PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing
items: Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing
items: Ultrasound-promoted synthesis of 2-organoselanyl-naphthalenes using Oxone® in aqueous medium as an oxidizing agent
items: Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
items: Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities
items: The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia
items: Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis
items: EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation
items: Temporally-aware algorithms for the classification of anuran sounds
items: The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps

A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing
type: item
type: AcademicArticle
description: Background Antibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor. Methods Self-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes. Results Of the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165). Discussion This study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic…
format: application/pdf
format: text/html
creator: Fatima Sinkala
creator: Richard Parsons
creator: Bruce Sunderland
creator: Kreshnik Hoti
creator: Petra Czarniak
subject: Health Policy
subject: Translational Medicine
description: doi:10.7717/peerj.4726
publisher: PeerJ Inc.
rights: © 2018 Sinkala et al.
abstract: Background Antibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor. Methods Self-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes. Results Of the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165). Discussion This study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic…
bibliographic citation: Sinkala et al. (2018) A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing. PeerJ 6:e4726 https://doi.org/10.7717/peerj.4726
date submitted: 2017-11-15
date accepted: 2018-04-17
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sinkala
  given name: Fatima
author list: Agent
  family name: Parsons
  given name: Richard
author list: Agent
  family name: Sunderland
  given name: Bruce
author list: Agent
  family name: Hoti
  given name: Kreshnik
author list: Agent
  family name: Czarniak
  given name: Petra
doi: 10.7717/peerj.4726
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: ©2018 Sinkala et al.
attribution name: Sinkala et al.

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing
type: item
type: AcademicArticle
description: Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In additio…
format: application/pdf
format: text/html
creator: Francisca Zepeda-Paulo
creator: Sebastían Ortiz-Martínez
creator: Andrea X. Silva
creator: Blas Lavandero
subject: Ecology
subject: Entomology
subject: Genomics
description: doi:10.7717/peerj.4725
publisher: PeerJ Inc.
rights: © 2018 Zepeda-Paulo et al.
abstract: Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In additio…
bibliographic citation: Zepeda-Paulo et al. (2018) Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing. PeerJ 6:e4725 https://doi.org/10.7717/peerj.4725
date submitted: 2018-01-11
date accepted: 2018-04-16
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zepeda-Paulo
  given name: Francisca
author list: Agent
  family name: Ortiz-Martínez
  given name: Sebastían
author list: Agent
  family name: Silva
  given name: Andrea X.
author list: Agent
  family name: Lavandero
  given name: Blas
doi: 10.7717/peerj.4725
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: ©2018 Zepeda-Paulo et al.
attribution name: Zepeda-Paulo et al.

Ultrasound-promoted synthesis of 2-organoselanyl-naphthalenes using Oxone® in aqueous medium as an oxidizing agent
type: item
type: AcademicArticle
description: A green methodology to synthesize 2-organoselanyl-naphthalenes based on the reaction of alkynols with diaryl diselenides is described. The electrophilic species of selenium were generated in situ, by the oxidative cleavage of the Se–Se bond of diaryl diselenides by Oxone® using water as the solvent. The reactions proceeded efficiently under ultrasonic irradiation as an alternative energy source, using a range of alkynols and diorganyl diselenides as starting materials. Through this methodology, the corresponding 2-organoselanyl-naphthalenes were obtained in moderate to good yields (56–94%) and in short reaction times (0.25–2.3 h).
format: application/pdf
format: text/html
creator: Gelson Perin
creator: Daniela Rodrigues Araujo
creator: Patrick Carvalho Nobre
creator: Eder João Lenardao
creator: Raquel Guimarães Jacob
creator: Marcio Santos Silva
creator: Juliano Alex Roehrs
subject: Natural Resource Management
subject: Food, Water and Energy Nexus
subject: Green Chemistry
description: doi:10.7717/peerj.4706
publisher: PeerJ Inc.
rights: © 2018 Perin et al.
abstract: A green methodology to synthesize 2-organoselanyl-naphthalenes based on the reaction of alkynols with diaryl diselenides is described. The electrophilic species of selenium were generated in situ, by the oxidative cleavage of the Se–Se bond of diaryl diselenides by Oxone® using water as the solvent. The reactions proceeded efficiently under ultrasonic irradiation as an alternative energy source, using a range of alkynols and diorganyl diselenides as starting materials. Through this methodology, the corresponding 2-organoselanyl-naphthalenes were obtained in moderate to good yields (56–94%) and in short reaction times (0.25–2.3 h).
bibliographic citation: Perin et al. (2018) Ultrasound-promoted synthesis of 2-organoselanyl-naphthalenes using Oxone® in aqueous medium as an oxidizing agent. PeerJ 6:e4706 https://doi.org/10.7717/peerj.4706
date submitted: 2018-03-22
date accepted: 2018-04-15
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Perin
  given name: Gelson
author list: Agent
  family name: Araujo
  given name: Daniela Rodrigues
author list: Agent
  family name: Nobre
  given name: Patrick Carvalho
author list: Agent
  family name: Lenardao
  given name: Eder João
author list: Agent
  family name: Jacob
  given name: Raquel Guimarães
author list: Agent
  family name: Silva
  given name: Marcio Santos
author list: Agent
  family name: Roehrs
  given name: Juliano Alex
doi: 10.7717/peerj.4706
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: © 2018 Perin et al.
attribution name: Perin et al.

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
type: item
type: AcademicArticle
description: Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
format: application/pdf
format: text/html
creator: Angela McCann
creator: Feargal J. Ryan
creator: Stephen R. Stockdale
creator: Marion Dalmasso
creator: Tony Blake
creator: C. Anthony Ryan
creator: Catherine Stanton
creator: Susan Mills
creator: Paul R. Ross
creator: Colin Hill
subject: Microbiology
subject: Virology
subject: Pediatrics
description: doi:10.7717/peerj.4694
publisher: PeerJ Inc.
rights: © 2018 McCann et al.
abstract: Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
bibliographic citation: McCann et al. (2018) Viromes of one year old infants reveal the impact of birth mode on microbiome diversity. PeerJ 6:e4694 https://doi.org/10.7717/peerj.4694
date submitted: 2018-01-23
date accepted: 2018-04-11
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McCann
  given name: Angela
author list: Agent
  family name: Ryan
  given name: Feargal J.
author list: Agent
  family name: Stockdale
  given name: Stephen R.
author list: Agent
  family name: Dalmasso
  given name: Marion
author list: Agent
  family name: Blake
  given name: Tony
author list: Agent
  family name: Ryan
  given name: C. Anthony
author list: Agent
  family name: Stanton
  given name: Catherine
author list: Agent
  family name: Mills
  given name: Susan
author list: Agent
  family name: Ross
  given name: Paul R.
author list: Agent
  family name: Hill
  given name: Colin
doi: 10.7717/peerj.4694
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: ©2018 McCann et al.
attribution name: McCann et al.

Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities
type: item
type: AcademicArticle
description: Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment c…
format: application/pdf
format: text/html
creator: Hauke F. Kegler
creator: Christiane Hassenrück
creator: Pia Kegler
creator: Tim C. Jennerjahn
creator: Muhammad Lukman
creator: Jamaluddin Jompa
creator: Astrid Gärdes
subject: Biodiversity
subject: Marine Biology
subject: Microbiology
subject: Environmental Impacts
description: doi:10.7717/peerj.4555
publisher: PeerJ Inc.
rights: © 2018 Kegler et al.
abstract: Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment c…
bibliographic citation: Kegler et al. (2018) Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities. PeerJ 6:e4555 https://doi.org/10.7717/peerj.4555
date submitted: 2017-12-14
date accepted: 2018-03-09
issued: 2018-05-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kegler
  given name: Hauke F.
author list: Agent
  family name: Hassenrück
  given name: Christiane
author list: Agent
  family name: Kegler
  given name: Pia
author list: Agent
  family name: Jennerjahn
  given name: Tim C.
author list: Agent
  family name: Lukman
  given name: Muhammad
author list: Agent
  family name: Jompa
  given name: Jamaluddin
author list: Agent
  family name: Gärdes
  given name: Astrid
doi: 10.7717/peerj.4555
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-07
copyright: © 2018 Kegler et al.
attribution name: Kegler et al.

The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia
type: item
type: AcademicArticle
description: Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.
format: application/pdf
format: text/html
creator: Marion Herisse
creator: Jessica L. Porter
creator: Romain Guerillot
creator: Takehiro Tomita
creator: Anders Goncalves Da Silva
creator: Torsten Seemann
creator: Benjamin P. Howden
creator: Timothy P. Stinear
creator: Sacha J. Pidot
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.4784
publisher: PeerJ Inc.
rights: © 2018 Herisse et al.
abstract: Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.
bibliographic citation: Herisse et al. (2018) The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia. PeerJ 6:e4784 https://doi.org/10.7717/peerj.4784
date submitted: 2018-02-23
date accepted: 2018-04-27
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Herisse
  given name: Marion
author list: Agent
  family name: Porter
  given name: Jessica L.
author list: Agent
  family name: Guerillot
  given name: Romain
author list: Agent
  family name: Tomita
  given name: Takehiro
author list: Agent
  family name: Goncalves Da Silva
  given name: Anders
author list: Agent
  family name: Seemann
  given name: Torsten
author list: Agent
  family name: Howden
  given name: Benjamin P.
author list: Agent
  family name: Stinear
  given name: Timothy P.
author list: Agent
  family name: Pidot
  given name: Sacha J.
doi: 10.7717/peerj.4784
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Herisse et al.
attribution name: Herisse et al.

Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis
type: item
type: AcademicArticle
description: Many infectious diseases disproportionately affect people in the developing world. Cryptococcal meningitis is one of the most common mycoses in HIV-AIDS patients, with the highest burden of disease in sub-Saharan Africa. Current best treatment regimens still result in unacceptably high mortality rates, and more effective antifungal agents are needed urgently. Drug development is hampered by the difficulty of developing effective antifungal agents that are not also toxic to human cells, and by a reluctance among pharmaceutical companies to invest in drugs that cannot guarantee a high financial return. Drug repurposing, where existing drugs are screened for alternative activities, is becoming an attractive approach in antimicrobial discovery programs, and various compound libraries are now commercially available. As these drugs have already undergone extensive optimisation and passed regulatory hurdles this can fast-track their progress to market for new uses. This study screened the Screen-Well Enzo library of 640 compounds for candidates that phenotypically inhibited the growth of Cryptococcus deuterogattii. The anthelminthic agent flubendazole, and L-type calcium channel blockers nifedipine, nisoldipine and felodipine, appeared particularly promising and were tested in additional strains and species. Flubendazole was very active against all pathogenic Cryptococcus species, with minimum inhibitory concentrations of 0.039–0.156 μg/mL, and was equally effective against isolates that were resistant to fluconazole. While nifedipine, nisoldipine and felodipine all inhibited Cryptococcus, nisoldipine was also effective against Candida, Saccharomyces and Aspergillus. This study validates repurposing as a rapid approach for finding new agents to treat neglected infectious diseases.
format: application/pdf
format: text/html
creator: Megan Truong
creator: Leigh G. Monahan
creator: Dee A. Carter
creator: Ian G. Charles
subject: Microbiology
subject: Mycology
subject: Drugs and Devices
subject: Infectious Diseases
description: doi:10.7717/peerj.4761
publisher: PeerJ Inc.
rights: © 2018 Truong et al.
abstract: Many infectious diseases disproportionately affect people in the developing world. Cryptococcal meningitis is one of the most common mycoses in HIV-AIDS patients, with the highest burden of disease in sub-Saharan Africa. Current best treatment regimens still result in unacceptably high mortality rates, and more effective antifungal agents are needed urgently. Drug development is hampered by the difficulty of developing effective antifungal agents that are not also toxic to human cells, and by a reluctance among pharmaceutical companies to invest in drugs that cannot guarantee a high financial return. Drug repurposing, where existing drugs are screened for alternative activities, is becoming an attractive approach in antimicrobial discovery programs, and various compound libraries are now commercially available. As these drugs have already undergone extensive optimisation and passed regulatory hurdles this can fast-track their progress to market for new uses. This study screened the Screen-Well Enzo library of 640 compounds for candidates that phenotypically inhibited the growth of Cryptococcus deuterogattii. The anthelminthic agent flubendazole, and L-type calcium channel blockers nifedipine, nisoldipine and felodipine, appeared particularly promising and were tested in additional strains and species. Flubendazole was very active against all pathogenic Cryptococcus species, with minimum inhibitory concentrations of 0.039–0.156 μg/mL, and was equally effective against isolates that were resistant to fluconazole. While nifedipine, nisoldipine and felodipine all inhibited Cryptococcus, nisoldipine was also effective against Candida, Saccharomyces and Aspergillus. This study validates repurposing as a rapid approach for finding new agents to treat neglected infectious diseases.
bibliographic citation: Truong et al. (2018) Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis. PeerJ 6:e4761 https://doi.org/10.7717/peerj.4761
date submitted: 2018-03-20
date accepted: 2018-04-21
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Truong
  given name: Megan
author list: Agent
  family name: Monahan
  given name: Leigh G.
author list: Agent
  family name: Carter
  given name: Dee A.
author list: Agent
  family name: Charles
  given name: Ian G.
doi: 10.7717/peerj.4761
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Truong et al.
attribution name: Truong et al.

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation
type: item
type: AcademicArticle
description: During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The two-layer architecture was investigated on a large dataset of 63,558 enzymes from the PDB and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.
format: application/pdf
format: text/html
creator: Afshine Amidi
creator: Shervine Amidi
creator: Dimitrios Vlachakis
creator: Vasileios Megalooikonomou
creator: Nikos Paragios
creator: Evangelia I. Zacharaki
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.4750
publisher: PeerJ Inc.
rights: © 2018 Amidi et al.
abstract: During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The two-layer architecture was investigated on a large dataset of 63,558 enzymes from the PDB and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet.
bibliographic citation: Amidi et al. (2018) EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation. PeerJ 6:e4750 https://doi.org/10.7717/peerj.4750
date submitted: 2017-07-25
date accepted: 2018-04-21
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amidi
  given name: Afshine
author list: Agent
  family name: Amidi
  given name: Shervine
author list: Agent
  family name: Vlachakis
  given name: Dimitrios
author list: Agent
  family name: Megalooikonomou
  given name: Vasileios
author list: Agent
  family name: Paragios
  given name: Nikos
author list: Agent
  family name: Zacharaki
  given name: Evangelia I.
doi: 10.7717/peerj.4750
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Amidi et al.
attribution name: Amidi et al.

Temporally-aware algorithms for the classification of anuran sounds
type: item
type: AcademicArticle
description: Several authors have shown that the sounds of anurans can be used as an indicator of climate change. Hence, the recording, storage and further processing of a huge number of anuran sounds, distributed over time and space, are required in order to obtain this indicator. Furthermore, it is desirable to have algorithms and tools for the automatic classification of the different classes of sounds. In this paper, six classification methods are proposed, all based on the data-mining domain, which strive to take advantage of the temporal character of the sounds. The definition and comparison of these classification methods is undertaken using several approaches. The main conclusions of this paper are that: (i) the sliding window method attained the best results in the experiments presented, and even outperformed the hidden Markov models usually employed in similar applications; (ii) noteworthy overall classification performance has been obtained, which is an especially striking result considering that the sounds analysed were affected by a highly noisy background; (iii) the instance selection for the determination of the sounds in the training dataset offers better results than cross-validation techniques; and (iv) the temporally-aware classifiers have revealed that they can obtain better performance than their non-temporally-aware counterparts.
format: application/pdf
format: text/html
creator: Amalia Luque
creator: Javier Romero-Lemos
creator: Alejandro Carrasco
creator: Luis Gonzalez-Abril
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
subject: Climate Change Biology
description: doi:10.7717/peerj.4732
publisher: PeerJ Inc.
rights: © 2018 Luque et al.
abstract: Several authors have shown that the sounds of anurans can be used as an indicator of climate change. Hence, the recording, storage and further processing of a huge number of anuran sounds, distributed over time and space, are required in order to obtain this indicator. Furthermore, it is desirable to have algorithms and tools for the automatic classification of the different classes of sounds. In this paper, six classification methods are proposed, all based on the data-mining domain, which strive to take advantage of the temporal character of the sounds. The definition and comparison of these classification methods is undertaken using several approaches. The main conclusions of this paper are that: (i) the sliding window method attained the best results in the experiments presented, and even outperformed the hidden Markov models usually employed in similar applications; (ii) noteworthy overall classification performance has been obtained, which is an especially striking result considering that the sounds analysed were affected by a highly noisy background; (iii) the instance selection for the determination of the sounds in the training dataset offers better results than cross-validation techniques; and (iv) the temporally-aware classifiers have revealed that they can obtain better performance than their non-temporally-aware counterparts.
bibliographic citation: Luque et al. (2018) Temporally-aware algorithms for the classification of anuran sounds. PeerJ 6:e4732 https://doi.org/10.7717/peerj.4732
date submitted: 2017-12-19
date accepted: 2018-04-18
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luque
  given name: Amalia
author list: Agent
  family name: Romero-Lemos
  given name: Javier
author list: Agent
  family name: Carrasco
  given name: Alejandro
author list: Agent
  family name: Gonzalez-Abril
  given name: Luis
doi: 10.7717/peerj.4732
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Luque et al.
attribution name: Luque et al.

The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps
type: item
type: AcademicArticle
description: Ecological traps attract biota to low-quality habitats. Landscape traps are zones caught in a vortex of spiralling degradation. Here, we demonstrate how short-range endemic (SRE) traits may make such taxa vulnerable to ecological and landscape traps. Three SRE species of mygalomorph spider were used in this study: Idiommata blackwalli, Idiosoma sigillatum and an undescribed Aganippe sp. Mygalomorphs can be long-lived (>43 years) and select sites for permanent burrows in their early dispersal phase. Spiderlings from two species, I. blackwalli (n = 20) and Aganippe sp. (n = 50), demonstrated choice for microhabitats under experimental conditions, that correspond to where adults typically occur in situ. An invasive veldt grass microhabitat was selected almost exclusively by spiderlings of I. sigillatum. At present, habitat dominated by veldt grass in Perth, Western Australia, has lower prey diversity and abundance than undisturbed habitats and therefore may act as an ecological trap for this species. Furthermore, as a homogenising force, veldt grass can spread to form a landscape trap in naturally heterogeneous ecosystems. Selection of specialised microhabitats of SREs may explain high extinction rates in old, stable landscapes undergoing (human-induced) rapid change.
format: application/pdf
format: text/html
creator: Leanda D. Mason
creator: Philip W. Bateman
creator: Grant W. Wardell-Johnson
subject: Animal Behaviour
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.4715
publisher: PeerJ Inc.
rights: © 2018 Mason et al.
abstract: Ecological traps attract biota to low-quality habitats. Landscape traps are zones caught in a vortex of spiralling degradation. Here, we demonstrate how short-range endemic (SRE) traits may make such taxa vulnerable to ecological and landscape traps. Three SRE species of mygalomorph spider were used in this study: Idiommata blackwalli, Idiosoma sigillatum and an undescribed Aganippe sp. Mygalomorphs can be long-lived (>43 years) and select sites for permanent burrows in their early dispersal phase. Spiderlings from two species, I. blackwalli (n = 20) and Aganippe sp. (n = 50), demonstrated choice for microhabitats under experimental conditions, that correspond to where adults typically occur in situ. An invasive veldt grass microhabitat was selected almost exclusively by spiderlings of I. sigillatum. At present, habitat dominated by veldt grass in Perth, Western Australia, has lower prey diversity and abundance than undisturbed habitats and therefore may act as an ecological trap for this species. Furthermore, as a homogenising force, veldt grass can spread to form a landscape trap in naturally heterogeneous ecosystems. Selection of specialised microhabitats of SREs may explain high extinction rates in old, stable landscapes undergoing (human-induced) rapid change.
bibliographic citation: Mason et al. (2018) The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps. PeerJ 6:e4715 https://doi.org/10.7717/peerj.4715
date submitted: 2018-02-09
date accepted: 2018-04-16
issued: 2018-05-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mason
  given name: Leanda D.
author list: Agent
  family name: Bateman
  given name: Philip W.
author list: Agent
  family name: Wardell-Johnson
  given name: Grant W.
doi: 10.7717/peerj.4715
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-04
copyright: © 2018 Mason et al.
attribution name: Mason et al.

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