PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Changes of liver transcriptome profiles following oxidative stress in streptozotocin-induced diabetes in mice
items: Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi
items: Prevalence and molecular characterization of some circulating strains of the peste-des-petits-ruminants virus in Saudi Arabia between 2014–2016
items: A new sponge-associated starfish, Astrolirus patricki sp. nov. (Asteroidea: Brisingida: Brisingidae), from the northwestern Pacific seamounts
items: Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics
items: Acute effects of air pollution on all-cause mortality: a natural experiment from haze control measures in Chiang Mai Province, Thailand
items: Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device
items: Effects of temperature on metabolic scaling in black carp
items: Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis
items: Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems

Changes of liver transcriptome profiles following oxidative stress in streptozotocin-induced diabetes in mice
type: item
type: AcademicArticle
description: Background Oxidative-stress (OS) was causal in the development of cell dysfunction and insulin resistance. Streptozotocin (STZ) was an alkylation agent that increased reactive oxygen species (ROS) levels. Here we aimed to explore the oxidative-stress and related RNAs in the liver of STZ-induced diabetic mice. Methods RNA-sequencing was performed using liver tissues from STZ induced diabetic mice and controls. Pathway and Gene Ontology (GO) analyses were utilized to annotate the target genes. The differentially expressed RNAs involved in the peroxisome pathway were validated by qRT-PCR. The glucose metabolite and OS markers were measured in the normal control (NC) and STZ-induced diabetic mellitus (DM) group. Results The levels of serum Fasting insulin, HbA1c, Malondialdehyde (MDA) and 8-iso-prostaglandin F2α (8-iso-PGF2α) were significant higher in DM groups than NC group, while SOD activity decreased significantly in DM groups. We found 416 lncRNAs and 910 mRNAs were differentially expressed in the STZ-induced diabetic mice compared to the control group. OS associated RNAs were differentially expressed in the liver of STZ-induced diabetic mice. Conclusion This study confirmed that the OS was increased in the STZ-induced DM mice as evidenced by the increase of lipid peroxidation product MDA and 8-iso-PGF2α, identified aberrantly expressed lncRNAs and mRNAs in STZ-induced diabetic mice.
format: application/pdf
format: text/html
creator: Shuren Guo
creator: Xiaohuan Mao
creator: Yunmeng Yan
creator: Yan Zhang
creator: Liang Ming
subject: Genomics
subject: Diabetes and Endocrinology
subject: Public Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.8983
publisher: PeerJ Inc.
rights: © 2020 Guo et al.
abstract: Background Oxidative-stress (OS) was causal in the development of cell dysfunction and insulin resistance. Streptozotocin (STZ) was an alkylation agent that increased reactive oxygen species (ROS) levels. Here we aimed to explore the oxidative-stress and related RNAs in the liver of STZ-induced diabetic mice. Methods RNA-sequencing was performed using liver tissues from STZ induced diabetic mice and controls. Pathway and Gene Ontology (GO) analyses were utilized to annotate the target genes. The differentially expressed RNAs involved in the peroxisome pathway were validated by qRT-PCR. The glucose metabolite and OS markers were measured in the normal control (NC) and STZ-induced diabetic mellitus (DM) group. Results The levels of serum Fasting insulin, HbA1c, Malondialdehyde (MDA) and 8-iso-prostaglandin F2α (8-iso-PGF2α) were significant higher in DM groups than NC group, while SOD activity decreased significantly in DM groups. We found 416 lncRNAs and 910 mRNAs were differentially expressed in the STZ-induced diabetic mice compared to the control group. OS associated RNAs were differentially expressed in the liver of STZ-induced diabetic mice. Conclusion This study confirmed that the OS was increased in the STZ-induced DM mice as evidenced by the increase of lipid peroxidation product MDA and 8-iso-PGF2α, identified aberrantly expressed lncRNAs and mRNAs in STZ-induced diabetic mice.
bibliographic citation: Guo et al. (2020) Changes of liver transcriptome profiles following oxidative stress in streptozotocin-induced diabetes in mice. PeerJ 8:e8983 https://doi.org/10.7717/peerj.8983
date submitted: 2019-11-11
date accepted: 2020-03-25
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Shuren
author list: Agent
  family name: Mao
  given name: Xiaohuan
author list: Agent
  family name: Yan
  given name: Yunmeng
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Ming
  given name: Liang
doi: 10.7717/peerj.8983
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Guo et al.
attribution name: Guo et al.

Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi
type: item
type: AcademicArticle
description: Background Especially on commodities crops like soybean, maize, cotton, coffee and others, high yields are reached mainly by the intensive use of pesticides and fertilizers. The biological management of crops is a relatively recent concept, and its application has increased expectations about a more sustainable agriculture. The use of fungi as plant bioinoculants has proven to be a useful alternative in this process, and research is deepening on genera and species with some already known potential. In this context, the present study focused on the analysis of the plant growth promotion potential of Purpureocillium lilacinum, Purpureocillium lavendulum and Metarhizium marquandii aiming its use as bioinoculants in maize, bean and soybean. Methods Purpureocillium spp. and M. marquandii strains were isolated from soil samples. They were screened for their ability to solubilize phosphorus (P) and produce indoleacetic acid (IAA) and the most promising strains were tested at greenhouse in maize, bean and soybean plants. Growth promotion parameters including plant height, dry mass and contents of P and nitrogen (N) in the plants and in the rhizospheric soil were assessed. Results Thirty strains were recovered and characterized as Purpureocillium lilacinum (25), Purpureocillium lavendulum (4) and Metarhizium marquandii (1). From the trial for P solubilization and IAA production, seven strains were selected and inoculated in maize, bean and soybean plants. These strains were able to modify in a different way the evaluated parameters involving plant growth in each crop, and some strains distinctly increased the availability of P and N, for the last, an uncommon occurrence involving these fungi. Moreover, the expected changes identified at the in vitro analysis were not necessarily found in planta. In addition, this study is the first to evaluate the effect of the isolated inoculation of these fungi on the growth promotion of maize, bean and soybean plants.
format: application/pdf
format: text/html
creator: Noemi Carla Baron
creator: Andressa de Souza Pollo
creator: Everlon Cid Rigobelo
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.9005
publisher: PeerJ Inc.
rights: © 2020 Baron et al.
abstract: Background Especially on commodities crops like soybean, maize, cotton, coffee and others, high yields are reached mainly by the intensive use of pesticides and fertilizers. The biological management of crops is a relatively recent concept, and its application has increased expectations about a more sustainable agriculture. The use of fungi as plant bioinoculants has proven to be a useful alternative in this process, and research is deepening on genera and species with some already known potential. In this context, the present study focused on the analysis of the plant growth promotion potential of Purpureocillium lilacinum, Purpureocillium lavendulum and Metarhizium marquandii aiming its use as bioinoculants in maize, bean and soybean. Methods Purpureocillium spp. and M. marquandii strains were isolated from soil samples. They were screened for their ability to solubilize phosphorus (P) and produce indoleacetic acid (IAA) and the most promising strains were tested at greenhouse in maize, bean and soybean plants. Growth promotion parameters including plant height, dry mass and contents of P and nitrogen (N) in the plants and in the rhizospheric soil were assessed. Results Thirty strains were recovered and characterized as Purpureocillium lilacinum (25), Purpureocillium lavendulum (4) and Metarhizium marquandii (1). From the trial for P solubilization and IAA production, seven strains were selected and inoculated in maize, bean and soybean plants. These strains were able to modify in a different way the evaluated parameters involving plant growth in each crop, and some strains distinctly increased the availability of P and N, for the last, an uncommon occurrence involving these fungi. Moreover, the expected changes identified at the in vitro analysis were not necessarily found in planta. In addition, this study is the first to evaluate the effect of the isolated inoculation of these fungi on the growth promotion of maize, bean and soybean plants.
bibliographic citation: Baron et al. (2020) Purpureocillium lilacinum and Metarhizium marquandii as plant growth-promoting fungi. PeerJ 8:e9005 https://doi.org/10.7717/peerj.9005
date submitted: 2019-12-18
date accepted: 2020-03-27
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Baron
  given name: Noemi Carla
author list: Agent
  family name: Souza Pollo
  given name: Andressa de
author list: Agent
  family name: Rigobelo
  given name: Everlon Cid
doi: 10.7717/peerj.9005
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: © 2020 Baron et al.
attribution name: Baron et al.

Prevalence and molecular characterization of some circulating strains of the peste-des-petits-ruminants virus in Saudi Arabia between 2014–2016
type: item
type: AcademicArticle
description: Background The peste-des-petits-ruminants virus (PPRV) is a highly devastating virus of small ruminants in many parts of the world, including the Kingdome of Saudi Arabia. Therefore, our objectives were (1) to conduct a molecular prevalence study of PPRV in sheep and goat across the KSA and (2) to isolate and identify currently circulating PPRV lineages. Swabs and tissue specimens were collected from 97 herds suspected to be infected with PPRV across the Kingdome of Saudi Arabia (KSA). Testing for the presence of the virus was done by the real-time PCR. Confirmation of the identity of the reactions was done by the gel-based-PCR then by sequencing of the partial PPRV genome. Results Our results revealed that 24.1% of the tested specimens were PPRV-positive. Isolation of PPRV was successful from samples using the Vero cell line. Sequence analysis of some partial PPRV genes (N, F, M, L, P, and H) revealed that these strains were belonging to lineage IV of the PPRV. Conclusions This is the first study to conduct both the nationwide prevalence, isolation, and molecular characterizations of the PPRV in the KSA. Continuous surveillance and monitoring of the circulating strains of PPRV among sheep and goats will contribute substantially to the global eradication campaign of such a virus.
format: application/pdf
format: text/html
creator: Maged Gomaa Hemida
creator: Hussain Mohammed Alghadeer
creator: Mohammed Alhammadi
creator: Sayed Ali
subject: Agricultural Science
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.9035
publisher: PeerJ Inc.
rights: © 2020 Hemida et al.
abstract: Background The peste-des-petits-ruminants virus (PPRV) is a highly devastating virus of small ruminants in many parts of the world, including the Kingdome of Saudi Arabia. Therefore, our objectives were (1) to conduct a molecular prevalence study of PPRV in sheep and goat across the KSA and (2) to isolate and identify currently circulating PPRV lineages. Swabs and tissue specimens were collected from 97 herds suspected to be infected with PPRV across the Kingdome of Saudi Arabia (KSA). Testing for the presence of the virus was done by the real-time PCR. Confirmation of the identity of the reactions was done by the gel-based-PCR then by sequencing of the partial PPRV genome. Results Our results revealed that 24.1% of the tested specimens were PPRV-positive. Isolation of PPRV was successful from samples using the Vero cell line. Sequence analysis of some partial PPRV genes (N, F, M, L, P, and H) revealed that these strains were belonging to lineage IV of the PPRV. Conclusions This is the first study to conduct both the nationwide prevalence, isolation, and molecular characterizations of the PPRV in the KSA. Continuous surveillance and monitoring of the circulating strains of PPRV among sheep and goats will contribute substantially to the global eradication campaign of such a virus.
bibliographic citation: Hemida et al. (2020) Prevalence and molecular characterization of some circulating strains of the peste-des-petits-ruminants virus in Saudi Arabia between 2014–2016. PeerJ 8:e9035 https://doi.org/10.7717/peerj.9035
date submitted: 2019-10-21
date accepted: 2020-03-31
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hemida
  given name: Maged Gomaa
author list: Agent
  family name: Alghadeer
  given name: Hussain Mohammed
author list: Agent
  family name: Alhammadi
  given name: Mohammed
author list: Agent
  family name: Ali
  given name: Sayed
doi: 10.7717/peerj.9035
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Hemida et al.
attribution name: Hemida et al.

A new sponge-associated starfish, Astrolirus patricki sp. nov. (Asteroidea: Brisingida: Brisingidae), from the northwestern Pacific seamounts
type: item
type: AcademicArticle
description: Seamounts are important deep ocean entities that serve as reservoirs for varied types of habitats and fauna. During the Chinese cruises in the northwestern Pacific seamount areas, a new starfish species of order Brisingida, Astrolirus patricki, was found at 1,458–2,125 m depth. All specimens of the new species were observed in situ attaching on hexactinellid sponges, suggesting a possible close relationship between the two taxa. A. patricki sp. nov. is the second known species of the genus, characterized by the abutting plates in the intercostal integument, separated first pair of adambulacral plates and densely distributed proximal spines. Phylogenetic analyses were conducted for order Brisingida to incorporate the new species as well as Hymenodiscus cf. fragilis (Fisher, 1906), Freyella cf. attenuata Sladen, 1889 and two Brisinga spp., for which we present the molecular data for the first time. Phylogenetic trees suggest a close relationship between A. patricki sp. nov. with Brisinga species rather than with Hymenodiscus species, which is inconsistent with morphological taxonomy. This study highlights the distinct morphological and ecological characters of the new species and provides new data for future investigation on Brisingida phylogeny.
format: application/pdf
format: text/html
creator: Ruiyan Zhang
creator: Yadong Zhou
creator: Ning Xiao
creator: Chunsheng Wang
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9071
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Seamounts are important deep ocean entities that serve as reservoirs for varied types of habitats and fauna. During the Chinese cruises in the northwestern Pacific seamount areas, a new starfish species of order Brisingida, Astrolirus patricki, was found at 1,458–2,125 m depth. All specimens of the new species were observed in situ attaching on hexactinellid sponges, suggesting a possible close relationship between the two taxa. A. patricki sp. nov. is the second known species of the genus, characterized by the abutting plates in the intercostal integument, separated first pair of adambulacral plates and densely distributed proximal spines. Phylogenetic analyses were conducted for order Brisingida to incorporate the new species as well as Hymenodiscus cf. fragilis (Fisher, 1906), Freyella cf. attenuata Sladen, 1889 and two Brisinga spp., for which we present the molecular data for the first time. Phylogenetic trees suggest a close relationship between A. patricki sp. nov. with Brisinga species rather than with Hymenodiscus species, which is inconsistent with morphological taxonomy. This study highlights the distinct morphological and ecological characters of the new species and provides new data for future investigation on Brisingida phylogeny.
bibliographic citation: Zhang et al. (2020) A new sponge-associated starfish, Astrolirus patricki sp. nov. (Asteroidea: Brisingida: Brisingidae), from the northwestern Pacific seamounts. PeerJ 8:e9071 https://doi.org/10.7717/peerj.9071
date submitted: 2020-01-24
date accepted: 2020-04-06
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ruiyan
author list: Agent
  family name: Zhou
  given name: Yadong
author list: Agent
  family name: Xiao
  given name: Ning
author list: Agent
  family name: Wang
  given name: Chunsheng
doi: 10.7717/peerj.9071
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics
type: item
type: AcademicArticle
description: Background Brasilonema is a cyanobacterial genus found on the surface of mineral substrates and plants such as bromeliads, orchids and eucalyptus. B. octagenarum stands out among cyanobacteria due to causing damage to the leaves of its host in an interaction not yet observed in other cyanobacteria. Previous studies revealed that B. octagenaum UFV-E1 is capable of leading eucalyptus leaves to suffer internal tissue damage and necrosis by unknown mechanisms. This work aimed to investigate the effects of B. octagenarum UFV-E1 inoculation on Eucalyptus urograndis and to uncover molecular mechanisms potentially involved in leaf damage by these cyanobacteria using a comparative genomics approach. Results Leaves from E. urograndis saplings were exposed for 30 days to B. octagenarum UFV-E1, which was followed by the characterization of its genome and its comparison with the genomes of four other Brasilonema strains isolated from phyllosphere and the surface of mineral substrates. While UFV-E1 inoculation caused an increase in root and stem dry mass of the host plants, the sites colonized by cyanobacteria on leaves presented a significant decrease in pigmentation, showing that the cyanobacterial mats have an effect on leaf cell structure. Genomic analyses revealed that all evaluated Brasilonema genomes harbored genes encoding molecules possibly involved in plant-pathogen interactions, such as hydrolases targeting plant cell walls and proteins similar to known virulence factors from plant pathogens. However, sequences related to the type III secretory system and effectors were not detected, suggesting that, even if any virulence factors could be expressed in contact with their hosts, they would not have the structural means to actively reach plant cytoplasm. Conclusions Leaf damage by this species is likely related to the blockage of access to sunlight by the efficient growth of cyanobacterial mats on the phyllosphere, which may hinder the photosynthetic machinery and prevent…
format: application/pdf
format: text/html
creator: Danillo O. Alvarenga
creator: Maione W. Franco
creator: Kaarina Sivonen
creator: Marli F. Fiore
creator: Alessandro M. Varani
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.9158
publisher: PeerJ Inc.
rights: © 2020 Alvarenga et al.
abstract: Background Brasilonema is a cyanobacterial genus found on the surface of mineral substrates and plants such as bromeliads, orchids and eucalyptus. B. octagenarum stands out among cyanobacteria due to causing damage to the leaves of its host in an interaction not yet observed in other cyanobacteria. Previous studies revealed that B. octagenaum UFV-E1 is capable of leading eucalyptus leaves to suffer internal tissue damage and necrosis by unknown mechanisms. This work aimed to investigate the effects of B. octagenarum UFV-E1 inoculation on Eucalyptus urograndis and to uncover molecular mechanisms potentially involved in leaf damage by these cyanobacteria using a comparative genomics approach. Results Leaves from E. urograndis saplings were exposed for 30 days to B. octagenarum UFV-E1, which was followed by the characterization of its genome and its comparison with the genomes of four other Brasilonema strains isolated from phyllosphere and the surface of mineral substrates. While UFV-E1 inoculation caused an increase in root and stem dry mass of the host plants, the sites colonized by cyanobacteria on leaves presented a significant decrease in pigmentation, showing that the cyanobacterial mats have an effect on leaf cell structure. Genomic analyses revealed that all evaluated Brasilonema genomes harbored genes encoding molecules possibly involved in plant-pathogen interactions, such as hydrolases targeting plant cell walls and proteins similar to known virulence factors from plant pathogens. However, sequences related to the type III secretory system and effectors were not detected, suggesting that, even if any virulence factors could be expressed in contact with their hosts, they would not have the structural means to actively reach plant cytoplasm. Conclusions Leaf damage by this species is likely related to the blockage of access to sunlight by the efficient growth of cyanobacterial mats on the phyllosphere, which may hinder the photosynthetic machinery and prevent…
bibliographic citation: Alvarenga et al. (2020) Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics. PeerJ 8:e9158 https://doi.org/10.7717/peerj.9158
date submitted: 2019-12-30
date accepted: 2020-04-18
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alvarenga
  given name: Danillo O.
author list: Agent
  family name: Franco
  given name: Maione W.
author list: Agent
  family name: Sivonen
  given name: Kaarina
author list: Agent
  family name: Fiore
  given name: Marli F.
author list: Agent
  family name: Varani
  given name: Alessandro M.
doi: 10.7717/peerj.9158
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Alvarenga et al.
attribution name: Alvarenga et al.

Acute effects of air pollution on all-cause mortality: a natural experiment from haze control measures in Chiang Mai Province, Thailand
type: item
type: AcademicArticle
description: Background Serious haze episodes have been a seasonal event in Chiang Mai province for more than a decade. In 2008, local government agencies introduced comprehensive measures to control haze and limit its impacts on public health. This study assessed the acute effects of ambient air pollutants on all-cause mortality before and after the introduction of those haze control measures. Methods We obtained daily mortality counts and data on mass concentrations of particulate matter <10 micron in aerodynamic diameter (PM10), gaseous pollutants (SO2, NO2, O3, and CO), and meteorology in Chiang Mai Province between January 2002 and December 2016. We analyzed the data using a case-crossover approach adjusting for temperature, relative humidity, seasonality, and day-of-week. We assessed change in the excess risks of all-cause mortality associated with an increase in interquartile range (IQR) of pollutant concentration before and after control measures came into force. Results We found decreased PM10 levels and markedly reduced excess risks of daily mortality associated with an IQR increase in PM10 concentrations in the years after haze-control measures were implemented (2009–2016). We found mixed results for gaseous pollutants: SO2 showed no significant change in excess risk of daily mortality throughout the study period, while NO2 and CO showed significant excess risks only in the period 2012–2016, and 8-h maximum O3 showed a decrease in excess risk despite an increase in its atmospheric levels after the introduction of haze control measures in 2008. Conclusions The findings indicate that the government haze control measures first introduced in Chiang Mai province in 2008 have successfully reduced episodic PM10 concentrations, which has led to a decrease in short-term all-cause mortality.
format: application/pdf
format: text/html
creator: Nitaya Vajanapoom
creator: Patcharee Kooncumchoo
creator: Thuan-Quoc Thach
subject: Epidemiology
subject: Public Health
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9207
publisher: PeerJ Inc.
rights: © 2020 Vajanapoom et al.
abstract: Background Serious haze episodes have been a seasonal event in Chiang Mai province for more than a decade. In 2008, local government agencies introduced comprehensive measures to control haze and limit its impacts on public health. This study assessed the acute effects of ambient air pollutants on all-cause mortality before and after the introduction of those haze control measures. Methods We obtained daily mortality counts and data on mass concentrations of particulate matter <10 micron in aerodynamic diameter (PM10), gaseous pollutants (SO2, NO2, O3, and CO), and meteorology in Chiang Mai Province between January 2002 and December 2016. We analyzed the data using a case-crossover approach adjusting for temperature, relative humidity, seasonality, and day-of-week. We assessed change in the excess risks of all-cause mortality associated with an increase in interquartile range (IQR) of pollutant concentration before and after control measures came into force. Results We found decreased PM10 levels and markedly reduced excess risks of daily mortality associated with an IQR increase in PM10 concentrations in the years after haze-control measures were implemented (2009–2016). We found mixed results for gaseous pollutants: SO2 showed no significant change in excess risk of daily mortality throughout the study period, while NO2 and CO showed significant excess risks only in the period 2012–2016, and 8-h maximum O3 showed a decrease in excess risk despite an increase in its atmospheric levels after the introduction of haze control measures in 2008. Conclusions The findings indicate that the government haze control measures first introduced in Chiang Mai province in 2008 have successfully reduced episodic PM10 concentrations, which has led to a decrease in short-term all-cause mortality.
bibliographic citation: Vajanapoom et al. (2020) Acute effects of air pollution on all-cause mortality: a natural experiment from haze control measures in Chiang Mai Province, Thailand. PeerJ 8:e9207 https://doi.org/10.7717/peerj.9207
date submitted: 2020-03-02
date accepted: 2020-04-27
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vajanapoom
  given name: Nitaya
author list: Agent
  family name: Kooncumchoo
  given name: Patcharee
author list: Agent
  family name: Thach
  given name: Thuan-Quoc
doi: 10.7717/peerj.9207
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Vajanapoom et al.
attribution name: Vajanapoom et al.

Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device
type: item
type: AcademicArticle
description: Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
format: application/pdf
format: text/html
creator: Kek Heng Chua
creator: E. Wei Tan
creator: Hwa Chia Chai
creator: SD Puthucheary
creator: Ping Chin Lee
creator: Suat Moi Puah
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.9238
publisher: PeerJ Inc.
rights: © 2020 Chua et al.
abstract: Background Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity. Method In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel. Results All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity. Conclusion This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.
bibliographic citation: Chua et al. (2020) Rapid identification of melioidosis agent by an insulated isothermal PCR on a field–deployable device. PeerJ 8:e9238 https://doi.org/10.7717/peerj.9238
date submitted: 2020-02-05
date accepted: 2020-05-05
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chua
  given name: Kek Heng
author list: Agent
  family name: Tan
  given name: E. Wei
author list: Agent
  family name: Chai
  given name: Hwa Chia
author list: Agent
  family name: Puthucheary
  given name: SD
author list: Agent
  family name: Lee
  given name: Ping Chin
author list: Agent
  family name: Puah
  given name: Suat Moi
doi: 10.7717/peerj.9238
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Chua et al.
attribution name: Chua et al.

Effects of temperature on metabolic scaling in black carp
type: item
type: AcademicArticle
description: The surface area (SA) of organs and cells may vary with temperature, which changes the SA exchange limitation on metabolic flows as well as the influence of temperature on metabolic scaling. The effect of SA change can intensify (when the effect is the same as that of temperature) or compensate for (when the effect is the opposite of that of temperature) the negative effects of temperature on metabolic scaling, which can result in multiple patterns of metabolic scaling with temperature among species. The present study aimed to examine whether metabolic scaling in black carp changes with temperature and to identify the link between metabolic scaling and SA at the organ and cellular levels at different temperatures. The resting metabolic rate (RMR), gill surface area (GSA) and red blood cell (RBC) size of black carp with different body masses were measured at 10 °C and 25 °C, and the scaling exponents of these parameters were compared. The results showed that both body mass and temperature independently affected the RMR, GSA and RBC size of black carp. A consistent scaling exponent of RMR (0.764, 95% CI [0.718–0.809]) was obtained for both temperatures. The RMR at 25 °C was 2.7 times higher than that at 10 °C. At both temperatures, the GSA scaled consistently with body mass by an exponent of 0.802 (95% CI [0.759–0.846]), while RBC size scaled consistently with body mass by an exponent of 0.042 (95% CI [0.010–0.075]). The constant GSA scaling can explain the constant metabolic scaling as temperature increases, as metabolism may be constrained by fluxes across surfaces. The GSA at 10 °C was 1.2 times higher than that at 25 °C, which suggests that the constraints of GSA on the metabolism of black carp is induced by the higher temperature. The RBC size at 10 °C was 1.1 times higher than that at 25 °C. The smaller RBC size (a larger surface-to-volume ratio) at higher temperature suggests an enhanced oxygen supply and a reduced surface boundary limit on bR, which offset the…
format: application/pdf
format: text/html
creator: Qian Li
creator: Xiaoling Zhu
creator: Wei Xiong
creator: Yanqiu Zhu
creator: Jianghui Zhang
creator: Pathe Karim Djiba
creator: Xiao Lv
creator: Yiping Luo
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.9242
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: The surface area (SA) of organs and cells may vary with temperature, which changes the SA exchange limitation on metabolic flows as well as the influence of temperature on metabolic scaling. The effect of SA change can intensify (when the effect is the same as that of temperature) or compensate for (when the effect is the opposite of that of temperature) the negative effects of temperature on metabolic scaling, which can result in multiple patterns of metabolic scaling with temperature among species. The present study aimed to examine whether metabolic scaling in black carp changes with temperature and to identify the link between metabolic scaling and SA at the organ and cellular levels at different temperatures. The resting metabolic rate (RMR), gill surface area (GSA) and red blood cell (RBC) size of black carp with different body masses were measured at 10 °C and 25 °C, and the scaling exponents of these parameters were compared. The results showed that both body mass and temperature independently affected the RMR, GSA and RBC size of black carp. A consistent scaling exponent of RMR (0.764, 95% CI [0.718–0.809]) was obtained for both temperatures. The RMR at 25 °C was 2.7 times higher than that at 10 °C. At both temperatures, the GSA scaled consistently with body mass by an exponent of 0.802 (95% CI [0.759–0.846]), while RBC size scaled consistently with body mass by an exponent of 0.042 (95% CI [0.010–0.075]). The constant GSA scaling can explain the constant metabolic scaling as temperature increases, as metabolism may be constrained by fluxes across surfaces. The GSA at 10 °C was 1.2 times higher than that at 25 °C, which suggests that the constraints of GSA on the metabolism of black carp is induced by the higher temperature. The RBC size at 10 °C was 1.1 times higher than that at 25 °C. The smaller RBC size (a larger surface-to-volume ratio) at higher temperature suggests an enhanced oxygen supply and a reduced surface boundary limit on bR, which offset the…
bibliographic citation: Li et al. (2020) Effects of temperature on metabolic scaling in black carp. PeerJ 8:e9242 https://doi.org/10.7717/peerj.9242
date submitted: 2020-01-15
date accepted: 2020-05-05
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Zhu
  given name: Xiaoling
author list: Agent
  family name: Xiong
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Yanqiu
author list: Agent
  family name: Zhang
  given name: Jianghui
author list: Agent
  family name: Djiba
  given name: Pathe Karim
author list: Agent
  family name: Lv
  given name: Xiao
author list: Agent
  family name: Luo
  given name: Yiping
doi: 10.7717/peerj.9242
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: © 2020 Li et al.
attribution name: Li et al.

Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis
type: item
type: AcademicArticle
description: Objectives To demonstrate the screening value of echocardiography for portopulmonary hypertension (POPH) in liver transplant candidates. Design Systematic review and meta-analysis. Background POPH is a complication of end-stage liver disease that adversely affects the outcome of orthotopic liver transplant. There are no specific symptoms in the early stage of POPH. POPH reduce the survival rate of patients with end-stage liver disease specially if they are not diagnosed. Therefore, early detection may improve prognosis. The objective of this study is to explore the screening value of echocardiography on liver transplant candidates for screening of POPH compared to right heart catheterization (RHC). Method PubMed, EMBASE and the Cochrane Library were searched by two independent reviewers for potentially eligible studies published up to 30 June 2019 to retrieve data based on per-patient analysis. STATA, Meta-DiSc, and RevMan were applied to perform this meta-analysis. Results Our search yielded 1576 studies, of which 11 satisfied the inclusion criteria. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve (AUC) of echocardiography for POPH were 0.85 (95% CI [0.65–0.94]), 0.83 (95% CI [0.73–0.90]), 4.99 (95% CI [3.03–8.21]), 0.19 (95% CI [0.07–0.46]), and 0.91 (95% CI [0.88–0.93]), respectively. Deeks’ funnel plot did not indicate the existence of publication bias (P = 0.66). Conclusions Echocardiography, a noninvasive modality, provides superior screening for POPH, but the diagnosis of POPH still requires RHC. PROSPERO registration number CRD42019144589.
format: application/pdf
format: text/html
creator: Xin Yin
creator: Yueming Shao
creator: Yu Zhang
creator: Hui Gao
creator: Tingting Qin
creator: Xiaoyu Wen
creator: Chen Yang
subject: Gastroenterology and Hepatology
subject: Internal Medicine
description: doi:10.7717/peerj.9243
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Objectives To demonstrate the screening value of echocardiography for portopulmonary hypertension (POPH) in liver transplant candidates. Design Systematic review and meta-analysis. Background POPH is a complication of end-stage liver disease that adversely affects the outcome of orthotopic liver transplant. There are no specific symptoms in the early stage of POPH. POPH reduce the survival rate of patients with end-stage liver disease specially if they are not diagnosed. Therefore, early detection may improve prognosis. The objective of this study is to explore the screening value of echocardiography on liver transplant candidates for screening of POPH compared to right heart catheterization (RHC). Method PubMed, EMBASE and the Cochrane Library were searched by two independent reviewers for potentially eligible studies published up to 30 June 2019 to retrieve data based on per-patient analysis. STATA, Meta-DiSc, and RevMan were applied to perform this meta-analysis. Results Our search yielded 1576 studies, of which 11 satisfied the inclusion criteria. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve (AUC) of echocardiography for POPH were 0.85 (95% CI [0.65–0.94]), 0.83 (95% CI [0.73–0.90]), 4.99 (95% CI [3.03–8.21]), 0.19 (95% CI [0.07–0.46]), and 0.91 (95% CI [0.88–0.93]), respectively. Deeks’ funnel plot did not indicate the existence of publication bias (P = 0.66). Conclusions Echocardiography, a noninvasive modality, provides superior screening for POPH, but the diagnosis of POPH still requires RHC. PROSPERO registration number CRD42019144589.
bibliographic citation: Yin et al. (2020) Role of echocardiography in screening for portopulmonary hypertension in liver transplant candidates: a meta-analysis. PeerJ 8:e9243 https://doi.org/10.7717/peerj.9243
date submitted: 2020-01-02
date accepted: 2020-05-06
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Xin
author list: Agent
  family name: Shao
  given name: Yueming
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Gao
  given name: Hui
author list: Agent
  family name: Qin
  given name: Tingting
author list: Agent
  family name: Wen
  given name: Xiaoyu
author list: Agent
  family name: Yang
  given name: Chen
doi: 10.7717/peerj.9243
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: ©2020 Yin et al.
attribution name: Yin et al.

Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems
type: item
type: AcademicArticle
description: The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and exact integer linear programing (EILP) solvers. Using a case study in BC, Canada, we compare the cost-effectiveness and processing times of SA used in Marxan versus EILP using both commercial and open-source algorithms. Plans for expanding protected area systems based on EILP algorithms were 12–30% cheaper than plans using SA, due to EILP’s ability to find optimal solutions as opposed to approximations. The best EILP solver we examined was on average 1,071 times faster than the SA algorithm tested. The performance advantages of EILP solvers were also observed when we aimed for spatially compact solutions by including a boundary penalty. One practical advantage of using EILP over SA is that the analysis does not require calibration, saving even more time. Given the performance of EILP solvers, they can be used to generate conservation plans in real-time during stakeholder meetings and can facilitate rapid sensitivity analysis, and contribute to a more transparent, inclusive, and defensible decision-making process.
format: application/pdf
format: text/html
creator: Richard Schuster
creator: Jeffrey O. Hanson
creator: Matthew Strimas-Mackey
creator: Joseph R. Bennett
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9258
publisher: PeerJ Inc.
rights: © 2020 Schuster et al.
abstract: The resources available for conserving biodiversity are limited, and so protected areas need to be established in places that will achieve objectives for minimal cost. Two of the main algorithms for solving systematic conservation planning problems are Simulated Annealing (SA) and exact integer linear programing (EILP) solvers. Using a case study in BC, Canada, we compare the cost-effectiveness and processing times of SA used in Marxan versus EILP using both commercial and open-source algorithms. Plans for expanding protected area systems based on EILP algorithms were 12–30% cheaper than plans using SA, due to EILP’s ability to find optimal solutions as opposed to approximations. The best EILP solver we examined was on average 1,071 times faster than the SA algorithm tested. The performance advantages of EILP solvers were also observed when we aimed for spatially compact solutions by including a boundary penalty. One practical advantage of using EILP over SA is that the analysis does not require calibration, saving even more time. Given the performance of EILP solvers, they can be used to generate conservation plans in real-time during stakeholder meetings and can facilitate rapid sensitivity analysis, and contribute to a more transparent, inclusive, and defensible decision-making process.
bibliographic citation: Schuster et al. (2020) Exact integer linear programming solvers outperform simulated annealing for solving conservation planning problems. PeerJ 8:e9258 https://doi.org/10.7717/peerj.9258
date submitted: 2020-01-16
date accepted: 2020-05-08
issued: 2020-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schuster
  given name: Richard
author list: Agent
  family name: Hanson
  given name: Jeffrey O.
author list: Agent
  family name: Strimas-Mackey
  given name: Matthew
author list: Agent
  family name: Bennett
  given name: Joseph R.
doi: 10.7717/peerj.9258
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-27
copyright: © 2020 Schuster et al.
attribution name: Schuster et al.

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