PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Self-rated mental health and race/ethnicity in the United States: support for the epidemiological paradox
items: Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
items: Harvesting and chewing as constraints to forage consumption by the African savanna elephant (Loxodonta africana)
items: Evolutionary morphology of the rabbit skull
items: In vitro and in vivo comparison of transport media for detecting nasopharyngeal carriage of Streptococcus pneumoniae
items: Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)
items: Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid
items: A genetic programming approach to oral cancer prognosis
items: Evaluation of the effectiveness of insecticide trunk injections for control of Latoia lepida (Cramer) in the sweet olive tree Osmanthus fragrans
items: Successful population establishment from small introductions appears to be less common than believed

Self-rated mental health and race/ethnicity in the United States: support for the epidemiological paradox
type: item
type: AcademicArticle
description: This paper evaluates racial/ethnic differences in self-rated mental health for adults in the United States, while controlling for demographic and socioeconomic characteristics as well as length of stay in the country. Using data from the 2010 National Health Interview Survey Cancer Control Supplement (NHIS-CCS), binomial logistic regression models are fit to estimate the association between race/ethnicity and poor/fair self-reported mental health among US Adults. The size of the analytical sample was 22,844 persons. Overall prevalence of poor/fair self-rated mental health was 7.72%, with lower prevalence among Hispanics (6.93%). Non-Hispanic blacks had the highest prevalence (10.38%). After controls for socioeconomic characteristics are incorporated in the models, Hispanics were found to have a lower probability of reporting poor/fair self-rated mental health in comparison to non-Hispanic whites (OR = 0.70; 95% CI [0.55–0.90]). No difference was found for other minority groups when compared to the reference group in the final model. Contrary to global self-rated health, Hispanics were found to have a lower probability of reporting poor/fair self-rated mental health in comparison to non-Hispanic whites. No difference was found for non-Hispanic blacks when they were compared to non-Hispanic whites. Self-rated mental health is therefore one case of a self-rating of health in which evidence supporting the epidemiological paradox is found among adults in the United States.
format: application/pdf
format: text/html
creator: Alexis R. Santos-Lozada
subject: Epidemiology
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.2508
publisher: PeerJ Inc.
rights: © 2016 Santos-Lozada
abstract: This paper evaluates racial/ethnic differences in self-rated mental health for adults in the United States, while controlling for demographic and socioeconomic characteristics as well as length of stay in the country. Using data from the 2010 National Health Interview Survey Cancer Control Supplement (NHIS-CCS), binomial logistic regression models are fit to estimate the association between race/ethnicity and poor/fair self-reported mental health among US Adults. The size of the analytical sample was 22,844 persons. Overall prevalence of poor/fair self-rated mental health was 7.72%, with lower prevalence among Hispanics (6.93%). Non-Hispanic blacks had the highest prevalence (10.38%). After controls for socioeconomic characteristics are incorporated in the models, Hispanics were found to have a lower probability of reporting poor/fair self-rated mental health in comparison to non-Hispanic whites (OR = 0.70; 95% CI [0.55–0.90]). No difference was found for other minority groups when compared to the reference group in the final model. Contrary to global self-rated health, Hispanics were found to have a lower probability of reporting poor/fair self-rated mental health in comparison to non-Hispanic whites. No difference was found for non-Hispanic blacks when they were compared to non-Hispanic whites. Self-rated mental health is therefore one case of a self-rating of health in which evidence supporting the epidemiological paradox is found among adults in the United States.
bibliographic citation: Santos-Lozada (2016) Self-rated mental health and race/ethnicity in the United States: support for the epidemiological paradox. PeerJ 4:e2508 https://doi.org/10.7717/peerj.2508
date submitted: 2016-06-15
date accepted: 2016-08-26
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos-Lozada
  given name: Alexis R.
doi: 10.7717/peerj.2508
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: ©2016 Santos-Lozada
attribution name: Santos-Lozada

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
type: item
type: AcademicArticle
description: High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
format: application/pdf
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creator: Christian Rinke
creator: Serene Low
creator: Ben J. Woodcroft
creator: Jean-Baptiste Raina
creator: Adam Skarshewski
creator: Xuyen H. Le
creator: Margaret K. Butler
creator: Roman Stocker
creator: Justin Seymour
creator: Gene W. Tyson
creator: Philip Hugenholtz
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.2486
publisher: PeerJ Inc.
rights: © 2016 Rinke et al.
abstract: High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.
bibliographic citation: Rinke et al. (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ 4:e2486 https://doi.org/10.7717/peerj.2486
date submitted: 2016-06-14
date accepted: 2016-08-24
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rinke
  given name: Christian
author list: Agent
  family name: Low
  given name: Serene
author list: Agent
  family name: Woodcroft
  given name: Ben J.
author list: Agent
  family name: Raina
  given name: Jean-Baptiste
author list: Agent
  family name: Skarshewski
  given name: Adam
author list: Agent
  family name: Le
  given name: Xuyen H.
author list: Agent
  family name: Butler
  given name: Margaret K.
author list: Agent
  family name: Stocker
  given name: Roman
author list: Agent
  family name: Seymour
  given name: Justin
author list: Agent
  family name: Tyson
  given name: Gene W.
author list: Agent
  family name: Hugenholtz
  given name: Philip
doi: 10.7717/peerj.2486
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: © 2016 Rinke et al.
attribution name: Rinke et al.

Harvesting and chewing as constraints to forage consumption by the African savanna elephant (Loxodonta africana)
type: item
type: AcademicArticle
description: As a foundation for understanding the diet of African savanna elephants (Loxodonta africana), adult bulls and cows were observed over an annual cycle to determine whether harvesting (Pt), chewing (Ct) and handling times (Ht) differed across food types and harvesting methods (handling time is defined as the time to harvest, chew and swallow a trunkload of food). Bulls and cows were observed 105 and 26 times, respectively (94 and 26 individuals), with a total of 64 h of feeding recorded across 32 vegetation types. Some food types took longer to harvest and chew than others, which may influence intake rate and affect choice of diet. The method used to gather a trunkload of food had a significant effect on harvesting time, with simple foraging actions being comparatively rapid and more difficult tasks taking longer. Handling time was constrained by chewing for bulls, except for the processing of roots from woody plants, which was limited by harvesting. Time to gather a trunkload had a greater influence on handling time for cows compared to bulls. Harvesting and handling times were longer for bulls than cows, with the sexes adopting foraging behaviors that best suited their energy requirements.
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format: text/html
creator: Bruce W. Clegg
creator: Timothy G. O’Connor
subject: Animal Behavior
subject: Conservation Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.2469
publisher: PeerJ Inc.
rights: © 2016 Clegg and O’Connor
abstract: As a foundation for understanding the diet of African savanna elephants (Loxodonta africana), adult bulls and cows were observed over an annual cycle to determine whether harvesting (Pt), chewing (Ct) and handling times (Ht) differed across food types and harvesting methods (handling time is defined as the time to harvest, chew and swallow a trunkload of food). Bulls and cows were observed 105 and 26 times, respectively (94 and 26 individuals), with a total of 64 h of feeding recorded across 32 vegetation types. Some food types took longer to harvest and chew than others, which may influence intake rate and affect choice of diet. The method used to gather a trunkload of food had a significant effect on harvesting time, with simple foraging actions being comparatively rapid and more difficult tasks taking longer. Handling time was constrained by chewing for bulls, except for the processing of roots from woody plants, which was limited by harvesting. Time to gather a trunkload had a greater influence on handling time for cows compared to bulls. Harvesting and handling times were longer for bulls than cows, with the sexes adopting foraging behaviors that best suited their energy requirements.
bibliographic citation: Clegg et al. (2016) Harvesting and chewing as constraints to forage consumption by the African savanna elephant (Loxodonta africana). PeerJ 4:e2469 https://doi.org/10.7717/peerj.2469
date submitted: 2016-06-20
date accepted: 2016-08-19
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clegg
  given name: Bruce W.
author list: Agent
  family name: O’Connor
  given name: Timothy G.
doi: 10.7717/peerj.2469
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: © 2016 Clegg and O’Connor
attribution name: Clegg and O’Connor

Evolutionary morphology of the rabbit skull
type: item
type: AcademicArticle
description: The skull of leporids (rabbits and hares) is highly transformed, typified by pronounced arching of the dorsal skull and ventral flexion of the facial region (i.e., facial tilt). Previous studies show that locomotor behavior influences aspects of cranial shape in leporids, and here we use an extensive 3D geometric morphometrics dataset to further explore what influences leporid cranial diversity. Facial tilt angle, a trait that strongly correlates with locomotor mode, significantly predicts the cranial shape variation captured by the primary axis of cranial shape space, and describes a small proportion (13.2%) of overall cranial shape variation in the clade. However, locomotor mode does not correlate with overall cranial shape variation in the clade, because there are two district morphologies of generalist species, and saltators and cursorial species have similar morphologies. Cranial shape changes due to phyletic size change (evolutionary allometry) also describes a small proportion (12.5%) of cranial shape variation in the clade, but this is largely driven by the smallest living leporid, the pygmy rabbit (Brachylagus idahoensis). By integrating phylogenetic history with our geometric morphometric data, we show that the leporid cranium exhibits weak phylogenetic signal and substantial homoplasy. Though these results make it difficult to reconstruct what the ‘ancestral’ leporid skull looked like, the fossil records suggest that dorsal arching and facial tilt could have occurred before the origin of the crown group. Lastly, our study highlights the diversity of cranial variation in crown leporids, and highlights a need for additional phylogenetic work that includes stem (fossil) leporids and includes morphological data that captures the transformed morphology of rabbits and hares.
format: application/pdf
format: text/html
creator: Brian Kraatz
creator: Emma Sherratt
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.2453
publisher: PeerJ Inc.
rights: © 2016 Kraatz and Sherratt
abstract: The skull of leporids (rabbits and hares) is highly transformed, typified by pronounced arching of the dorsal skull and ventral flexion of the facial region (i.e., facial tilt). Previous studies show that locomotor behavior influences aspects of cranial shape in leporids, and here we use an extensive 3D geometric morphometrics dataset to further explore what influences leporid cranial diversity. Facial tilt angle, a trait that strongly correlates with locomotor mode, significantly predicts the cranial shape variation captured by the primary axis of cranial shape space, and describes a small proportion (13.2%) of overall cranial shape variation in the clade. However, locomotor mode does not correlate with overall cranial shape variation in the clade, because there are two district morphologies of generalist species, and saltators and cursorial species have similar morphologies. Cranial shape changes due to phyletic size change (evolutionary allometry) also describes a small proportion (12.5%) of cranial shape variation in the clade, but this is largely driven by the smallest living leporid, the pygmy rabbit (Brachylagus idahoensis). By integrating phylogenetic history with our geometric morphometric data, we show that the leporid cranium exhibits weak phylogenetic signal and substantial homoplasy. Though these results make it difficult to reconstruct what the ‘ancestral’ leporid skull looked like, the fossil records suggest that dorsal arching and facial tilt could have occurred before the origin of the crown group. Lastly, our study highlights the diversity of cranial variation in crown leporids, and highlights a need for additional phylogenetic work that includes stem (fossil) leporids and includes morphological data that captures the transformed morphology of rabbits and hares.
bibliographic citation: Kraatz et al. (2016) Evolutionary morphology of the rabbit skull. PeerJ 4:e2453 https://doi.org/10.7717/peerj.2453
date submitted: 2015-10-05
date accepted: 2016-08-16
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraatz
  given name: Brian
author list: Agent
  family name: Sherratt
  given name: Emma
doi: 10.7717/peerj.2453
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: ©2016 Kraatz and Sherratt
attribution name: Kraatz and Sherratt

In vitro and in vivo comparison of transport media for detecting nasopharyngeal carriage of Streptococcus pneumoniae
type: item
type: AcademicArticle
description: Background As a standard method for pneumococcal carriage studies, the World Health Organization recommends nasopharyngeal swabs be transported and stored at cool temperatures in a medium containing skim-milk, tryptone, glucose and glycerol (STGG). An enrichment broth used for transport at room temperature in three carriage studies performed in Norway may have a higher sensitivity than STGG. We therefore compared the media in vitro and in vivo. Methods For the in vitro component, three strains (serotype 4, 19F and 3) were suspended in STGG and enrichment broth. Recovery was compared using latex agglutination, quantification of bacterial loads by real-time PCR of the lytA gene, and counting colonies from incubated plates. For the in vivo comparison, paired swabs were obtained from 100 children and transported in STGG at cool temperatures or in enrichment broth at room temperature. Carriage was identified by latex agglutination and confirmed by Quellung reaction. Results In vitro, the cycle threshold values obtained by PCR did not differ between the two media (p = 0.853) and no clear difference in colony counts was apparent after incubation (p = 0.593). In vivo, pneumococci were recovered in 46% of swabs transported in STGG and 51% of those transported in enrichment broth (Kappa statistic 0.90, p = 0.063). Discussion Overall, no statistical differences in sensitivity were found between STGG and enrichment broth. Nevertheless, some serotype differences were observed and STGG appeared slightly less sensitive than enrichment broth for detection of nasopharyngeal carriage of pneumococci by culturing. We recommend the continued use of STGG for transport and storage of nasopharyngeal swabs in pneumococcal carriage studies for the benefit of comparability between studies and settings, including more resource-limited settings.
format: application/pdf
format: text/html
creator: Anneke Steens
creator: Natacha Milhano
creator: Ingeborg S. Aaberge
creator: Didrik F. Vestrheim
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.2449
publisher: PeerJ Inc.
rights: © 2016 Steens et al.
abstract: Background As a standard method for pneumococcal carriage studies, the World Health Organization recommends nasopharyngeal swabs be transported and stored at cool temperatures in a medium containing skim-milk, tryptone, glucose and glycerol (STGG). An enrichment broth used for transport at room temperature in three carriage studies performed in Norway may have a higher sensitivity than STGG. We therefore compared the media in vitro and in vivo. Methods For the in vitro component, three strains (serotype 4, 19F and 3) were suspended in STGG and enrichment broth. Recovery was compared using latex agglutination, quantification of bacterial loads by real-time PCR of the lytA gene, and counting colonies from incubated plates. For the in vivo comparison, paired swabs were obtained from 100 children and transported in STGG at cool temperatures or in enrichment broth at room temperature. Carriage was identified by latex agglutination and confirmed by Quellung reaction. Results In vitro, the cycle threshold values obtained by PCR did not differ between the two media (p = 0.853) and no clear difference in colony counts was apparent after incubation (p = 0.593). In vivo, pneumococci were recovered in 46% of swabs transported in STGG and 51% of those transported in enrichment broth (Kappa statistic 0.90, p = 0.063). Discussion Overall, no statistical differences in sensitivity were found between STGG and enrichment broth. Nevertheless, some serotype differences were observed and STGG appeared slightly less sensitive than enrichment broth for detection of nasopharyngeal carriage of pneumococci by culturing. We recommend the continued use of STGG for transport and storage of nasopharyngeal swabs in pneumococcal carriage studies for the benefit of comparability between studies and settings, including more resource-limited settings.
bibliographic citation: Steens et al. (2016) In vitro and in vivo comparison of transport media for detecting nasopharyngeal carriage of Streptococcus pneumoniae. PeerJ 4:e2449 https://doi.org/10.7717/peerj.2449
date submitted: 2016-06-27
date accepted: 2016-08-15
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Steens
  given name: Anneke
author list: Agent
  family name: Milhano
  given name: Natacha
author list: Agent
  family name: Aaberge
  given name: Ingeborg S.
author list: Agent
  family name: Vestrheim
  given name: Didrik F.
doi: 10.7717/peerj.2449
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: ©2016 Steens et al.
attribution name: Steens et al.

Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)
type: item
type: AcademicArticle
description: The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.
format: application/pdf
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creator: Catherine Jan
creator: Luca Fumagalli
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.2416
publisher: PeerJ Inc.
rights: © 2016 Jan & Fumagalli
abstract: The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.
bibliographic citation: Jan et al. (2016) Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae). PeerJ 4:e2416 https://doi.org/10.7717/peerj.2416
date submitted: 2016-06-17
date accepted: 2016-08-05
issued: 2016-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jan
  given name: Catherine
author list: Agent
  family name: Fumagalli
  given name: Luca
doi: 10.7717/peerj.2416
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-22
copyright: © 2016 Jan & Fumagalli
attribution name: Jan & Fumagalli

Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid
type: item
type: AcademicArticle
description: Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. Methods In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratory Mtb. Results Genome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratory Mtb genomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated with Streptococcus pneumoniae meningitis and Neisseria meningitidis virulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study. Discussion The occurrence of in silico genetic differences in CSF-derived but not respiratory Mtb suggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infe…
format: application/pdf
format: text/html
creator: Seow Hoon Saw
creator: Joon Liang Tan
creator: Xin Yue Chan
creator: Kok Gan Chan
creator: Yun Fong Ngeow
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2484
publisher: PeerJ Inc.
rights: © 2016 Saw et al.
abstract: Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. Methods In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratory Mtb. Results Genome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratory Mtb genomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated with Streptococcus pneumoniae meningitis and Neisseria meningitidis virulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study. Discussion The occurrence of in silico genetic differences in CSF-derived but not respiratory Mtb suggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infe…
bibliographic citation: Saw et al. (2016) Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid. PeerJ 4:e2484 https://doi.org/10.7717/peerj.2484
date submitted: 2015-12-18
date accepted: 2016-08-24
issued: 2016-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saw
  given name: Seow Hoon
author list: Agent
  family name: Tan
  given name: Joon Liang
author list: Agent
  family name: Chan
  given name: Xin Yue
author list: Agent
  family name: Chan
  given name: Kok Gan
author list: Agent
  family name: Ngeow
  given name: Yun Fong
doi: 10.7717/peerj.2484
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-21
copyright: © 2016 Saw et al.
attribution name: Saw et al.

A genetic programming approach to oral cancer prognosis
type: item
type: AcademicArticle
description: Background The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. Method GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. Result The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Discussion Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.
format: application/pdf
format: text/html
creator: Mei Sze Tan
creator: Jing Wei Tan
creator: Siow-Wee Chang
creator: Hwa Jen Yap
creator: Sameem Abdul Kareem
creator: Rosnah Binti Zain
subject: Computational Biology
subject: Oncology
subject: Computational Science
description: doi:10.7717/peerj.2482
publisher: PeerJ Inc.
rights: © 2016 Tan et al.
abstract: Background The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. Method GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. Result The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Discussion Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.
bibliographic citation: Tan et al. (2016) A genetic programming approach to oral cancer prognosis. PeerJ 4:e2482 https://doi.org/10.7717/peerj.2482
date submitted: 2016-06-11
date accepted: 2016-08-24
issued: 2016-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Mei Sze
author list: Agent
  family name: Tan
  given name: Jing Wei
author list: Agent
  family name: Chang
  given name: Siow-Wee
author list: Agent
  family name: Yap
  given name: Hwa Jen
author list: Agent
  family name: Abdul Kareem
  given name: Sameem
author list: Agent
  family name: Zain
  given name: Rosnah Binti
doi: 10.7717/peerj.2482
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-21
copyright: ©2016 Tan et al.
attribution name: Tan et al.

Evaluation of the effectiveness of insecticide trunk injections for control of Latoia lepida (Cramer) in the sweet olive tree Osmanthus fragrans
type: item
type: AcademicArticle
description: The screening of suitable insecticides is a key factor in successfully applying trunk injection technology to ornamental plants. In this study, six chemical pesticides were selected and injected into the trunks of Osmanthus fragrans to control the nettle caterpillar, Latoia lepida (Lepidoptera: Limacodidae), using a no-pressure injection system. The absorption rate of the insecticides, the leaf loss due to insect damage, and the mortality and frass amount of L. lepida larvae were evaluated after 77 and 429 days. The results showed that 4% imidacloprid + carbosulfan and 21% abamectin + imidacloprid + omethoate had the fastest conductivity and were completely absorbed into the trunkswithin14 days; however, the efficiencies of these insecticides in controlling L. lepidawere extremely low. Additionally, the treatment 10% emamectin benzoate + clothianidin and 2.5% emamectin benzoate was almost completely absorbed within 30 days and exhibited a longer duration of insecticide efficiency (>80% mortality) in the upper and lower leaves of the canopy. Treatment with these insecticides also resulted in significantly lower leaf loss and frass amounts. We conclude that emamectin benzoate and emamectin benzoate + clothianidin have a rapid uptake into O. fragrans, and are effective as insecticides over long durations. Hence, they may be a suitable control option for L. lepida in O. fragrans plants.
format: application/pdf
format: text/html
creator: Jun Huang
creator: Juan Zhang
creator: Yan Li
creator: Jun Li
creator: Xiao-Hua Shi
subject: Agricultural Science
subject: Entomology
description: doi:10.7717/peerj.2480
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: The screening of suitable insecticides is a key factor in successfully applying trunk injection technology to ornamental plants. In this study, six chemical pesticides were selected and injected into the trunks of Osmanthus fragrans to control the nettle caterpillar, Latoia lepida (Lepidoptera: Limacodidae), using a no-pressure injection system. The absorption rate of the insecticides, the leaf loss due to insect damage, and the mortality and frass amount of L. lepida larvae were evaluated after 77 and 429 days. The results showed that 4% imidacloprid + carbosulfan and 21% abamectin + imidacloprid + omethoate had the fastest conductivity and were completely absorbed into the trunkswithin14 days; however, the efficiencies of these insecticides in controlling L. lepidawere extremely low. Additionally, the treatment 10% emamectin benzoate + clothianidin and 2.5% emamectin benzoate was almost completely absorbed within 30 days and exhibited a longer duration of insecticide efficiency (>80% mortality) in the upper and lower leaves of the canopy. Treatment with these insecticides also resulted in significantly lower leaf loss and frass amounts. We conclude that emamectin benzoate and emamectin benzoate + clothianidin have a rapid uptake into O. fragrans, and are effective as insecticides over long durations. Hence, they may be a suitable control option for L. lepida in O. fragrans plants.
bibliographic citation: Huang et al. (2016) Evaluation of the effectiveness of insecticide trunk injections for control of Latoia lepida (Cramer) in the sweet olive tree Osmanthus fragrans. PeerJ 4:e2480 https://doi.org/10.7717/peerj.2480
date submitted: 2016-05-29
date accepted: 2016-08-23
issued: 2016-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Jun
author list: Agent
  family name: Zhang
  given name: Juan
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Shi
  given name: Xiao-Hua
doi: 10.7717/peerj.2480
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-21
copyright: ©2016 Huang et al.
attribution name: Huang et al.

Successful population establishment from small introductions appears to be less common than believed
type: item
type: AcademicArticle
description: Although small populations are at high risk of extinction, there are regular reports in the scientific literature of purported small, isolated, persistent populations. One source of evidence of the viability of small populations comes from the alleged successful introduction of species to areas outside their original range from introductions of few individuals. We reviewed the examples from introduction compendia on deliberate translocations of birds, and the original sources, to identify and evaluate purported examples of successful establishments from small introductions. We found 23 purportedly successful introductions from few (<30) individuals. After assessing original sources, we found that two of the claims were substantiated; the rest were ambiguous or could be rejected as examples, primarily due to a lack of evidence in original sources of the number of birds released and because of supplemental individuals from other releases, releases in nearby regions, and the possibility of natural invasion. Our results suggest that reports of successful establishment of birds from introductions of few individuals have been overstated. These results strengthen the relationship previously reported between propagule pressure and likelihood of establishment, and support the lack of viability of small populations presumed by population theory. We suggest that analyses of introduction failure and success would benefit from excluding studies where introduction effort is unknown or unreliably documented.
format: application/pdf
format: text/html
creator: Alyssa Corbett King
creator: J. Michael Reed
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2440
publisher: PeerJ Inc.
rights: © 2016 Corbett King and Reed
abstract: Although small populations are at high risk of extinction, there are regular reports in the scientific literature of purported small, isolated, persistent populations. One source of evidence of the viability of small populations comes from the alleged successful introduction of species to areas outside their original range from introductions of few individuals. We reviewed the examples from introduction compendia on deliberate translocations of birds, and the original sources, to identify and evaluate purported examples of successful establishments from small introductions. We found 23 purportedly successful introductions from few (<30) individuals. After assessing original sources, we found that two of the claims were substantiated; the rest were ambiguous or could be rejected as examples, primarily due to a lack of evidence in original sources of the number of birds released and because of supplemental individuals from other releases, releases in nearby regions, and the possibility of natural invasion. Our results suggest that reports of successful establishment of birds from introductions of few individuals have been overstated. These results strengthen the relationship previously reported between propagule pressure and likelihood of establishment, and support the lack of viability of small populations presumed by population theory. We suggest that analyses of introduction failure and success would benefit from excluding studies where introduction effort is unknown or unreliably documented.
bibliographic citation: Corbett King et al. (2016) Successful population establishment from small introductions appears to be less common than believed. PeerJ 4:e2440 https://doi.org/10.7717/peerj.2440
date submitted: 2016-07-25
date accepted: 2016-08-13
issued: 2016-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Corbett King
  given name: Alyssa
author list: Agent
  family name: Reed
  given name: J. Michael
doi: 10.7717/peerj.2440
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-21
copyright: ©2016 Corbett King and Reed
attribution name: Corbett King and Reed

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