: Lin Ye
subject: Biodiversity
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12103
publisher: PeerJ Inc.
rights: © 2021 Chen et al.
abstract: Small waterbodies are a unique aquatic ecosystem with an increasing recognition for their important role in maintaining regional biodiversity and delivering ecosystem services. However, small waterbodies in Northwest Yunnan, one of the most concerned global biodiversity hot-spots, remain largely unknown. Here, we investigated the community structure of crustacean zooplankton and their relationships with limnological, morphometric and spatial variables in the highland small waterbodies in Northwest Yunnan in both the dry (October 2015) and rainy (June 2016) seasons. A total of 38 species of crustacean zooplankton were identified in our study, which is significantly higher than many other reported waterbodies in the Yunnan–Guizhou plateau as well as in the Yangtze River basin. This suggests that the highland small waterbodies are critical in maintaining regional zooplankton diversity in Northwest Yunnan. Meanwhile, we found limnological variables could explain most variation of crustacean zooplankton community, comparing to the morphometric and spatial variables in both the rainy and dry seasons. Our study revealed the diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan and highlighted the importance of small waterbodies in maintaining regional biodiversity.
bibliographic citation: Chen et al. (2021) Species diversity and community structure of crustacean zooplankton in the highland small waterbodies in Northwest Yunnan, China. PeerJ 9:e12103 https://doi.org/10.7717/peerj.12103
date submitted: 2020-06-04
date accepted: 2021-08-11
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Xing
author list: Agent
  family name: Cai
  given name: Qinghua
author list: Agent
  family name: Tan
  given name: Lu
author list: Agent
  family name: Liu
  given name: Shuoran
author list: Agent
  family name: Xiao
  given name: Wen
author list: Agent
  family name: Ye
  given name: Lin
doi: 10.7717/peerj.12103
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02
copyright: © 2021 Chen et al.
attribution name: Chen et al.

Extending density surface models to include multiple and double-observer survey data
type: item
type: AcademicArticle
description: Spatial models of density and abundance are widely used in both ecological research (e.g., to study habitat use) and wildlife management (e.g., for population monitoring and environmental impact assessment). Increasingly, modellers are tasked with integrating data from multiple sources, collected via different observation processes. Distance sampling is an efficient and widely used survey and analysis technique. Within this framework, observation processes are modelled via detection functions. We seek to take multiple data sources and fit them in a single spatial model. Density surface models (DSMs) are a two-stage approach: first accounting for detectability via distance sampling methods, then modelling distribution via a generalized additive model. However, current software and theory does not address the issue of multiple data sources. We extend the DSM approach to accommodate data from multiple surveys, collected via conventional distance sampling, double-observer distance sampling (used to account for incomplete detection at zero distance) and strip transects. Variance propagation ensures that uncertainty is correctly accounted for in final estimates of abundance. Methods described here are implemented in the dsm R package. We briefly analyse two datasets to illustrate these new developments. Our new methodology enables data from multiple distance sampling surveys of different types to be treated in a single spatial model, enabling more robust abundance estimation, potentially over wider geographical or temporal domains.
format: application/pdf
format: text/html
creator: David L. Miller
creator: David Fifield
creator: Ewan Wakefield
creator: Douglas B. Sigourney
subject: Statistics
subject: Natural Resource Management
description: doi:10.7717/peerj.12113
publisher: PeerJ Inc.
rights: © 2021
abstract: Spatial models of density and abundance are widely used in both ecological research (e.g., to study habitat use) and wildlife management (e.g., for population monitoring and environmental impact assessment). Increasingly, modellers are tasked with integrating data from multiple sources, collected via different observation processes. Distance sampling is an efficient and widely used survey and analysis technique. Within this framework, observation processes are modelled via detection functions. We seek to take multiple data sources and fit them in a single spatial model. Density surface models (DSMs) are a two-stage approach: first accounting for detectability via distance sampling methods, then modelling distribution via a generalized additive model. However, current software and theory does not address the issue of multiple data sources. We extend the DSM approach to accommodate data from multiple surveys, collected via conventional distance sampling, double-observer distance sampling (used to account for incomplete detection at zero distance) and strip transects. Variance propagation ensures that uncertainty is correctly accounted for in final estimates of abundance. Methods described here are implemented in the dsm R package. We briefly analyse two datasets to illustrate these new developments. Our new methodology enables data from multiple distance sampling surveys of different types to be treated in a single spatial model, enabling more robust abundance estimation, potentially over wider geographical or temporal domains.
bibliographic citation: Miller et al. (2021) Extending density surface models to include multiple and double-observer survey data. PeerJ 9:e12113 https://doi.org/10.7717/peerj.12113
date submitted: 2021-04-23
date accepted: 2021-08-14
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Miller
  given name: David L.
author list: Agent
  family name: Fifield
  given name: David
author list: Agent
  family name: Wakefield
  given name: Ewan
author list: Agent
  family name: Sigourney
  given name: Douglas B.
doi: 10.7717/peerj.12113
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02

Level of anxiety among healthcare providers during COVID-19 pandemic in Saudi Arabia: cross-sectional study
type: item
type: AcademicArticle
description: Background The burden of the spread of the COVID-19 pandemic has impacted widely on the healthcare providers physically and mentally. Many healthcare providers are exposed to psychological stressors due to their high risk of contracting the virus. Aims This study aimed to measure the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia. In addition, this study aimed to measure the level of anxiety based on demographic characteristics. Method A cross-sectional survey was employed to recruit a convenience sample of healthcare providers. A pencil and paper self-administered questionnaires were used to collect data from demographic and generalized anxiety disorder GAD-7 data. However, this study received written informed consent from participants of the study. In addition, the study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-03). Results A total of 650 participants were recruited, results of GAD-7 showed that 43.5%, 28.9% and 27.5% of healthcare providers in Saudi Arabia experienced mild, moderate and severe anxiety, respectively, during the COVID-19 pandemic. Results indicated that age, health specialty, nationality, and sleeping disorders before COVID-19 were associated with anxiety levels. Conclusion The generalized anxiety among healthcare providers in Saudi Arabia was mild. Older healthcare providers were found to have a higher level of anxiety compared to other participating healthcare providers. Several factors may contribute to a higher level of anxiety including age, socioeconomic status, marital status, having chronic conditions, and sleeping disorder before the COVID-19 pandemic. To further understand the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia, longitudinal and mixed-method research is needed.
format: application/pdf
format: text/html
creator: Abbas Al Mutair
creator: Alya Al Mutairi
creator: Yasmine Alabbasi
creator: Abbas Shamsan
creator: Sana Al-Mahmoud
creator: Saad Alhumaid
creator: Muhammad zeshan Arshad
creator: Mansour Awad
creator: Ali Rabaan
subject: Infectious Diseases
subject: Nursing
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12119
publisher: PeerJ Inc.
rights: © 2021 Al Mutair et al.
abstract: Background The burden of the spread of the COVID-19 pandemic has impacted widely on the healthcare providers physically and mentally. Many healthcare providers are exposed to psychological stressors due to their high risk of contracting the virus. Aims This study aimed to measure the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia. In addition, this study aimed to measure the level of anxiety based on demographic characteristics. Method A cross-sectional survey was employed to recruit a convenience sample of healthcare providers. A pencil and paper self-administered questionnaires were used to collect data from demographic and generalized anxiety disorder GAD-7 data. However, this study received written informed consent from participants of the study. In addition, the study was approved by the Institutional Review Board at Dr. Sulaiman Al Habib Medical Group (IRB Log No. RC20.06.88-03). Results A total of 650 participants were recruited, results of GAD-7 showed that 43.5%, 28.9% and 27.5% of healthcare providers in Saudi Arabia experienced mild, moderate and severe anxiety, respectively, during the COVID-19 pandemic. Results indicated that age, health specialty, nationality, and sleeping disorders before COVID-19 were associated with anxiety levels. Conclusion The generalized anxiety among healthcare providers in Saudi Arabia was mild. Older healthcare providers were found to have a higher level of anxiety compared to other participating healthcare providers. Several factors may contribute to a higher level of anxiety including age, socioeconomic status, marital status, having chronic conditions, and sleeping disorder before the COVID-19 pandemic. To further understand the level of anxiety among healthcare providers during the COVID-19 pandemic in Saudi Arabia, longitudinal and mixed-method research is needed.
bibliographic citation: Al Mutair et al. (2021) Level of anxiety among healthcare providers during COVID-19 pandemic in Saudi Arabia: cross-sectional study. PeerJ 9:e12119 https://doi.org/10.7717/peerj.12119
date submitted: 2021-05-05
date accepted: 2021-08-15
issued: 2021-09-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Mutair
  given name: Abbas
author list: Agent
  family name: Al Mutairi
  given name: Alya
author list: Agent
  family name: Alabbasi
  given name: Yasmine
author list: Agent
  family name: Shamsan
  given name: Abbas
author list: Agent
  family name: Al-Mahmoud
  given name: Sana
author list: Agent
  family name: Alhumaid
  given name: Saad
author list: Agent
  family name: Arshad
  given name: Muhammad zeshan
author list: Agent
  family name: Awad
  given name: Mansour
author list: Agent
  family name: Rabaan
  given name: Ali
doi: 10.7717/peerj.12119
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-02
copyright: © 2021 Al Mutair et al.
attribution name: Al Mutair et al.

https://peerj.com/articles/11940
type: item
type: AcademicArticle
title: Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements
description: The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and water-soluble classification of vitamins remains consistent with their respective absorption and dissolution potentials, underpinned by numerous physiological functions. Vitamins, largely absorbed in the small intestine, have their bioavailability dependent on the food composition, its associated interactions, as well as alignment with their metabolic functions, which involves antioxidants, coenzymes, electron acceptor/donor, and hormones. Moreover, vitamin deficiencies, in every form, pose a serious threat to human health. Vitamin toxicities remain rare, but can still occur mainly from supplementation, although it appears much less in water-soluble vitamins of which some excesses get readily removed by the human body, different from the fat-soluble ones that are stored in tissues and organs. Besides discussions of absorption, transport, and cellular uptake of vitamins, this perspective review…
format: application/pdf
format: text/html
creator: Chigozie E. Ofoedu
creator: Jude O. Iwouno
creator: Ebelechukwu O. Ofoedu
creator: Chika C. Ogueke
creator: Victory S. Igwe
creator: Ijeoma M. Agunwah
creator: Arinze F. Ofoedum
creator: James S. Chacha
creator: Onyinye P. Muobike
creator: Adedoyin O. Agunbiade
creator: Njideka E. Njoku
creator: Angela A. Nwakaudu
creator: Nkiru E. Odimegwu
creator: Onyekachi E. Ndukauba
creator: Chukwuka U. Ogbonna
creator: Joncer Naibaho
creator: Maciej Korus
creator: Charles Odilichukwu R. Okpala
subject: Biochemistry
subject: Food Science and Technology
subject: Nutrition
description: doi:10.7717/peerj.11940
publisher: PeerJ Inc.
rights: © 2021 Ofoedu et al.
abstract: The significant attention gained by food-sourced vitamins has provided insights into numerous current researches; for instance, the potential reversal of epigenetic age using a diet and lifestyle intervention, the balance between food and dietary supplements in the general population, the role of diet and food intake in age-related macular degeneration, and the association of dietary supplement use, nutrient intake and mortality among adults. As relevant literature about food-sourced vitamin increases, continuous synthesis is warranted. To supplement existing information, this perspective review discussed food-sourced vitamins for consumer diet and health needs, scoping from vitamin absorption, metabolic functions, utilization, to balancing nutritional requirements. Relevant literatures were identified through a search of databases like Google Scholar, Web of Science, the Interscience Online Library, ScienceDirect, and PubMed. We demonstrated that vitamins whether from plant- and animal-based sources are prerequisites for the metabolic functions of the human body. The fat- and water-soluble classification of vitamins remains consistent with their respective absorption and dissolution potentials, underpinned by numerous physiological functions. Vitamins, largely absorbed in the small intestine, have their bioavailability dependent on the food composition, its associated interactions, as well as alignment with their metabolic functions, which involves antioxidants, coenzymes, electron acceptor/donor, and hormones. Moreover, vitamin deficiencies, in every form, pose a serious threat to human health. Vitamin toxicities remain rare, but can still occur mainly from supplementation, although it appears much less in water-soluble vitamins of which some excesses get readily removed by the human body, different from the fat-soluble ones that are stored in tissues and organs. Besides discussions of absorption, transport, and cellular uptake of vitamins, this perspective review…
bibliographic citation: Ofoedu et al. (2021) Revisiting food-sourced vitamins for consumer diet and health needs: a perspective review, from vitamin classification, metabolic functions, absorption, utilization, to balancing nutritional requirements. PeerJ 9:e11940 https://doi.org/10.7717/peerj.11940
date submitted: 2021-03-26
date accepted: 2021-07-19
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ofoedu
  given name: Chigozie E.
author list: Agent
  family name: Iwouno
  given name: Jude O.
author list: Agent
  family name: Ofoedu
  given name: Ebelechukwu O.
author list: Agent
  family name: Ogueke
  given name: Chika C.
author list: Agent
  family name: Igwe
  given name: Victory S.
author list: Agent
  family name: Agunwah
  given name: Ijeoma M.
author list: Agent
  family name: Ofoedum
  given name: Arinze F.
author list: Agent
  family name: Chacha
  given name: James S.
author list: Agent
  family name: Muobike
  given name: Onyinye P.
author list: Agent
  family name: Agunbiade
  given name: Adedoyin O.
author list: Agent
  family name: Njoku
  given name: Njideka E.
author list: Agent
  family name: Nwakaudu
  given name: Angela A.
author list: Agent
  family name: Odimegwu
  given name: Nkiru E.
author list: Agent
  family name: Ndukauba
  given name: Onyekachi E.
author list: Agent
  family name: Ogbonna
  given name: Chukwuka U.
author list: Agent
  family name: Naibaho
  given name: Joncer
author list: Agent
  family name: Korus
  given name: Maciej
author list: Agent
  family name: Okpala
  given name: Charles Odilichukwu R.
doi: 10.7717/peerj.11940
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Ofoedu et al.
attribution name: Ofoedu et al.

Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya
type: item
type: AcademicArticle
description: Background Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya. Methods This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates. Results A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024). Conclu…
format: application/pdf
format: text/html
creator: Jennifer Lord
creator: Anthony Gikonyo
creator: Amos Miwa
creator: Agricola Odoi
subject: Microbiology
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.11958
publisher: PeerJ Inc.
rights: © 2021 Lord et al.
abstract: Background Antimicrobial resistance among pathogens of public health importance is an emerging problem in sub-Saharan Africa. Unfortunately, published information on the burden and patterns of antimicrobial resistance (AMR) in this region is sparse. There is evidence that the burden and patterns of AMR vary by geography and facility. Knowledge of local epidemiology of AMR is thus important for guiding clinical decisions and mitigation strategies. Therefore, the objective of this study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Nairobi, Kenya. Methods This retrospective study used laboratory records of 1,217 clinical specimens submitted for bacterial culture and sensitivity testing at the diagnostic laboratory of The Karen Hospital in Nairobi, Kenya between 2012 and 2016. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis. Firth logistic models, which minimize small sample bias, were used to investigate determinants of AMR and MDR of the isolates. Results A total of 222 specimens had bacterial growth. Most Enterobacteriaceae isolates were resistant to commonly used drugs such as penicillin/β-lactamase inhibitor combinations (91.2%) and folate pathway inhibitors (83.7%). Resistance to extended-spectrum cephalosporins was also high (52.9%). Levels of AMR and MDR for Enterobacteriaceae were 88.5% and 51%, respectively. Among S. aureus isolates, 57.1% were AMR, while 16.7% were MDR. As many as 42.1% of the Pseudomonas spp. isolates were aminoglycoside-resistant and 15% were fluoroquinolone-resistant, but none exhibited resistance to antipseudomonal carbapenems. Half of Pseudomonas spp. isolates were AMR but none were MDR. Significant predictors of MDR among Enterobacteriaceae were organism species (p = 0.002) and patient gender (p = 0.024). Conclu…
bibliographic citation: Lord et al. (2021) Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya. PeerJ 9:e11958 https://doi.org/10.7717/peerj.11958
date submitted: 2021-05-10
date accepted: 2021-07-21
issued: 2021-09-01
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: Gikonyo
  given name: Anthony
author list: Agent
  family name: Miwa
  given name: Amos
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.11958
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 Lord et al.
attribution name: Lord et al.

To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere
type: item
type: AcademicArticle
description: Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.
format: application/pdf
format: text/html
creator: Ankit Hinsu
creator: Ashvin Dumadiya
creator: Anjali Joshi
creator: Rohitkumar Kotadiya
creator: Kavan Andharia
creator: Prakash Koringa
creator: Ramesh Kothari
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.12035
publisher: PeerJ Inc.
rights: © 2021 Hinsu et al.
abstract: Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.
bibliographic citation: Hinsu et al. (2021) To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere. PeerJ 9:e12035 https://doi.org/10.7717/peerj.12035
date submitted: 2021-06-03
date accepted: 2021-08-01
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hinsu
  given name: Ankit
author list: Agent
  family name: Dumadiya
  given name: Ashvin
author list: Agent
  family name: Joshi
  given name: Anjali
author list: Agent
  family name: Kotadiya
  given name: Rohitkumar
author list: Agent
  family name: Andharia
  given name: Kavan
author list: Agent
  family name: Koringa
  given name: Prakash
author list: Agent
  family name: Kothari
  given name: Ramesh
doi: 10.7717/peerj.12035
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Hinsu et al.
attribution name: Hinsu et al.

https://peerj.com/articles/12062
type: item
type: AcademicArticle
title: Oral health-related quality-of-life scores differ by socioeconomic status, mother’s level of education, dental visits and severity of malocclusion in mixed dentition of eight-to-ten-year-old schoolchildren
description: Objective To determinate the association among socioeconomic status subject’s mother’s level of educational attainment, dental visits, and malocclusion in mixed dentition with on the OHRQoL of eight-to-ten-year-old children. Methods A cross-sectional study conducted, in 2019, on Mexican children from households of different socioeconomic status (SES). The prevalence of malocclusion was evaluated using the Dental Aesthetic Index (DAI), while the SES of the participants’ households was evaluated using the three categories (corresponding to a high, middle, or low-income household) stipulated by the Consejo Nacional de Población (CONAPO or National Population Council). Oral Health-related Quality of Life (OHRQoL) was evaluated using the Child Perceptions Questionnaire (CPQ8-10). Poisson regression models were performed for the analysis of the data obtained. Results A total of 79.4% of the subjects presented some type of malocclusion in mixed dentition, which was, by severity, as follows: definite (31.3%); severe (25.6%); and, very severe (22.5%). The Poisson regression model revealed a greater negative impact on the following four CPQ8-10domains for children with severe/very severe malocclusion [RR]: oral symptoms [2.78]; functional limitations [2.72]; emotional well-being [2.59]; and, social well-being [3.99]. A greater impact on the four CPQ8-10domains was found for children from a low-income household than for children from a high-income (p < 0.001) household. Furthermore, poor oral hygiene, lack of dental visits, and the mother’s level of educational attainment (<9 years) were found to have a negative impact on OHRQoL. Conclusion The findings of the present study demonstrated that the severity of malocclusion was associated with a greater negative impact on the OHRQoL of children, while those children who face greater health inequalities are likely to report a greater negative impact on their OHRQoL.
format: application/pdf
format: text/html
creator: Alvaro García Pérez
creator: Álvaro Edgar González-Aragón Pineda
creator: Hilda Gonzalez Olivares
subject: Dentistry
subject: Epidemiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.12062
publisher: PeerJ Inc.
rights: © 2021 García Pérez et al.
abstract: Objective To determinate the association among socioeconomic status subject’s mother’s level of educational attainment, dental visits, and malocclusion in mixed dentition with on the OHRQoL of eight-to-ten-year-old children. Methods A cross-sectional study conducted, in 2019, on Mexican children from households of different socioeconomic status (SES). The prevalence of malocclusion was evaluated using the Dental Aesthetic Index (DAI), while the SES of the participants’ households was evaluated using the three categories (corresponding to a high, middle, or low-income household) stipulated by the Consejo Nacional de Población (CONAPO or National Population Council). Oral Health-related Quality of Life (OHRQoL) was evaluated using the Child Perceptions Questionnaire (CPQ8-10). Poisson regression models were performed for the analysis of the data obtained. Results A total of 79.4% of the subjects presented some type of malocclusion in mixed dentition, which was, by severity, as follows: definite (31.3%); severe (25.6%); and, very severe (22.5%). The Poisson regression model revealed a greater negative impact on the following four CPQ8-10domains for children with severe/very severe malocclusion [RR]: oral symptoms [2.78]; functional limitations [2.72]; emotional well-being [2.59]; and, social well-being [3.99]. A greater impact on the four CPQ8-10domains was found for children from a low-income household than for children from a high-income (p < 0.001) household. Furthermore, poor oral hygiene, lack of dental visits, and the mother’s level of educational attainment (<9 years) were found to have a negative impact on OHRQoL. Conclusion The findings of the present study demonstrated that the severity of malocclusion was associated with a greater negative impact on the OHRQoL of children, while those children who face greater health inequalities are likely to report a greater negative impact on their OHRQoL.
bibliographic citation: García Pérez et al. (2021) Oral health-related quality-of-life scores differ by socioeconomic status, mother’s level of education, dental visits and severity of malocclusion in mixed dentition of eight-to-ten-year-old schoolchildren. PeerJ 9:e12062 https://doi.org/10.7717/peerj.12062
date submitted: 2021-03-04
date accepted: 2021-08-04
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García Pérez
  given name: Alvaro
author list: Agent
  family name: González-Aragón Pineda
  given name: Álvaro Edgar
author list: Agent
  family name: Gonzalez Olivares
  given name: Hilda
doi: 10.7717/peerj.12062
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 García Pérez et al.
attribution name: García Pérez et al.

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