PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The first report of the prevalence of Nosema ceranae in Bulgaria
items: Signals of forest degradation in the demography of common Asian amphibians
items: Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing
items: Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A
items: Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies
items: Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method
items: Positive end expiratory pressure in acute hypoxemic respiratory failure due to community acquired pneumonia: do we need a personalized approach?
items: Comparative proteomics reveals that YK51, a 4-Hydroxypandurantin-A analogue, downregulates the expression of proteins associated with dengue virus infection
items: Incidence of and social-demographic and obstetric factors associated with postpartum depression: differences among ethnic Han and Kazak women of Northwestern China
items: Evaluating outcomes of young forest management on a target species of conservation concern

The first report of the prevalence of Nosema ceranae in Bulgaria
type: item
type: AcademicArticle
description: Nosema apis and Nosema ceranae are the two main microsporidian parasites causing nosematosis in the honey bee Apis mellifera. The aim of the present study is to investigate the presence of Nosema apis and Nosema ceranae in the area of Bulgaria. The 16S (SSU) rDNA gene region was chosen for analysis. A duplex PCR assay was performed on 108 honey bee samples from three different parts of the country (South, North and West Bulgaria). The results showed that the samples from the northern part of the country were with the highest prevalence (77.2%) for Nosema ceranae while those from the mountainous parts (the Rodopa Mountains, South Bulgaria) were with the lowest rate (13.9%). Infection with Nosema apis alone and co-infection N. apis/N. ceranae were not detected in any samples. These findings suggest that Nosema ceranae is the dominant species in the Bulgarian honey bee. It is not known when the introduction of Nosema ceranae in Bulgaria has occurred, but as in the rest of the world, this species has become the dominant one in Bulgarian Apis mellifera. In conclusion, this is the first report for molecular detection of Nosema infection of honey bee in Bulgaria. The results showed that N. ceranae is the main Nosema species in Bulgaria.
format: application/pdf
format: text/html
creator: Rositsa Shumkova
creator: Ani Georgieva
creator: Georgi Radoslavov
creator: Daniela Sirakova
creator: Gyulnas Dzhebir
creator: Boyko Neov
creator: Maria Bouga
creator: Peter Hristov
subject: Entomology
subject: Genetics
subject: Parasitology
subject: Veterinary Medicine
description: doi:10.7717/peerj.4252
publisher: PeerJ Inc.
rights: © 2018 Shumkova et al.
abstract: Nosema apis and Nosema ceranae are the two main microsporidian parasites causing nosematosis in the honey bee Apis mellifera. The aim of the present study is to investigate the presence of Nosema apis and Nosema ceranae in the area of Bulgaria. The 16S (SSU) rDNA gene region was chosen for analysis. A duplex PCR assay was performed on 108 honey bee samples from three different parts of the country (South, North and West Bulgaria). The results showed that the samples from the northern part of the country were with the highest prevalence (77.2%) for Nosema ceranae while those from the mountainous parts (the Rodopa Mountains, South Bulgaria) were with the lowest rate (13.9%). Infection with Nosema apis alone and co-infection N. apis/N. ceranae were not detected in any samples. These findings suggest that Nosema ceranae is the dominant species in the Bulgarian honey bee. It is not known when the introduction of Nosema ceranae in Bulgaria has occurred, but as in the rest of the world, this species has become the dominant one in Bulgarian Apis mellifera. In conclusion, this is the first report for molecular detection of Nosema infection of honey bee in Bulgaria. The results showed that N. ceranae is the main Nosema species in Bulgaria.
bibliographic citation: Shumkova et al. (2018) The first report of the prevalence of Nosema ceranae in Bulgaria. PeerJ 6:e4252 https://doi.org/10.7717/peerj.4252
date submitted: 2017-10-10
date accepted: 2017-12-19
issued: 2018-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shumkova
  given name: Rositsa
author list: Agent
  family name: Georgieva
  given name: Ani
author list: Agent
  family name: Radoslavov
  given name: Georgi
author list: Agent
  family name: Sirakova
  given name: Daniela
author list: Agent
  family name: Dzhebir
  given name: Gyulnas
author list: Agent
  family name: Neov
  given name: Boyko
author list: Agent
  family name: Bouga
  given name: Maria
author list: Agent
  family name: Hristov
  given name: Peter
doi: 10.7717/peerj.4252
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-31
copyright: ©2018 Shumkova et al.
attribution name: Shumkova et al.

Signals of forest degradation in the demography of common Asian amphibians
type: item
type: AcademicArticle
description: Background Lowland areas in tropical East and Southeast Asia have a long history of conversion from forestland to agricultural land, with many remaining forests being chronically degraded by wood cutting, livestock grazing, and burning. Wetland-breeding amphibians that have evolved in lowland forests in the region have adjusted to changes in habitat composition caused by humans’ activities, and populations continue to persist. However, we have little understanding of the impacts of forest disturbance on these species beyond assessments of abundance and distribution, and species considered to be common and widespread have been largely neglected. Methods We examined body condition and sex ratios of toads (Duttaphrynus melanostictus), predation risk in treefrogs (2 Polypedates spp.), and growth and survival of leaf litter frogs (2 Microhyla spp.) in agricultural land, degraded forest, and intact forest in two study areas, Thailand and Hong Kong. Results Toad populations exhibited higher body condition and female-biased sex ratios in intact forest. Predation of treefrog embryos by flies was lower in intact and degraded forests than in agricultural land. Embryonic survival and larval growth and survival in leaf litter frogs were lower in intact forests than in agricultural land. Results for each study were similar between study areas. Discussion For three of five of these common amphibian species, we documented signals of forest loss and disturbance in their populations. Although these species occur in disturbed habitats, loss of forest cover continues to degrade aspects of their population demography. We urge conservation biologists to consider that populations of species appearing to be common, widespread, and tolerant of human disturbance may be eroding over time.
format: application/pdf
format: text/html
creator: Nancy E. Karraker
creator: Samantha Fischer
creator: Anchalee Aowphol
creator: Jennifer Sheridan
creator: Sinlan Poo
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.4220
publisher: PeerJ Inc.
rights: © 2018 Karraker et al.
abstract: Background Lowland areas in tropical East and Southeast Asia have a long history of conversion from forestland to agricultural land, with many remaining forests being chronically degraded by wood cutting, livestock grazing, and burning. Wetland-breeding amphibians that have evolved in lowland forests in the region have adjusted to changes in habitat composition caused by humans’ activities, and populations continue to persist. However, we have little understanding of the impacts of forest disturbance on these species beyond assessments of abundance and distribution, and species considered to be common and widespread have been largely neglected. Methods We examined body condition and sex ratios of toads (Duttaphrynus melanostictus), predation risk in treefrogs (2 Polypedates spp.), and growth and survival of leaf litter frogs (2 Microhyla spp.) in agricultural land, degraded forest, and intact forest in two study areas, Thailand and Hong Kong. Results Toad populations exhibited higher body condition and female-biased sex ratios in intact forest. Predation of treefrog embryos by flies was lower in intact and degraded forests than in agricultural land. Embryonic survival and larval growth and survival in leaf litter frogs were lower in intact forests than in agricultural land. Results for each study were similar between study areas. Discussion For three of five of these common amphibian species, we documented signals of forest loss and disturbance in their populations. Although these species occur in disturbed habitats, loss of forest cover continues to degrade aspects of their population demography. We urge conservation biologists to consider that populations of species appearing to be common, widespread, and tolerant of human disturbance may be eroding over time.
bibliographic citation: Karraker et al. (2018) Signals of forest degradation in the demography of common Asian amphibians. PeerJ 6:e4220 https://doi.org/10.7717/peerj.4220
date submitted: 2017-09-28
date accepted: 2017-12-12
issued: 2018-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karraker
  given name: Nancy E.
author list: Agent
  family name: Fischer
  given name: Samantha
author list: Agent
  family name: Aowphol
  given name: Anchalee
author list: Agent
  family name: Sheridan
  given name: Jennifer
author list: Agent
  family name: Poo
  given name: Sinlan
doi: 10.7717/peerj.4220
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-31
copyright: ©2018 Karraker et al.
attribution name: Karraker et al.

Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing
type: item
type: AcademicArticle
description: Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.
format: application/pdf
format: text/html
creator: Nikolett Csizmár
creator: Sándor Mihók
creator: András Jávor
creator: Szilvia Kusza
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.4198
publisher: PeerJ Inc.
rights: © 2018 Csizmár et al.
abstract: Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while.
bibliographic citation: Csizmár et al. (2018) Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing. PeerJ 6:e4198 https://doi.org/10.7717/peerj.4198
date submitted: 2017-07-24
date accepted: 2017-12-05
issued: 2018-01-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Csizmár
  given name: Nikolett
author list: Agent
  family name: Mihók
  given name: Sándor
author list: Agent
  family name: Jávor
  given name: András
author list: Agent
  family name: Kusza
  given name: Szilvia
doi: 10.7717/peerj.4198
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-31
copyright: ©2018 Csizmár et al.
attribution name: Csizmár et al.

Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A
type: item
type: AcademicArticle
description: Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
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creator: Shelby S. Calkins
creator: Nicole C. Elledge
creator: Katherine E. Mueller
creator: Stephen M. Marek
creator: MB Couger
creator: Mostafa S. Elshahed
creator: Noha H. Youssef
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.4276
publisher: PeerJ Inc.
rights: © 2018 Calkins et al.
abstract: Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
bibliographic citation: Calkins et al. (2018) Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ 6:e4276 https://doi.org/10.7717/peerj.4276
date submitted: 2017-08-18
date accepted: 2017-12-29
issued: 2018-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calkins
  given name: Shelby S.
author list: Agent
  family name: Elledge
  given name: Nicole C.
author list: Agent
  family name: Mueller
  given name: Katherine E.
author list: Agent
  family name: Marek
  given name: Stephen M.
author list: Agent
  family name: Couger
  given name: MB
author list: Agent
  family name: Elshahed
  given name: Mostafa S.
author list: Agent
  family name: Youssef
  given name: Noha H.
doi: 10.7717/peerj.4276
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-30
copyright: ©2018 Calkins et al.
attribution name: Calkins et al.

Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies
type: item
type: AcademicArticle
description: Background N-acetylcarnosine (NAC), a dipeptide with powerful antioxidant properties that is extensively used as a pharmaceutical prodrug for the treatment of cataract and acute gastric disease, was investigated by molecular dynamics with the GROMACS program in order to understand the solvent effect on peptide conformation of the peptide molecule used as a component of a drug and which presents substantial information on where drug molecules bind and how they exert their effects. Besides, molecular docking simulation was performed by using the AutoDock Vina program which identify the kind of interaction between the drug and proteins. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with NAC (NAC-PLGA-NPs) for the treatment of cataract was prepared for the first time in this study in order to enhance drug bioavailability and biocompatibility. The objective of this work was to prepare and evaluate the structural formulation, characterization, and cytotoxicity studies of NAC-loaded NPs based on PLGA for cataract treatment. Methods PLGA and NAC-loaded PLGA NPs were prepared using the double emulsion (w/o/w) method, and characterizations of the NPs were carried out with UV–Vis spectrometer to determine drug concentration, the Zeta-sizer system to analyze size and zeta potential, FTIR spectrometer to determine the incorporation of drug and PLGA, and TEM analysis for morphological evaluation. Results NAC-loaded PLGA NPs were successfully obtained according to UV–Vis and FTIR spectroscopy, Zeta-sizer system. And it was clearly observed from the TEM analysis that the peptide-loaded NPs had spherical and non-aggregated morphology. Also, the NPs had low toxicity at lower concentrations, and toxicity was augmented by increasing the concentration of the drug. Discussion The NAC molecule, which has been investigated as a drug molecule due to its antioxidant and oxidative stress-reducing properties, especially in cataract treatment, was en…
format: application/pdf
format: text/html
creator: Yasemin Budama-Kilinc
creator: Rabia Cakir-Koc
creator: Serda Kecel-Gunduz
creator: Yagmur Kokcu
creator: Bilge Bicak
creator: Hande Mutlu
creator: Aysen E. Ozel
subject: Bioengineering
subject: Biophysics
subject: Computational Science
description: doi:10.7717/peerj.4270
publisher: PeerJ Inc.
rights: © 2018 Budama-Kilinc et al.
abstract: Background N-acetylcarnosine (NAC), a dipeptide with powerful antioxidant properties that is extensively used as a pharmaceutical prodrug for the treatment of cataract and acute gastric disease, was investigated by molecular dynamics with the GROMACS program in order to understand the solvent effect on peptide conformation of the peptide molecule used as a component of a drug and which presents substantial information on where drug molecules bind and how they exert their effects. Besides, molecular docking simulation was performed by using the AutoDock Vina program which identify the kind of interaction between the drug and proteins. A delivery system based on poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) loaded with NAC (NAC-PLGA-NPs) for the treatment of cataract was prepared for the first time in this study in order to enhance drug bioavailability and biocompatibility. The objective of this work was to prepare and evaluate the structural formulation, characterization, and cytotoxicity studies of NAC-loaded NPs based on PLGA for cataract treatment. Methods PLGA and NAC-loaded PLGA NPs were prepared using the double emulsion (w/o/w) method, and characterizations of the NPs were carried out with UV–Vis spectrometer to determine drug concentration, the Zeta-sizer system to analyze size and zeta potential, FTIR spectrometer to determine the incorporation of drug and PLGA, and TEM analysis for morphological evaluation. Results NAC-loaded PLGA NPs were successfully obtained according to UV–Vis and FTIR spectroscopy, Zeta-sizer system. And it was clearly observed from the TEM analysis that the peptide-loaded NPs had spherical and non-aggregated morphology. Also, the NPs had low toxicity at lower concentrations, and toxicity was augmented by increasing the concentration of the drug. Discussion The NAC molecule, which has been investigated as a drug molecule due to its antioxidant and oxidative stress-reducing properties, especially in cataract treatment, was en…
bibliographic citation: Budama-Kilinc et al. (2018) Novel NAC-loaded poly(lactide-co-glycolide acid) nanoparticles for cataract treatment: preparation, characterization, evaluation of structure, cytotoxicity, and molecular docking studies. PeerJ 6:e4270 https://doi.org/10.7717/peerj.4270
date submitted: 2017-12-04
date accepted: 2017-12-27
issued: 2018-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Budama-Kilinc
  given name: Yasemin
author list: Agent
  family name: Cakir-Koc
  given name: Rabia
author list: Agent
  family name: Kecel-Gunduz
  given name: Serda
author list: Agent
  family name: Kokcu
  given name: Yagmur
author list: Agent
  family name: Bicak
  given name: Bilge
author list: Agent
  family name: Mutlu
  given name: Hande
author list: Agent
  family name: E. Ozel
  given name: Aysen
doi: 10.7717/peerj.4270
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-30
copyright: © 2018 Budama-Kilinc et al.
attribution name: Budama-Kilinc et al.

Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method
type: item
type: AcademicArticle
description: Background Competitive interactions in biological communities can be thought of as giving rise to “assembly rules” that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an “ant mosaic”, in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess presence of ant mosaics in a hitherto under-investigated forest stratum, the emergent trees of the high canopy in primary tropical rain forest, and explore how the strength of any ant mosaics is affected by spatial scale, time of day, and sampling method. Methods To test whether these factors might impact the detection of ant mosaics in pristine habitats, we sampled ant communities from emergent trees, which rise above the highest canopy layers in lowland dipterocarp rain forests in North Borneo (38.8–60.2 m), using both baiting and insecticide fogging. Critically, we restricted sampling to only the canopy of each focal tree. For baiting, we carried out sampling during both the day and the night. We used null models of species co-occurrence to assess patterns of segregation at within-tree and between-tree scales. Results The numerically dominant ant species on the emergent trees sampled formed a diverse community, with differences in the identity of dominant species between times of day and sampling methods. Between trees, we found patterns of ant species segregation consistent with the existence of ant mosaics using both methods. Within trees, fogged ants were segregated, while baited ants were segregated only at night. Discussion We conclude that ant mosaics are present within the emergent trees of the high canopy of tropical rain forest in Malaysian Borneo, and that sampling technique, spatial scale, and time of day interact to determine o…
format: application/pdf
format: text/html
creator: Kalsum M. Yusah
creator: William A. Foster
creator: Glen Reynolds
creator: Tom M. Fayle
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.4231
publisher: PeerJ Inc.
rights: © 2018 Yusah et al.
abstract: Background Competitive interactions in biological communities can be thought of as giving rise to “assembly rules” that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an “ant mosaic”, in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess presence of ant mosaics in a hitherto under-investigated forest stratum, the emergent trees of the high canopy in primary tropical rain forest, and explore how the strength of any ant mosaics is affected by spatial scale, time of day, and sampling method. Methods To test whether these factors might impact the detection of ant mosaics in pristine habitats, we sampled ant communities from emergent trees, which rise above the highest canopy layers in lowland dipterocarp rain forests in North Borneo (38.8–60.2 m), using both baiting and insecticide fogging. Critically, we restricted sampling to only the canopy of each focal tree. For baiting, we carried out sampling during both the day and the night. We used null models of species co-occurrence to assess patterns of segregation at within-tree and between-tree scales. Results The numerically dominant ant species on the emergent trees sampled formed a diverse community, with differences in the identity of dominant species between times of day and sampling methods. Between trees, we found patterns of ant species segregation consistent with the existence of ant mosaics using both methods. Within trees, fogged ants were segregated, while baited ants were segregated only at night. Discussion We conclude that ant mosaics are present within the emergent trees of the high canopy of tropical rain forest in Malaysian Borneo, and that sampling technique, spatial scale, and time of day interact to determine o…
bibliographic citation: Yusah et al. (2018) Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method. PeerJ 6:e4231 https://doi.org/10.7717/peerj.4231
date submitted: 2016-01-22
date accepted: 2017-12-14
issued: 2018-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yusah
  given name: Kalsum M.
author list: Agent
  family name: Foster
  given name: William A.
author list: Agent
  family name: Reynolds
  given name: Glen
author list: Agent
  family name: Fayle
  given name: Tom M.
doi: 10.7717/peerj.4231
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-30
copyright: ©2018 Yusah et al.
attribution name: Yusah et al.

Positive end expiratory pressure in acute hypoxemic respiratory failure due to community acquired pneumonia: do we need a personalized approach?
type: item
type: AcademicArticle
description: Background Acute respiratory failure (ARF) is a life-threatening complication in patients with community acquired pneumonia (CAP). The use of non-invasive ventilation is controversial. With this prospective, observational study we aimed to describe a protocol to assess whether a patient with moderate-to-severe hypoxemic ARF secondary to CAP benefits, in clinical and laboratoristic terms, from the application of a positive end expiratory pressure (PEEP) + oxygen vs oxygen alone. Methods Patients who benefit from PEEP application (PEEP-responders) were defined as those with partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2) increase >20% and/or reduction of respiratory distress during PEEP + oxygen therapy compared to oxygen therapy alone. Clinical characteristics and outcomes were compared between PEEP-responders and PEEP-non responders. Results Out of 41 patients, 27 (66%) benefit from PEEP application (PEEP-responders), the best response was obtained with a PEEP of 10 cmH2O in 13 patients, 7.5 cmH2O in eight and 5 cmH2O in six. PEEP-responders were less likely to present comorbidities compared to PEEP-non responders. No differences between groups were found in regards to endotracheal intubation criteria fullfillment, intensive care unit admission and in-hospital mortality, while PEEP-responders had a shorter length of hospital stay. Discussion The application of a protocol to evaluate PEEP responsiveness might be useful in patients with moderate-to-severe hypoxemic ARF due to CAP in order to personalize and maximize the effectiveness of therapy, and prevent the inappropriate PEEP use. PEEP responsiveness does not seem to be associated with better outcomes, with the exception of a shorter length of hospital stay.
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format: text/html
creator: Valentina Paolini
creator: Paola Faverio
creator: Stefano Aliberti
creator: Grazia Messinesi
creator: Giuseppe Foti
creator: Oriol Sibila
creator: Anna Monzani
creator: Federica De Giacomi
creator: Anna Stainer
creator: Alberto Pesci
subject: Evidence Based Medicine
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.4211
publisher: PeerJ Inc.
rights: © 2018 Paolini et al.
abstract: Background Acute respiratory failure (ARF) is a life-threatening complication in patients with community acquired pneumonia (CAP). The use of non-invasive ventilation is controversial. With this prospective, observational study we aimed to describe a protocol to assess whether a patient with moderate-to-severe hypoxemic ARF secondary to CAP benefits, in clinical and laboratoristic terms, from the application of a positive end expiratory pressure (PEEP) + oxygen vs oxygen alone. Methods Patients who benefit from PEEP application (PEEP-responders) were defined as those with partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2) increase >20% and/or reduction of respiratory distress during PEEP + oxygen therapy compared to oxygen therapy alone. Clinical characteristics and outcomes were compared between PEEP-responders and PEEP-non responders. Results Out of 41 patients, 27 (66%) benefit from PEEP application (PEEP-responders), the best response was obtained with a PEEP of 10 cmH2O in 13 patients, 7.5 cmH2O in eight and 5 cmH2O in six. PEEP-responders were less likely to present comorbidities compared to PEEP-non responders. No differences between groups were found in regards to endotracheal intubation criteria fullfillment, intensive care unit admission and in-hospital mortality, while PEEP-responders had a shorter length of hospital stay. Discussion The application of a protocol to evaluate PEEP responsiveness might be useful in patients with moderate-to-severe hypoxemic ARF due to CAP in order to personalize and maximize the effectiveness of therapy, and prevent the inappropriate PEEP use. PEEP responsiveness does not seem to be associated with better outcomes, with the exception of a shorter length of hospital stay.
bibliographic citation: Paolini et al. (2018) Positive end expiratory pressure in acute hypoxemic respiratory failure due to community acquired pneumonia: do we need a personalized approach?. PeerJ 6:e4211 https://doi.org/10.7717/peerj.4211
date submitted: 2017-11-02
date accepted: 2017-12-09
issued: 2018-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paolini
  given name: Valentina
author list: Agent
  family name: Faverio
  given name: Paola
author list: Agent
  family name: Aliberti
  given name: Stefano
author list: Agent
  family name: Messinesi
  given name: Grazia
author list: Agent
  family name: Foti
  given name: Giuseppe
author list: Agent
  family name: Sibila
  given name: Oriol
author list: Agent
  family name: Monzani
  given name: Anna
author list: Agent
  family name: De Giacomi
  given name: Federica
author list: Agent
  family name: Stainer
  given name: Anna
author list: Agent
  family name: Pesci
  given name: Alberto
doi: 10.7717/peerj.4211
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-30
copyright: ©2018 Paolini et al.
attribution name: Paolini et al.

Comparative proteomics reveals that YK51, a 4-Hydroxypandurantin-A analogue, downregulates the expression of proteins associated with dengue virus infection
type: item
type: AcademicArticle
description: Dengue is endemic throughout tropical and subtropical regions of the world. Currently, there is no clinically approved therapeutic drug available for this acute viral infection. Although the first dengue vaccine Dengvaxia has been approved for use in certain countries, it is limited to those without a previous dengue infection while the safety and efficacy of the vaccine in those elderly and younger children still need to be identified. Therefore, it is becoming increasingly important to develop therapeutics/drugs to combat dengue virus (DENV) infection. YK51 is a synthetic analogue of 4-Hydroxypandurantin A (a compound found in the crude extract of the rhizomes of Boesenbergia rotunda) that has been extensively studied by our research group. It has been shown to possess outstanding antiviral activity due to its inhibitory activity against NS2B/NS3 DENV2 protease. However, it is not known how YK51 affects the proteome of DENV infected cells. Therefore, we performed a comparative proteomics analysis to identify changes in protein expression in DENV infected HepG2 cells treated with YK51. Classical two-dimensional gel electrophoresis followed by protein identification using tandem mass spectrometry was employed in this study. Thirty proteins were found to be down-regulated with YK51 treatment. In silico analysis predicted that the down-regulation of eight of these proteins may inhibit viral infection. Our results suggested that apart from inhibiting the NS2B/NS3 DENV2 protease, YK51 may also be causing the down-regulation of a number of proteins that may be responsible in, and/or essential to virus infection. However, functional characterization of these proteins will be necessary before we can conclusively determine their roles in DENV infection.
format: application/pdf
format: text/html
creator: Wei-Lian Tan
creator: Yean Kee Lee
creator: Yen Fong Ho
creator: Rohana Yusof
creator: Noorsaadah Abdul Rahman
creator: Saiful Anuar Karsani
subject: Molecular Biology
subject: Evidence Based Medicine
subject: Infectious Diseases
description: doi:10.7717/peerj.3939
publisher: PeerJ Inc.
rights: © 2018 Tan et al.
abstract: Dengue is endemic throughout tropical and subtropical regions of the world. Currently, there is no clinically approved therapeutic drug available for this acute viral infection. Although the first dengue vaccine Dengvaxia has been approved for use in certain countries, it is limited to those without a previous dengue infection while the safety and efficacy of the vaccine in those elderly and younger children still need to be identified. Therefore, it is becoming increasingly important to develop therapeutics/drugs to combat dengue virus (DENV) infection. YK51 is a synthetic analogue of 4-Hydroxypandurantin A (a compound found in the crude extract of the rhizomes of Boesenbergia rotunda) that has been extensively studied by our research group. It has been shown to possess outstanding antiviral activity due to its inhibitory activity against NS2B/NS3 DENV2 protease. However, it is not known how YK51 affects the proteome of DENV infected cells. Therefore, we performed a comparative proteomics analysis to identify changes in protein expression in DENV infected HepG2 cells treated with YK51. Classical two-dimensional gel electrophoresis followed by protein identification using tandem mass spectrometry was employed in this study. Thirty proteins were found to be down-regulated with YK51 treatment. In silico analysis predicted that the down-regulation of eight of these proteins may inhibit viral infection. Our results suggested that apart from inhibiting the NS2B/NS3 DENV2 protease, YK51 may also be causing the down-regulation of a number of proteins that may be responsible in, and/or essential to virus infection. However, functional characterization of these proteins will be necessary before we can conclusively determine their roles in DENV infection.
bibliographic citation: Tan et al. (2018) Comparative proteomics reveals that YK51, a 4-Hydroxypandurantin-A analogue, downregulates the expression of proteins associated with dengue virus infection. PeerJ 5:e3939 https://doi.org/10.7717/peerj.3939
date submitted: 2017-06-13
date accepted: 2017-09-25
issued: 2018-01-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Wei-Lian
author list: Agent
  family name: Lee
  given name: Yean Kee
author list: Agent
  family name: Ho
  given name: Yen Fong
author list: Agent
  family name: Yusof
  given name: Rohana
author list: Agent
  family name: Abdul Rahman
  given name: Noorsaadah
author list: Agent
  family name: Karsani
  given name: Saiful Anuar
doi: 10.7717/peerj.3939
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-30
copyright: ©2018 Tan et al.
attribution name: Tan et al.

Incidence of and social-demographic and obstetric factors associated with postpartum depression: differences among ethnic Han and Kazak women of Northwestern China
type: item
type: AcademicArticle
description: Background Studies on postpartum depression (PPD) in China have focused primarily on women of Han ethnicity, whereas work on other ethnic groups has proven limited. This study explored the ethnic differences of associated social-demographic and obstetric factors for PPD between Han-majority and Kazak-minority women in northwestern China. Methods Han and Kazak women who received routine examinations at four hospitals in a multi-ethnic area of China six weeks after childbirth between March 2016 and December 2016 were included in the study. Data on the women’s socio-demographic characteristics, obstetric factors, and possible depression at six weeks after childbirth were collected. We examined the associated factors of PPD using multivariable logistic regression analyses by ethnic group. Results The overall incidence of PPD was 14.6% (184/1,263) at six weeks after childbirth. PPD was detected more frequently among Kazak (16.1%) than Han women (13.1%). Kazak women exhibited a higher risk of PPD (adjusted OR = 1.561, 95% CI [1.108–2.198], P = 0.011). Urinary incontinence (UI) represented a significant risk factor of PPD for Kazak compared with Han women (OR = 1.720, 95% CI [1.056–2.804], P = 0.003). In contrast, the presence of the mother-in-law as a caregiver after childbirth demonstrated a positive association with PPD among Han (OR = 2.600, 95% CI [1.499–4.512], P = 0.001), but not with Kazak women. Conclusions Kazak women were more likely to develop PPD than Han women, even after controlling for confounders. Moreover, distinct risk factors for PPD existed for Han and Kazak women. Future research that explores the relationships between Han women and their mothers-in-law as well as Kazak women’s attitudes toward UI could help us further understand PPD in these populations.
format: application/pdf
format: text/html
creator: Ling Chen
creator: Li Ding
creator: Ming Qi
creator: Chao Jiang
creator: Xin-Min Mao
creator: Wen-Zhi Cai
subject: Gynecology and Obstetrics
subject: Nursing
subject: Psychiatry and Psychology
subject: Women’s Health
description: doi:10.7717/peerj.4335
publisher: PeerJ Inc.
rights: © 2018 Chen et al.
abstract: Background Studies on postpartum depression (PPD) in China have focused primarily on women of Han ethnicity, whereas work on other ethnic groups has proven limited. This study explored the ethnic differences of associated social-demographic and obstetric factors for PPD between Han-majority and Kazak-minority women in northwestern China. Methods Han and Kazak women who received routine examinations at four hospitals in a multi-ethnic area of China six weeks after childbirth between March 2016 and December 2016 were included in the study. Data on the women’s socio-demographic characteristics, obstetric factors, and possible depression at six weeks after childbirth were collected. We examined the associated factors of PPD using multivariable logistic regression analyses by ethnic group. Results The overall incidence of PPD was 14.6% (184/1,263) at six weeks after childbirth. PPD was detected more frequently among Kazak (16.1%) than Han women (13.1%). Kazak women exhibited a higher risk of PPD (adjusted OR = 1.561, 95% CI [1.108–2.198], P = 0.011). Urinary incontinence (UI) represented a significant risk factor of PPD for Kazak compared with Han women (OR = 1.720, 95% CI [1.056–2.804], P = 0.003). In contrast, the presence of the mother-in-law as a caregiver after childbirth demonstrated a positive association with PPD among Han (OR = 2.600, 95% CI [1.499–4.512], P = 0.001), but not with Kazak women. Conclusions Kazak women were more likely to develop PPD than Han women, even after controlling for confounders. Moreover, distinct risk factors for PPD existed for Han and Kazak women. Future research that explores the relationships between Han women and their mothers-in-law as well as Kazak women’s attitudes toward UI could help us further understand PPD in these populations.
bibliographic citation: Chen et al. (2018) Incidence of and social-demographic and obstetric factors associated with postpartum depression: differences among ethnic Han and Kazak women of Northwestern China. PeerJ 6:e4335 https://doi.org/10.7717/peerj.4335
date submitted: 2017-10-24
date accepted: 2018-01-17
issued: 2018-01-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ling
author list: Agent
  family name: Ding
  given name: Li
author list: Agent
  family name: Qi
  given name: Ming
author list: Agent
  family name: Jiang
  given name: Chao
author list: Agent
  family name: Mao
  given name: Xin-Min
author list: Agent
  family name: Cai
  given name: Wen-Zhi
doi: 10.7717/peerj.4335
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-29
copyright: ©2018 Chen et al.
attribution name: Chen et al.

Evaluating outcomes of young forest management on a target species of conservation concern
type: item
type: AcademicArticle
description: Background Assessing outcomes of habitat management is critical for informing and adapting conservation plans. From 2013–2019, a multi-stage management initiative aims to create >26,000 ha of shrubland and early-successional vegetation to benefit Golden-winged Warblers (Vermivora chrysoptera) in managed forested landscapes of the western Great Lakes region. We studied a dense breeding population of Golden-winged Warblers at Rice Lake National Wildlife Refuge (NWR) in Minnesota, USA, where shrubs and young trees were sheared during the winter of 2014–2015 in a single treatment supported in part by the American Bird Conservancy (ABC) and in part by other funding source(s) to benefit Golden-winged Warblers and other species associated with young forest [e.g., American Woodcock (Scalopax minor)] and as part of maintenance of early successional forest cover on the refuge. Methods We monitored abundance of Golden-winged Warblers before (2013–2014) and after (2015–2016) management at the treatment site and a control site, and we estimated full-season productivity (i.e., young recruited into the fall population) on the treatment site from predictive, spatially explicit models, informed by nest and fledgling survival data collected at sites in the western Great Lakes region, including Rice Lake NWR, during 2011 and 2012. Then, using biologically informed models of Golden-winged Warbler response to observed and predicted vegetation succession, we estimated the cumulative change in population recruitment over various scenarios of vegetation succession and demographic response. Results We observed a 32% decline in abundance of Golden-winged Warbler breeding pairs on the treatment site and estimated a 27% decline in per-pair full-season productivity following management, compared to no change in a nearby control site. In models that ranged from highly optimistic to progressively more realistic scenarios, we estimated a net loss of 72–460 juvenile Golden-winged Warblers produced …
format: application/pdf
format: text/html
creator: Henry M. Streby
creator: Gunnar R. Kramer
creator: Sean M. Peterson
creator: David E. Andersen
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.4319
publisher: PeerJ Inc.
rights: © 2018
abstract: Background Assessing outcomes of habitat management is critical for informing and adapting conservation plans. From 2013–2019, a multi-stage management initiative aims to create >26,000 ha of shrubland and early-successional vegetation to benefit Golden-winged Warblers (Vermivora chrysoptera) in managed forested landscapes of the western Great Lakes region. We studied a dense breeding population of Golden-winged Warblers at Rice Lake National Wildlife Refuge (NWR) in Minnesota, USA, where shrubs and young trees were sheared during the winter of 2014–2015 in a single treatment supported in part by the American Bird Conservancy (ABC) and in part by other funding source(s) to benefit Golden-winged Warblers and other species associated with young forest [e.g., American Woodcock (Scalopax minor)] and as part of maintenance of early successional forest cover on the refuge. Methods We monitored abundance of Golden-winged Warblers before (2013–2014) and after (2015–2016) management at the treatment site and a control site, and we estimated full-season productivity (i.e., young recruited into the fall population) on the treatment site from predictive, spatially explicit models, informed by nest and fledgling survival data collected at sites in the western Great Lakes region, including Rice Lake NWR, during 2011 and 2012. Then, using biologically informed models of Golden-winged Warbler response to observed and predicted vegetation succession, we estimated the cumulative change in population recruitment over various scenarios of vegetation succession and demographic response. Results We observed a 32% decline in abundance of Golden-winged Warbler breeding pairs on the treatment site and estimated a 27% decline in per-pair full-season productivity following management, compared to no change in a nearby control site. In models that ranged from highly optimistic to progressively more realistic scenarios, we estimated a net loss of 72–460 juvenile Golden-winged Warblers produced …
bibliographic citation: Streby et al. (2018) Evaluating outcomes of young forest management on a target species of conservation concern. PeerJ 6:e4319 https://doi.org/10.7717/peerj.4319
date submitted: 2017-12-01
date accepted: 2018-01-12
issued: 2018-01-29
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Streby
  given name: Henry M.
author list: Agent
  family name: Kramer
  given name: Gunnar R.
author list: Agent
  family name: Peterson
  given name: Sean M.
author list: Agent
  family name: Andersen
  given name: David E.
doi: 10.7717/peerj.4319
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-29

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