PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis
items: New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti)
items: A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
items: Spermatozoon ultrastructure in two monorchiid digeneans
items: CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients
items: Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth
items: Overland movement in African clawed frogs (Xenopus laevis): a systematic review
items: Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information

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

A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis
type: item
type: AcademicArticle
description: Inferring growth for aquatic species is dependent upon accurate descriptions of age-length relationships, which may be degraded by measurement error in observed ages. Ageing error arises from biased and/or imprecise age determinations as a consequence of misinterpretation by readers or inability of ageing structures to accurately reflect true age. A Bayesian errors-in-variables (EIV) approach (i.e., measurement-error modeling) can account for ageing uncertainty during nonlinear growth curve estimation by allowing observed ages to be parametrically modeled as random deviates. Information on the latent age composition then comes from the specified prior distribution, which represents the true age structure of the sampled fish population. In this study, weakfish growth was modeled by means of traditional and measurement-error von Bertalanffy growth curves using otolith- or scale-estimated ages. Age determinations were assumed to be log-normally distributed, thereby incorporating multiplicative error with respect to ageing uncertainty. The prior distribution for true age was assumed to be uniformly distributed between ±4 of the observed age (yr) for each individual. Measurement-error growth models described weakfish that reached larger sizes but at slower rates, with median length-at-age being overestimated by traditional growth curves for the observed age range. In addition, measurement-error models produced slightly narrower credible intervals for parameters of the von Bertalanffy growth function, which may be an artifact of the specified prior distributions. Subjectivity is always apparent in the ageing of fishes and it is recommended that measurement-error growth models be used in conjunction with otolith-estimated ages to accurately capture the age-length relationship that is subsequently used in fisheries stock assessment and management.
format: application/pdf
format: text/html
creator: Joshua Hatch
creator: Yan Jiao
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Mathematical Biology
description: doi:10.7717/peerj.2431
publisher: PeerJ Inc.
rights: © 2016 Hatch & Jiao
abstract: Inferring growth for aquatic species is dependent upon accurate descriptions of age-length relationships, which may be degraded by measurement error in observed ages. Ageing error arises from biased and/or imprecise age determinations as a consequence of misinterpretation by readers or inability of ageing structures to accurately reflect true age. A Bayesian errors-in-variables (EIV) approach (i.e., measurement-error modeling) can account for ageing uncertainty during nonlinear growth curve estimation by allowing observed ages to be parametrically modeled as random deviates. Information on the latent age composition then comes from the specified prior distribution, which represents the true age structure of the sampled fish population. In this study, weakfish growth was modeled by means of traditional and measurement-error von Bertalanffy growth curves using otolith- or scale-estimated ages. Age determinations were assumed to be log-normally distributed, thereby incorporating multiplicative error with respect to ageing uncertainty. The prior distribution for true age was assumed to be uniformly distributed between ±4 of the observed age (yr) for each individual. Measurement-error growth models described weakfish that reached larger sizes but at slower rates, with median length-at-age being overestimated by traditional growth curves for the observed age range. In addition, measurement-error models produced slightly narrower credible intervals for parameters of the von Bertalanffy growth function, which may be an artifact of the specified prior distributions. Subjectivity is always apparent in the ageing of fishes and it is recommended that measurement-error growth models be used in conjunction with otolith-estimated ages to accurately capture the age-length relationship that is subsequently used in fisheries stock assessment and management.
bibliographic citation: Hatch et al. (2016) A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis. PeerJ 4:e2431 https://doi.org/10.7717/peerj.2431
date submitted: 2016-02-24
date accepted: 2016-08-11
issued: 2016-09-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hatch
  given name: Joshua
author list: Agent
  family name: Jiao
  given name: Yan
doi: 10.7717/peerj.2431
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-21
copyright: © 2016 Hatch & Jiao
attribution name: Hatch & Jiao

New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti)
type: item
type: AcademicArticle
description: The Ziphiidae (beaked whales) represent a large group of open-ocean odontocetes (toothed cetaceans), whose elusive and deep diving behavior prevents direct observation in their natural habitat. Despite their generally large body size, broad geographical distribution, and high species number, ziphiids thus remain poorly known. Furthermore, the evolutionary processes that have led to their extreme adaptations and impressive extant diversity are still poorly understood. Here we report new fossil beaked whales from the late Miocene of the Pisco Formation (southern Peru). The best preserved remains here described are referred to two new genera and species, the Messinian Chavinziphius maxillocristatus and the Tortonian Chimuziphius coloradensis, based on skull remains from two marine vertebrate-rich localities: Cerro Los Quesos and Cerro Colorado, respectively. C. maxillocristatus is medium sized retains a complete set of functional lower teeth, and bears robust rostral maxillary crests similar to those of the extant Berardius. By contrast, C. coloradensis is small and characterized by large triangular nasals and moderately thickened premaxillae that dorsally close the mesorostral groove. Both species confirm the high past diversity of Ziphiidae, the richest cetacean family in terms of the number of genera and species. Our new phylogenetic and biogeographical analyses depart markedly from earlier studies in dividing beaked whales into two major clades: the Messapicetus clade, which, along with other stem ziphiids, once dominated the southeastern Pacific and North Atlantic; and crown Ziphiidae, the majority of which are found in deep-water regions of the Southern Ocean, with possible subsequent dispersal both globally (Mesoplodon and Ziphius) and to the cooler waters of the northern oceans (Berardius and Hyperoodon). Despite this relatively clear separation, both lineages seem to follow similar evolutionary trends, including (1) a progressive reduction of dentition; (2) an…
format: application/pdf
format: text/html
creator: Giovanni Bianucci
creator: Claudio Di Celma
creator: Mario Urbina
creator: Olivier Lambert
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2479
publisher: PeerJ Inc.
rights: © 2016 Bianucci et al.
abstract: The Ziphiidae (beaked whales) represent a large group of open-ocean odontocetes (toothed cetaceans), whose elusive and deep diving behavior prevents direct observation in their natural habitat. Despite their generally large body size, broad geographical distribution, and high species number, ziphiids thus remain poorly known. Furthermore, the evolutionary processes that have led to their extreme adaptations and impressive extant diversity are still poorly understood. Here we report new fossil beaked whales from the late Miocene of the Pisco Formation (southern Peru). The best preserved remains here described are referred to two new genera and species, the Messinian Chavinziphius maxillocristatus and the Tortonian Chimuziphius coloradensis, based on skull remains from two marine vertebrate-rich localities: Cerro Los Quesos and Cerro Colorado, respectively. C. maxillocristatus is medium sized retains a complete set of functional lower teeth, and bears robust rostral maxillary crests similar to those of the extant Berardius. By contrast, C. coloradensis is small and characterized by large triangular nasals and moderately thickened premaxillae that dorsally close the mesorostral groove. Both species confirm the high past diversity of Ziphiidae, the richest cetacean family in terms of the number of genera and species. Our new phylogenetic and biogeographical analyses depart markedly from earlier studies in dividing beaked whales into two major clades: the Messapicetus clade, which, along with other stem ziphiids, once dominated the southeastern Pacific and North Atlantic; and crown Ziphiidae, the majority of which are found in deep-water regions of the Southern Ocean, with possible subsequent dispersal both globally (Mesoplodon and Ziphius) and to the cooler waters of the northern oceans (Berardius and Hyperoodon). Despite this relatively clear separation, both lineages seem to follow similar evolutionary trends, including (1) a progressive reduction of dentition; (2) an…
bibliographic citation: Bianucci et al. (2016) New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti). PeerJ 4:e2479 https://doi.org/10.7717/peerj.2479
date submitted: 2016-06-08
date accepted: 2016-08-23
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bianucci
  given name: Giovanni
author list: Agent
  family name: Di Celma
  given name: Claudio
author list: Agent
  family name: Urbina
  given name: Mario
author list: Agent
  family name: Lambert
  given name: Olivier
doi: 10.7717/peerj.2479
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: © 2016 Bianucci et al.
attribution name: Bianucci et al.

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
type: item
type: AcademicArticle
description: Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. Conclusions This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.
format: application/pdf
format: text/html
creator: Catherine M. Burke
creator: Aaron E. Darling
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.2492
publisher: PeerJ Inc.
rights: © 2016 Burke & Darling
abstract: Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. Conclusions This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.
bibliographic citation: Burke et al. (2016) A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq. PeerJ 4:e2492 https://doi.org/10.7717/peerj.2492
date submitted: 2015-12-16
date accepted: 2016-08-25
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burke
  given name: Catherine M.
author list: Agent
  family name: Darling
  given name: Aaron E.
doi: 10.7717/peerj.2492
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: © 2016 Burke & Darling
attribution name: Burke & Darling

Spermatozoon ultrastructure in two monorchiid digeneans
type: item
type: AcademicArticle
description: Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris share several characters such as the presence of two axonemes of different lengths showing the 9+“1” pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, granules of glycogen and similar morphologies of the anterior and posterior extremities. The slight differences between the male gamete of O. dinema and P. selaris are the length of the first axoneme and the position of the second mitochondrion. This study also elucidates the general morphology of the spermatozoon in all monorchiid species described so far, which corresponds to a unique spermatozoon type. Other interesting finds concern the spermatological similarities between monorchiid spermatozoa and the mature spermatozoon reported in the apocreadiid Neoapocreadium chabaudi. These similarities allow us to suggest a close phylogenetical relationship between the Monorchiidae and the Apocreadiidae, although more studies are needed, especially in the unexplored taxa.
format: application/pdf
format: text/html
creator: Yann Quilichini
creator: Abdoulaye J.S. Bakhoum
creator: Jean-Lou Justine
creator: Rodney A. Bray
creator: Cheikh T. Bâ
creator: Bernard Marchand
subject: Cell Biology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.2488
publisher: PeerJ Inc.
rights: © 2016 Quilichini et al.
abstract: Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris share several characters such as the presence of two axonemes of different lengths showing the 9+“1” pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, granules of glycogen and similar morphologies of the anterior and posterior extremities. The slight differences between the male gamete of O. dinema and P. selaris are the length of the first axoneme and the position of the second mitochondrion. This study also elucidates the general morphology of the spermatozoon in all monorchiid species described so far, which corresponds to a unique spermatozoon type. Other interesting finds concern the spermatological similarities between monorchiid spermatozoa and the mature spermatozoon reported in the apocreadiid Neoapocreadium chabaudi. These similarities allow us to suggest a close phylogenetical relationship between the Monorchiidae and the Apocreadiidae, although more studies are needed, especially in the unexplored taxa.
bibliographic citation: Quilichini et al. (2016) Spermatozoon ultrastructure in two monorchiid digeneans. PeerJ 4:e2488 https://doi.org/10.7717/peerj.2488
date submitted: 2016-06-28
date accepted: 2016-08-25
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quilichini
  given name: Yann
author list: Agent
  family name: Bakhoum
  given name: Abdoulaye J.S.
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Bray
  given name: Rodney A.
author list: Agent
  family name: Bâ
  given name: Cheikh T.
author list: Agent
  family name: Marchand
  given name: Bernard
doi: 10.7717/peerj.2488
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: ©2016 Quilichini et al.
attribution name: Quilichini et al.

CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients
type: item
type: AcademicArticle
description: Introduction Rituximab (RTX) is a B cell-depleting agent approved for the treatment of granulomatosis with polyangiitis (GPA). RTX reduces antibody producing precursor plasma cells and inhibits B and T cells interaction. Infections related to T cell immunodeficiency are not infrequent during RTX treatment. Our study investigated CD4 cell count and CD4/CD8 ratio in GPA patients during the first two years of long-term RTX treatment. Methods A single centre cohort study of 35 patients who received median total cumulative dose of cyclophosphamide (CYC) of 15 g and were treated with RTX 2 g followed by retreatment with either 2 g once annually or 1 g biannually. Serum levels of total immunoglobulin (Ig) and lymphocytes subsets were recorded at RTX initiation and at 3, 6, 12, 18 and 24 months. Low CD4 count and inverted CD4/CD8 ratio were defined as CD4 < 0.3 × 109/l and ratio < 1. Results The CD4 cell count and CD4/CD8 ratio decreased slightly following the initial RTX treatment and then increased gradually during maintenance treatment. While the proportion of patients with low CD4 cell count decreased from 43% at baseline to 18% at 24 months, the ratio remained inverted in 40%. Oral daily prednisolone dose at baseline, CYC exposure and the maintenance regimen did not influence the CD4 cell count and ratio. Being older (p = 0.012) and having a higher CRP (p = 0.044) and ESR (p = 0.024) at baseline significantly increased the risk of inverted CD4/CD8 ratio at 24 months. Inverted ratio at baseline associated with lower total Ig levels during the study. Conclusions Overall, the CD4 and CD4/CD8 ratio increased during maintenance RTX therapy in GPA with no discernible impact of other immunosuppressive therapy. However the increase in CD4 was not followed by an increase in the CD4/CD8 ratio, especially in older patients. Inverted CD4/CD8 ratio associated with lower Ig levels, suggesting a more profound B cell depleting effect of RTX with a relative increase in CD8+ lymphocytes…
format: application/pdf
format: text/html
creator: Emilio Besada
creator: Johannes C. Nossent
subject: Allergy and Clinical Immunology
subject: Internal Medicine
subject: Rheumatology
description: doi:10.7717/peerj.2487
publisher: PeerJ Inc.
rights: © 2016 Besada & Nossent
abstract: Introduction Rituximab (RTX) is a B cell-depleting agent approved for the treatment of granulomatosis with polyangiitis (GPA). RTX reduces antibody producing precursor plasma cells and inhibits B and T cells interaction. Infections related to T cell immunodeficiency are not infrequent during RTX treatment. Our study investigated CD4 cell count and CD4/CD8 ratio in GPA patients during the first two years of long-term RTX treatment. Methods A single centre cohort study of 35 patients who received median total cumulative dose of cyclophosphamide (CYC) of 15 g and were treated with RTX 2 g followed by retreatment with either 2 g once annually or 1 g biannually. Serum levels of total immunoglobulin (Ig) and lymphocytes subsets were recorded at RTX initiation and at 3, 6, 12, 18 and 24 months. Low CD4 count and inverted CD4/CD8 ratio were defined as CD4 < 0.3 × 109/l and ratio < 1. Results The CD4 cell count and CD4/CD8 ratio decreased slightly following the initial RTX treatment and then increased gradually during maintenance treatment. While the proportion of patients with low CD4 cell count decreased from 43% at baseline to 18% at 24 months, the ratio remained inverted in 40%. Oral daily prednisolone dose at baseline, CYC exposure and the maintenance regimen did not influence the CD4 cell count and ratio. Being older (p = 0.012) and having a higher CRP (p = 0.044) and ESR (p = 0.024) at baseline significantly increased the risk of inverted CD4/CD8 ratio at 24 months. Inverted ratio at baseline associated with lower total Ig levels during the study. Conclusions Overall, the CD4 and CD4/CD8 ratio increased during maintenance RTX therapy in GPA with no discernible impact of other immunosuppressive therapy. However the increase in CD4 was not followed by an increase in the CD4/CD8 ratio, especially in older patients. Inverted CD4/CD8 ratio associated with lower Ig levels, suggesting a more profound B cell depleting effect of RTX with a relative increase in CD8+ lymphocytes…
bibliographic citation: Besada et al. (2016) CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients. PeerJ 4:e2487 https://doi.org/10.7717/peerj.2487
date submitted: 2016-06-16
date accepted: 2016-08-25
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Besada
  given name: Emilio
author list: Agent
  family name: Nossent
  given name: Johannes C.
doi: 10.7717/peerj.2487
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: © 2016 Besada & Nossent
attribution name: Besada & Nossent

Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth
type: item
type: AcademicArticle
description: Background Parenteral nutrition associated cholestasis (PNAC) is a frequently observed pathology in extremely low birth weight (ELBW) infants. Its pathogenesis is determined by the composition and duration of parenteral nutrition (PN) as well as the tolerance of enteral feeds (EF). “Aggressive” nutrition is increasingly used in ELBW infants to improve postnatal growth. Little is known about the effect of “aggressive” nutrition on the incidence of PNAC. We analyzed the influence of implementing an “aggressive” nutritional regimen on the incidence of PNAC and growth in a cohort of ELBW infants. Methods ELBW infants were nourished using a “conservative” (2005–6; n = 77) or “aggressive” (2007–9; n = 85) nutritional regimen that differed in the composition of PN after birth as well as the composition and timing of advancement of EFs. We analyzed the incidence of PNAC (conjugated bilirubin > 1.5 mg/dl (25 µmol/l)) corrected for confounders of cholestasis (i.e., NEC and/or gastrointestinal surgery, sepsis, birth weight, Z-score of birth weight, time on PN and male sex), growth until discharge (as the most important secondary outcome) and neonatal morbidities. Results The incidence of PNAC was significantly lower during the period of “aggressive” vs. “conservative “nutrition (27% vs. 46%, P < 0.05; adjusted OR 0.275 [0.116–0.651], P < 0.01). Body weight (+411g), head circumference (+1 cm) and length (+1 cm) at discharge were significantly higher. Extra-uterine growth failure (defined as a Z-score difference from birth to discharge lower than −1) was significantly reduced for body weight (85% vs. 35%), head circumference (77% vs. 45%) and length (85% vs. 65%) (P < 0.05). The body mass index (BMI) at discharge was significantly higher (11.1 vs. 12.4) using “aggressive” nutrition and growth became more proportionate with significantly less infants being discharged below the 10th BMI percentile (44% vs. 9%), while the percentage of infants discharged over the 90th BMI percentil…
format: application/pdf
format: text/html
creator: Andreas Repa
creator: Ruth Lochmann
creator: Lukas Unterasinger
creator: Michael Weber
creator: Angelika Berger
creator: Nadja Haiden
subject: Gastroenterology and Hepatology
subject: Nutrition
subject: Pediatrics
description: doi:10.7717/peerj.2483
publisher: PeerJ Inc.
rights: © 2016 Repa et al.
abstract: Background Parenteral nutrition associated cholestasis (PNAC) is a frequently observed pathology in extremely low birth weight (ELBW) infants. Its pathogenesis is determined by the composition and duration of parenteral nutrition (PN) as well as the tolerance of enteral feeds (EF). “Aggressive” nutrition is increasingly used in ELBW infants to improve postnatal growth. Little is known about the effect of “aggressive” nutrition on the incidence of PNAC. We analyzed the influence of implementing an “aggressive” nutritional regimen on the incidence of PNAC and growth in a cohort of ELBW infants. Methods ELBW infants were nourished using a “conservative” (2005–6; n = 77) or “aggressive” (2007–9; n = 85) nutritional regimen that differed in the composition of PN after birth as well as the composition and timing of advancement of EFs. We analyzed the incidence of PNAC (conjugated bilirubin > 1.5 mg/dl (25 µmol/l)) corrected for confounders of cholestasis (i.e., NEC and/or gastrointestinal surgery, sepsis, birth weight, Z-score of birth weight, time on PN and male sex), growth until discharge (as the most important secondary outcome) and neonatal morbidities. Results The incidence of PNAC was significantly lower during the period of “aggressive” vs. “conservative “nutrition (27% vs. 46%, P < 0.05; adjusted OR 0.275 [0.116–0.651], P < 0.01). Body weight (+411g), head circumference (+1 cm) and length (+1 cm) at discharge were significantly higher. Extra-uterine growth failure (defined as a Z-score difference from birth to discharge lower than −1) was significantly reduced for body weight (85% vs. 35%), head circumference (77% vs. 45%) and length (85% vs. 65%) (P < 0.05). The body mass index (BMI) at discharge was significantly higher (11.1 vs. 12.4) using “aggressive” nutrition and growth became more proportionate with significantly less infants being discharged below the 10th BMI percentile (44% vs. 9%), while the percentage of infants discharged over the 90th BMI percentil…
bibliographic citation: Repa et al. (2016) Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth. PeerJ 4:e2483 https://doi.org/10.7717/peerj.2483
date submitted: 2016-06-05
date accepted: 2016-08-24
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Repa
  given name: Andreas
author list: Agent
  family name: Lochmann
  given name: Ruth
author list: Agent
  family name: Unterasinger
  given name: Lukas
author list: Agent
  family name: Weber
  given name: Michael
author list: Agent
  family name: Berger
  given name: Angelika
author list: Agent
  family name: Haiden
  given name: Nadja
doi: 10.7717/peerj.2483
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: ©2016 Repa et al.
attribution name: Repa et al.

Overland movement in African clawed frogs (Xenopus laevis): a systematic review
type: item
type: AcademicArticle
description: African clawed frogs (Xenopus laevis) are often referred to as ‘purely aquatic’ but there are many publications which suggest extensive overland movements. Previous reviews which considered the topic have not answered the following questions: (1) is there evidence for overland dispersal in native and invasive ranges; (2) what is the range of distances moved overland; (3) when does overland movement occur; and (4) is there evidence of breeding migratory behaviour? A systematic review was chosen to synthesise and critically analyse all literature on the overland movement in Xenopus laevis. Database searches resulted in 57 documents which revealed a paucity of empirical studies, with 28 containing no data, and 19 having anecdotal content. Overwhelming evidence shows that both native and invasive populations of X. laevis move overland, with well documented examples for several other members of the genus (X. borealis, X. gilli, X. muelleri, X. fraseriand X. tropicalis). Reports of distances moved overland were from 40 m to 2 km, with no apparent difference between native and invasive ranges. Overland movements are not confined to wet seasons or conditions, but the literature suggests that moving overland does not occur in the middle of the day. Migrations to temporary water-bodies for breeding have been suggested, but without any corroborating data.
format: application/pdf
format: text/html
creator: John Measey
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2474
publisher: PeerJ Inc.
rights: © 2016 Measey
abstract: African clawed frogs (Xenopus laevis) are often referred to as ‘purely aquatic’ but there are many publications which suggest extensive overland movements. Previous reviews which considered the topic have not answered the following questions: (1) is there evidence for overland dispersal in native and invasive ranges; (2) what is the range of distances moved overland; (3) when does overland movement occur; and (4) is there evidence of breeding migratory behaviour? A systematic review was chosen to synthesise and critically analyse all literature on the overland movement in Xenopus laevis. Database searches resulted in 57 documents which revealed a paucity of empirical studies, with 28 containing no data, and 19 having anecdotal content. Overwhelming evidence shows that both native and invasive populations of X. laevis move overland, with well documented examples for several other members of the genus (X. borealis, X. gilli, X. muelleri, X. fraseriand X. tropicalis). Reports of distances moved overland were from 40 m to 2 km, with no apparent difference between native and invasive ranges. Overland movements are not confined to wet seasons or conditions, but the literature suggests that moving overland does not occur in the middle of the day. Migrations to temporary water-bodies for breeding have been suggested, but without any corroborating data.
bibliographic citation: Measey (2016) Overland movement in African clawed frogs (Xenopus laevis): a systematic review. PeerJ 4:e2474 https://doi.org/10.7717/peerj.2474
date submitted: 2016-04-26
date accepted: 2016-08-23
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Measey
  given name: John
doi: 10.7717/peerj.2474
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: ©2016 Measey
attribution name: Measey

Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information
type: item
type: AcademicArticle
description: Background Highlighted text in the Internet (i.e., hypertext) is predominantly blue and underlined. The perceptibility of these hypertext characteristics was heavily questioned by applied research and empirical tests resulted in inconclusive results. The ability to recognize blue text in foveal and parafoveal vision was identified as potentially constrained by the low number of foveally centered blue light sensitive retinal cells. The present study investigates if foveal and parafoveal perceptibility of blue hypertext is reduced in comparison to normal black text during reading. Methods A silent-sentence reading study with simultaneous eye movement recordings and the invisible boundary paradigm, which allows the investigation of foveal and parafoveal perceptibility, separately, was realized (comparing fixation times after degraded vs. un-degraded parafoveal previews). Target words in sentences were presented in either black or blue and either underlined or normal. Results No effect of color and underlining, but a preview benefit could be detected for first pass reading measures. Fixation time measures that included re-reading, e.g., total viewing times, showed, in addition to a preview effect, a reduced fixation time for not highlighted (black not underlined) in contrast to highlighted target words (either blue or underlined or both). Discussion The present pattern reflects no detectable perceptual disadvantage of hyperlink stimuli but increased attraction of attention resources, after first pass reading, through highlighting. Blue or underlined text allows readers to easily perceive hypertext and at the same time readers re-visited highlighted words longer. On the basis of the present evidence, blue hypertext can be safely recommended to web designers for future use.
format: application/pdf
format: text/html
creator: Benjamin Gagl
subject: Human-Computer Interaction
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2467
publisher: PeerJ Inc.
rights: © 2016 Gagl
abstract: Background Highlighted text in the Internet (i.e., hypertext) is predominantly blue and underlined. The perceptibility of these hypertext characteristics was heavily questioned by applied research and empirical tests resulted in inconclusive results. The ability to recognize blue text in foveal and parafoveal vision was identified as potentially constrained by the low number of foveally centered blue light sensitive retinal cells. The present study investigates if foveal and parafoveal perceptibility of blue hypertext is reduced in comparison to normal black text during reading. Methods A silent-sentence reading study with simultaneous eye movement recordings and the invisible boundary paradigm, which allows the investigation of foveal and parafoveal perceptibility, separately, was realized (comparing fixation times after degraded vs. un-degraded parafoveal previews). Target words in sentences were presented in either black or blue and either underlined or normal. Results No effect of color and underlining, but a preview benefit could be detected for first pass reading measures. Fixation time measures that included re-reading, e.g., total viewing times, showed, in addition to a preview effect, a reduced fixation time for not highlighted (black not underlined) in contrast to highlighted target words (either blue or underlined or both). Discussion The present pattern reflects no detectable perceptual disadvantage of hyperlink stimuli but increased attraction of attention resources, after first pass reading, through highlighting. Blue or underlined text allows readers to easily perceive hypertext and at the same time readers re-visited highlighted words longer. On the basis of the present evidence, blue hypertext can be safely recommended to web designers for future use.
bibliographic citation: Gagl (2016) Blue hypertext is a good design decision: no perceptual disadvantage in reading and successful highlighting of relevant information. PeerJ 4:e2467 https://doi.org/10.7717/peerj.2467
date submitted: 2016-04-25
date accepted: 2016-08-20
issued: 2016-09-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gagl
  given name: Benjamin
doi: 10.7717/peerj.2467
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-20
copyright: ©2016 Gagl
attribution name: Gagl

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