PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings
items: Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species
items: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna
items: Artificial light at night alters life history in a nocturnal orb-web spider
items: Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use?
items: The CCB-ID approach to tree species mapping with airborne imaging spectroscopy
items: Patient-centered care interventions to reduce the inappropriate prescription and use of benzodiazepines and z-drugs: a systematic review
items: Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
items: Trophic state (TSISD) and mixing type significantly influence pelagic zooplankton biodiversity in temperate lakes (NW Poland)
items: Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada

strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings
type: item
type: AcademicArticle
description: Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.
format: application/pdf
format: text/html
creator: Camilo Saavedra
subject: Computational Biology
subject: Algorithms and Analysis of Algorithms
subject: Software Engineering
description: doi:10.7717/peerj.5768
publisher: PeerJ Inc.
rights: © 2018 Saavedra
abstract: Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.
bibliographic citation: Saavedra (2018) strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings. PeerJ 6:e5768 https://doi.org/10.7717/peerj.5768
date submitted: 2018-02-16
date accepted: 2018-09-16
issued: 2018-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saavedra
  given name: Camilo
doi: 10.7717/peerj.5768
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-09
copyright: © 2018 Saavedra
attribution name: Saavedra

Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species
type: item
type: AcademicArticle
description: Background The plight of the white rhinoceros (Ceratotherium simum) and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs in comparison to the horse. While the reason for the differences is unknown, a likely cause may be a difference in present cytochrome P450 (CYP450), which may result in the rhino being genetically deficient in certain enzyme families. Methods For this paper we assess the degree of similarity of the CYP genome sequences across the different species, using BLAT (BLAST-like alignment tool) for the alignment of the nucleotide sequences of the equine CYP450 with potential homologous nucleotide sequences of the published database from white rhinos and other mammalian species (cow, pig, dog, sheep, elephant, mouse and human). Results The white rhino nucleotide sequences were 90.74% identical to the equine sequences. This was higher than the degree of similarity between any of the other evaluated species sequences. While no specific CYP family were found to be deficient in the published rhino genome, the horse genome contained additional genetic sequence for a larger number of iso-enzymes that were not present in the rhino. Discussion In pharmacokinetic study, it is well known that absence of a metabolic enzyme will result in constraints in drug metabolism and drug elimination. While this was our speculation, comparison to the horse and other mammalian species indicate that all the described CYP genes required for metabolism are present within the rhino g…
format: application/pdf
format: text/html
creator: Marion Leiberich
creator: Hendrik Johannes Marais
creator: Vinny Naidoo
subject: Genetics
subject: Veterinary Medicine
description: doi:10.7717/peerj.5718
publisher: PeerJ Inc.
rights: © 2018 Leiberich et al.
abstract: Background The plight of the white rhinoceros (Ceratotherium simum) and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs in comparison to the horse. While the reason for the differences is unknown, a likely cause may be a difference in present cytochrome P450 (CYP450), which may result in the rhino being genetically deficient in certain enzyme families. Methods For this paper we assess the degree of similarity of the CYP genome sequences across the different species, using BLAT (BLAST-like alignment tool) for the alignment of the nucleotide sequences of the equine CYP450 with potential homologous nucleotide sequences of the published database from white rhinos and other mammalian species (cow, pig, dog, sheep, elephant, mouse and human). Results The white rhino nucleotide sequences were 90.74% identical to the equine sequences. This was higher than the degree of similarity between any of the other evaluated species sequences. While no specific CYP family were found to be deficient in the published rhino genome, the horse genome contained additional genetic sequence for a larger number of iso-enzymes that were not present in the rhino. Discussion In pharmacokinetic study, it is well known that absence of a metabolic enzyme will result in constraints in drug metabolism and drug elimination. While this was our speculation, comparison to the horse and other mammalian species indicate that all the described CYP genes required for metabolism are present within the rhino g…
bibliographic citation: Leiberich et al. (2018) Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species. PeerJ 6:e5718 https://doi.org/10.7717/peerj.5718
date submitted: 2018-03-16
date accepted: 2018-09-08
issued: 2018-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leiberich
  given name: Marion
author list: Agent
  family name: Marais
  given name: Hendrik Johannes
author list: Agent
  family name: Naidoo
  given name: Vinny
doi: 10.7717/peerj.5718
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-09
copyright: © 2018 Leiberich et al.
attribution name: Leiberich et al.

Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna
type: item
type: AcademicArticle
description: Background Ecosystem engineers are species that transform habitats in ways that influence other species.While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated—the gradients themselves can be altered by engineers—doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods We conducted our research in South America’s Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes are consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion Atta laevigat…
format: application/pdf
format: text/html
creator: Alan N. Costa
creator: Emilio M. Bruna
creator: Heraldo L. Vasconcelos
subject: Biodiversity
subject: Biogeography
subject: Ecosystem Science
subject: Entomology
subject: Soil Science
description: doi:10.7717/peerj.5612
publisher: PeerJ Inc.
rights: © 2018 Costa et al.
abstract: Background Ecosystem engineers are species that transform habitats in ways that influence other species.While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated—the gradients themselves can be altered by engineers—doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods We conducted our research in South America’s Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes are consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion Atta laevigat…
bibliographic citation: Costa et al. (2018) Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna. PeerJ 6:e5612 https://doi.org/10.7717/peerj.5612
date submitted: 2016-06-01
date accepted: 2018-08-14
issued: 2018-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costa
  given name: Alan N.
author list: Agent
  family name: Bruna
  given name: Emilio M.
author list: Agent
  family name: Vasconcelos
  given name: Heraldo L.
doi: 10.7717/peerj.5612
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-09
copyright: ©2018 Costa et al.
attribution name: Costa et al.

Artificial light at night alters life history in a nocturnal orb-web spider
type: item
type: AcademicArticle
description: The prevalence of artificial light at night (ALAN) is increasing rapidly around the world. The potential physiological costs of this night lighting are often evident in life history shifts. We investigated the effects of chronic night-time exposure to ecologically relevant levels of LED lighting on the life history traits of the nocturnal Australian garden orb-web spider (Eriophora biapicata). We reared spiders under a 12-h day and either a 12-h natural darkness (∼0 lux) or a 12-h dim light (∼20 lux) night and assessed juvenile development, growth and mortality, and adult reproductive success and survival. We found that exposure to ALAN accelerated juvenile development, resulting in spiders progressing through fewer moults, and maturing earlier and at a smaller size. There was a significant increase in daily juvenile mortality for spiders reared under 20 lux, but the earlier maturation resulted in a comparable number of 0 lux and 20 lux spiders reaching maturity. Exposure to ALAN also considerably reduced the number of eggs produced by females, and this was largely associated with ALAN-induced reductions in body size. Despite previous observations of increased fitness for some orb-web spiders in urban areas and near night lighting, it appears that exposure to artificial night lighting may lead to considerable developmental costs. Future research will need to consider the detrimental effects of ALAN combined with foraging benefits when studying nocturnal insectivores that forage around artificial lights.
format: application/pdf
format: text/html
creator: Nikolas J. Willmott
creator: Jessica Henneken
creator: Caitlin J. Selleck
creator: Therésa M. Jones
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.5599
publisher: PeerJ Inc.
rights: © 2018 Willmott et al.
abstract: The prevalence of artificial light at night (ALAN) is increasing rapidly around the world. The potential physiological costs of this night lighting are often evident in life history shifts. We investigated the effects of chronic night-time exposure to ecologically relevant levels of LED lighting on the life history traits of the nocturnal Australian garden orb-web spider (Eriophora biapicata). We reared spiders under a 12-h day and either a 12-h natural darkness (∼0 lux) or a 12-h dim light (∼20 lux) night and assessed juvenile development, growth and mortality, and adult reproductive success and survival. We found that exposure to ALAN accelerated juvenile development, resulting in spiders progressing through fewer moults, and maturing earlier and at a smaller size. There was a significant increase in daily juvenile mortality for spiders reared under 20 lux, but the earlier maturation resulted in a comparable number of 0 lux and 20 lux spiders reaching maturity. Exposure to ALAN also considerably reduced the number of eggs produced by females, and this was largely associated with ALAN-induced reductions in body size. Despite previous observations of increased fitness for some orb-web spiders in urban areas and near night lighting, it appears that exposure to artificial night lighting may lead to considerable developmental costs. Future research will need to consider the detrimental effects of ALAN combined with foraging benefits when studying nocturnal insectivores that forage around artificial lights.
bibliographic citation: Willmott et al. (2018) Artificial light at night alters life history in a nocturnal orb-web spider. PeerJ 6:e5599 https://doi.org/10.7717/peerj.5599
date submitted: 2018-05-15
date accepted: 2018-08-17
issued: 2018-10-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Willmott
  given name: Nikolas J.
author list: Agent
  family name: Henneken
  given name: Jessica
author list: Agent
  family name: Selleck
  given name: Caitlin J.
author list: Agent
  family name: Jones
  given name: Therésa M.
doi: 10.7717/peerj.5599
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-09
copyright: © 2018 Willmott et al.
attribution name: Willmott et al.

Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use?
type: item
type: AcademicArticle
description: Background Prescription pain reliever (PPR) overdoses differentially affect ‘American Indian/Alaskan Natives’ in the United States (US). Here, studying onset of extra-medical PPR use in 12-24-year-olds, we examine subgroup variations in rates of starting to use prescription pain relievers extra-medically (i.e., to get ‘high’ or for other reasons outside boundaries of prescriber’s intent). Risk differences (RD) are estimated for US-born versus non-US-born young people, stratified by American Indian/Alaskan Natives versus other ethnic self-identities. Methods Between 2002–2009, nationally representative cross-sectional samples of 12–24-year-old non-institutionalized civilians completed interviews for the US National Surveys of Drug Use and Health. Analysis-weighted annual incidence estimates, RD, and confidence intervals (CI) are from the Restricted-use Data Analysis System, an online software tool for US National Surveys of Drug Use and Health. Results Each year, an estimated 2.5% of 12-24-year-olds in the US start using PPR extra-medically (95% CI [2.1%–3.0%]). Estimates for the US-born (3.8%; 95% CI [3.7%–3.9%]) are larger (non-US-born: 1.8%; 95% CI [1.5%–2.0%]; RD = 2.0; p < 0.05). US-born American Indian/Alaskan Natives youths have the largest incidence rate (4.8%). Robust RD for US-born can be seen for ‘non-Hispanic White’ subgroups, and for others (e.g., ‘Cuban’, ‘Dominican’). Discussion Each year, one in 20 of US-born American Indian/Alaskan Natives starts using PPR extra-medically. Overdose prevention is important, but is no substitute for primary prevention initiatives for all young people. The observed epidemiological patterns can guide targeted prevention initiatives for the identified higher risk subgroups in complement with more universal prevention efforts intended to reduce incidence of first extra-medical PPR use, a crucial rate-limiting step on the path toward more serious drug involvement (i.e., progressing past initial use).
format: application/pdf
format: text/html
creator: Maria A. Parker
creator: Catalina Lopez-Quintero
creator: James C. Anthony
subject: Drugs and Devices
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.5713
publisher: PeerJ Inc.
rights: © 2018 Parker et al.
abstract: Background Prescription pain reliever (PPR) overdoses differentially affect ‘American Indian/Alaskan Natives’ in the United States (US). Here, studying onset of extra-medical PPR use in 12-24-year-olds, we examine subgroup variations in rates of starting to use prescription pain relievers extra-medically (i.e., to get ‘high’ or for other reasons outside boundaries of prescriber’s intent). Risk differences (RD) are estimated for US-born versus non-US-born young people, stratified by American Indian/Alaskan Natives versus other ethnic self-identities. Methods Between 2002–2009, nationally representative cross-sectional samples of 12–24-year-old non-institutionalized civilians completed interviews for the US National Surveys of Drug Use and Health. Analysis-weighted annual incidence estimates, RD, and confidence intervals (CI) are from the Restricted-use Data Analysis System, an online software tool for US National Surveys of Drug Use and Health. Results Each year, an estimated 2.5% of 12-24-year-olds in the US start using PPR extra-medically (95% CI [2.1%–3.0%]). Estimates for the US-born (3.8%; 95% CI [3.7%–3.9%]) are larger (non-US-born: 1.8%; 95% CI [1.5%–2.0%]; RD = 2.0; p < 0.05). US-born American Indian/Alaskan Natives youths have the largest incidence rate (4.8%). Robust RD for US-born can be seen for ‘non-Hispanic White’ subgroups, and for others (e.g., ‘Cuban’, ‘Dominican’). Discussion Each year, one in 20 of US-born American Indian/Alaskan Natives starts using PPR extra-medically. Overdose prevention is important, but is no substitute for primary prevention initiatives for all young people. The observed epidemiological patterns can guide targeted prevention initiatives for the identified higher risk subgroups in complement with more universal prevention efforts intended to reduce incidence of first extra-medical PPR use, a crucial rate-limiting step on the path toward more serious drug involvement (i.e., progressing past initial use).
bibliographic citation: Parker et al. (2018) Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use?. PeerJ 6:e5713 https://doi.org/10.7717/peerj.5713
date submitted: 2018-06-05
date accepted: 2018-09-10
issued: 2018-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parker
  given name: Maria A.
author list: Agent
  family name: Lopez-Quintero
  given name: Catalina
author list: Agent
  family name: Anthony
  given name: James C.
doi: 10.7717/peerj.5713
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-08
copyright: ©2018 Parker et al.
attribution name: Parker et al.

The CCB-ID approach to tree species mapping with airborne imaging spectroscopy
type: item
type: AcademicArticle
description: Background Biogeographers assess how species distributions and abundances affect the structure, function, and composition of ecosystems. Yet we face a major challenge: it is difficult to precisely map species across landscapes. Novel Earth observations could overcome this challenge for vegetation mapping. Airborne imaging spectrometers measure plant functional traits at high resolution, and these measurements can be used to identify tree species. In this paper, I describe a trait-based approach to species identification with imaging spectroscopy, the Center for Conservation Biology species identification (CCB-ID) method, which was developed as part of an ecological data science evaluation competition. Methods These methods were developed using airborne imaging spectroscopy data from the National Ecological Observatory Network (NEON). CCB-ID classified tree species using trait-based reflectance variation and decision tree-based machine learning models, approximating a morphological trait and dichotomous key method inspired by botanical classification. First, outliers were removed using a spectral variance threshold. The remaining samples were transformed using principal components analysis (PCA) and resampled to reduce common species biases. Gradient boosting and random forest classifiers were trained using the transformed and resampled feature data. Prediction probabilities were calibrated using sigmoid regression, and sample-scale predictions were averaged to the crown scale. Results CCB-ID received a rank-1 accuracy score of 0.919, and a cross-entropy cost score of 0.447 on the competition test data. Accuracy and specificity scores were high for all species, but precision and recall scores varied for rare species. PCA transformation improved accuracy scores compared to models trained using reflectance data, but outlier removal and data resampling exacerbated class imbalance problems. Discussion CCB-ID accurately classified tree species using NEON data, reporting t…
format: application/pdf
format: text/html
creator: Christopher B. Anderson
subject: Biogeography
subject: Ecology
subject: Data Mining and Machine Learning
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5666
publisher: PeerJ Inc.
rights: © 2018 Anderson
abstract: Background Biogeographers assess how species distributions and abundances affect the structure, function, and composition of ecosystems. Yet we face a major challenge: it is difficult to precisely map species across landscapes. Novel Earth observations could overcome this challenge for vegetation mapping. Airborne imaging spectrometers measure plant functional traits at high resolution, and these measurements can be used to identify tree species. In this paper, I describe a trait-based approach to species identification with imaging spectroscopy, the Center for Conservation Biology species identification (CCB-ID) method, which was developed as part of an ecological data science evaluation competition. Methods These methods were developed using airborne imaging spectroscopy data from the National Ecological Observatory Network (NEON). CCB-ID classified tree species using trait-based reflectance variation and decision tree-based machine learning models, approximating a morphological trait and dichotomous key method inspired by botanical classification. First, outliers were removed using a spectral variance threshold. The remaining samples were transformed using principal components analysis (PCA) and resampled to reduce common species biases. Gradient boosting and random forest classifiers were trained using the transformed and resampled feature data. Prediction probabilities were calibrated using sigmoid regression, and sample-scale predictions were averaged to the crown scale. Results CCB-ID received a rank-1 accuracy score of 0.919, and a cross-entropy cost score of 0.447 on the competition test data. Accuracy and specificity scores were high for all species, but precision and recall scores varied for rare species. PCA transformation improved accuracy scores compared to models trained using reflectance data, but outlier removal and data resampling exacerbated class imbalance problems. Discussion CCB-ID accurately classified tree species using NEON data, reporting t…
bibliographic citation: Anderson (2018) The CCB-ID approach to tree species mapping with airborne imaging spectroscopy. PeerJ 6:e5666 https://doi.org/10.7717/peerj.5666
date submitted: 2018-06-01
date accepted: 2018-08-29
issued: 2018-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Christopher B.
doi: 10.7717/peerj.5666
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-08
copyright: © 2018 Anderson
attribution name: Anderson

Patient-centered care interventions to reduce the inappropriate prescription and use of benzodiazepines and z-drugs: a systematic review
type: item
type: AcademicArticle
description: Background Benzodiazepines (BZDs) and z-drugs are effective drugs, but they are prescribed excessively worldwide. International guidelines recommend a maximum treatment duration of 4 weeks. Although these drugs are effective in the short-term, long-term BZD therapy is associated with considerable adverse effects, the development of tolerance and, finally, addiction. However, there are different interventions in terms of patient-centered care that aim to reduce the use of BZDs and z-drugs as well as assist health care professionals (HCPs) in preventing the inappropriate prescription of BZDs. Aim The aim of this systematic review was to identify interventions that promote patient-centered treatments for inappropriate BZD and z-drug use and to analyze their effectiveness in reducing the inappropriate use of these drugs. Methods To identify relevant studies, the PubMed, EMBASE, PsycINFO, Psyndex, and Cochrane Library databases were searched. Studies with controlled designs focusing on adult patients were included. Trials with chronically or mentally ill patients were excluded if long-term BZD and z-drug use was indicated. Study extraction was performed based on the Cochrane Form for study extraction. To assess the quality of the studies, we used a tool based on the Cochrane Collaboration’s tool for assessing the risk of bias in randomized trials. Results We identified 7,068 studies and selected 20 for systematic review. Nine interventions focused on patients, nine on HCPs, and two on both patients and HCPs. Intervention types ranged from simple to multifaceted. Patient-centered interventions that provided patient information effectively increased the appropriate use of BZDs. The educational approaches for HCPs that aimed to achieve appropriate prescription reported inconsistent results. The methods that combined informing patients and HCPs led to a significant reduction in BZD use. Conclusions This is the first review of studies focused on patient-centered approaches to…
format: application/pdf
format: text/html
creator: Aliaksandra Mokhar
creator: Janine Topp
creator: Martin Härter
creator: Holger Schulz
creator: Silke Kuhn
creator: Uwe Verthein
creator: Jörg Dirmaier
subject: Geriatrics
subject: Pharmacology
description: doi:10.7717/peerj.5535
publisher: PeerJ Inc.
rights: © 2018 Mokhar et al.
abstract: Background Benzodiazepines (BZDs) and z-drugs are effective drugs, but they are prescribed excessively worldwide. International guidelines recommend a maximum treatment duration of 4 weeks. Although these drugs are effective in the short-term, long-term BZD therapy is associated with considerable adverse effects, the development of tolerance and, finally, addiction. However, there are different interventions in terms of patient-centered care that aim to reduce the use of BZDs and z-drugs as well as assist health care professionals (HCPs) in preventing the inappropriate prescription of BZDs. Aim The aim of this systematic review was to identify interventions that promote patient-centered treatments for inappropriate BZD and z-drug use and to analyze their effectiveness in reducing the inappropriate use of these drugs. Methods To identify relevant studies, the PubMed, EMBASE, PsycINFO, Psyndex, and Cochrane Library databases were searched. Studies with controlled designs focusing on adult patients were included. Trials with chronically or mentally ill patients were excluded if long-term BZD and z-drug use was indicated. Study extraction was performed based on the Cochrane Form for study extraction. To assess the quality of the studies, we used a tool based on the Cochrane Collaboration’s tool for assessing the risk of bias in randomized trials. Results We identified 7,068 studies and selected 20 for systematic review. Nine interventions focused on patients, nine on HCPs, and two on both patients and HCPs. Intervention types ranged from simple to multifaceted. Patient-centered interventions that provided patient information effectively increased the appropriate use of BZDs. The educational approaches for HCPs that aimed to achieve appropriate prescription reported inconsistent results. The methods that combined informing patients and HCPs led to a significant reduction in BZD use. Conclusions This is the first review of studies focused on patient-centered approaches to…
bibliographic citation: Mokhar et al. (2018) Patient-centered care interventions to reduce the inappropriate prescription and use of benzodiazepines and z-drugs: a systematic review. PeerJ 6:e5535 https://doi.org/10.7717/peerj.5535
date submitted: 2018-01-17
date accepted: 2018-08-08
issued: 2018-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mokhar
  given name: Aliaksandra
author list: Agent
  family name: Topp
  given name: Janine
author list: Agent
  family name: Härter
  given name: Martin
author list: Agent
  family name: Schulz
  given name: Holger
author list: Agent
  family name: Kuhn
  given name: Silke
author list: Agent
  family name: Verthein
  given name: Uwe
author list: Agent
  family name: Dirmaier
  given name: Jörg
doi: 10.7717/peerj.5535
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-08
copyright: © 2018 Mokhar et al.
attribution name: Mokhar et al.

Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
type: item
type: AcademicArticle
description: Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
format: application/pdf
format: text/html
creator: Kevin Winker
creator: Travis C. Glenn
creator: Brant C. Faircloth
subject: Biodiversity
subject: Evolutionary Studies
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.5735
publisher: PeerJ Inc.
rights: © 2018 Winker et al.
abstract: Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
bibliographic citation: Winker et al. (2018) Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. PeerJ 6:e5735 https://doi.org/10.7717/peerj.5735
date submitted: 2018-04-04
date accepted: 2018-09-05
issued: 2018-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Winker
  given name: Kevin
author list: Agent
  family name: Glenn
  given name: Travis C.
author list: Agent
  family name: Faircloth
  given name: Brant C.
doi: 10.7717/peerj.5735
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-05
copyright: © 2018 Winker et al.
attribution name: Winker et al.

Trophic state (TSISD) and mixing type significantly influence pelagic zooplankton biodiversity in temperate lakes (NW Poland)
type: item
type: AcademicArticle
description: Background Lake depth and the consequent mixing regime and thermal structure have profound effects on ecosystem functioning, because depth strongly affects the availability of nutrients, light, and oxygen. All these conditions influence patterns of zooplankton diversity. Zooplankton are a key component of the aquatic environment and are essential to maintaining natural processes in freshwater ecosystems. However, zooplankton biodiversity can be different regard to depth, mixing type and trophic state. Therefore, the aim of this study was to examine how depth and mixing regime affect zooplankton diversity in lakes. We also investigated the vertical distribution of diversity across a trophic gradient of lakes. Methods A total of 329 zooplankton samples from 79 temperate lakes (36 polymictic and 43 dimictic) were collected. The biodiversity of zooplankton was calculated using species richness (SR) and the Shannon index (SI). An index based on Secchi disc visibility was used to determine the trophic state index (TSISD) of lakes. The one-way ANOVA with Duncan’s post hoc test were used to determine differences in zooplankton biodiversity between mictic lake types and thermal layers. To find the best predictors for zooplankton biodiversity a multiple stepwise regression was used. The rarefaction method was used to evaluate the impact of mixing types, thermal layers, and the TSISDon zooplankton biodiversity indices. A Sørensen similarity analysis and nonmetric multidimensional scaling (NMDS) were performed to describe the similarity patterns in species composition among lakes. Results We identified a total of 151 taxa from 36 polymictic and 43 dimictic lakes. Lake depth and the TSISD were significantly correlated with the biodiversity of lake zooplankton. The results of ANOVA and Duncan tests show that mictic type and thermal zones had a significant effect on zooplankton biodiversity. The rarefaction curve showed significant differences in zooplankton biodiversity, which wa…
format: application/pdf
format: text/html
creator: Łukasz Sługocki
creator: Robert Czerniawski
subject: Biodiversity
subject: Ecosystem Science
subject: Zoology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.5731
publisher: PeerJ Inc.
rights: © 2018 Sługocki and Czerniawski
abstract: Background Lake depth and the consequent mixing regime and thermal structure have profound effects on ecosystem functioning, because depth strongly affects the availability of nutrients, light, and oxygen. All these conditions influence patterns of zooplankton diversity. Zooplankton are a key component of the aquatic environment and are essential to maintaining natural processes in freshwater ecosystems. However, zooplankton biodiversity can be different regard to depth, mixing type and trophic state. Therefore, the aim of this study was to examine how depth and mixing regime affect zooplankton diversity in lakes. We also investigated the vertical distribution of diversity across a trophic gradient of lakes. Methods A total of 329 zooplankton samples from 79 temperate lakes (36 polymictic and 43 dimictic) were collected. The biodiversity of zooplankton was calculated using species richness (SR) and the Shannon index (SI). An index based on Secchi disc visibility was used to determine the trophic state index (TSISD) of lakes. The one-way ANOVA with Duncan’s post hoc test were used to determine differences in zooplankton biodiversity between mictic lake types and thermal layers. To find the best predictors for zooplankton biodiversity a multiple stepwise regression was used. The rarefaction method was used to evaluate the impact of mixing types, thermal layers, and the TSISDon zooplankton biodiversity indices. A Sørensen similarity analysis and nonmetric multidimensional scaling (NMDS) were performed to describe the similarity patterns in species composition among lakes. Results We identified a total of 151 taxa from 36 polymictic and 43 dimictic lakes. Lake depth and the TSISD were significantly correlated with the biodiversity of lake zooplankton. The results of ANOVA and Duncan tests show that mictic type and thermal zones had a significant effect on zooplankton biodiversity. The rarefaction curve showed significant differences in zooplankton biodiversity, which wa…
bibliographic citation: Sługocki et al. (2018) Trophic state (TSISD) and mixing type significantly influence pelagic zooplankton biodiversity in temperate lakes (NW Poland). PeerJ 6:e5731 https://doi.org/10.7717/peerj.5731
date submitted: 2018-01-08
date accepted: 2018-09-12
issued: 2018-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sługocki
  given name: Łukasz
author list: Agent
  family name: Czerniawski
  given name: Robert
doi: 10.7717/peerj.5731
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-05
copyright: ©2018 Sługocki and Czerniawski
attribution name: Sługocki and Czerniawski

Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada
type: item
type: AcademicArticle
description: Eelgrass (Zostera marina) has been designated an Ecologically Significant Species in Atlantic Canada. The development and rapid expansion of netpen finfish aquaculture into sensitive coastal habitats has raised concerns about the impacts of finfish aquaculture on eelgrass habitats. To date, no studies have been done in Atlantic Canada to examine these impacts or to identify potential monitoring variables that would aid in the development of specific conservation and management objectives. As a first step in addressing this gap, we examined differences in environmental variables, eelgrass bed structure and macroinfauna communities at increasing distances from a finfish farm in Port Mouton Bay, a reference site in adjacent Port Joli Bay, and published survey results from other sites without finfish farms along the Atlantic Coast of Nova Scotia. Drawing on research done elsewhere and our results, we then identified possible metrics for assessing and monitoring local impacts of finfish aquaculture on eelgrass habitats. Our results suggest some nutrient and organic enrichment, higher epiphyte loads, lower eelgrass cover and biomass, and lower macroinfauna biomass closer to the farm. Moreover, community structure significantly differed between sites with some species increasing and others decreasing closer to the farm. Changes in the macroinfauna community could be linked to observed differences in environmental and eelgrass bed variables. These results provide new insights into the potential impacts of finfish aquaculture on eelgrass habitats in Atlantic Canada. We recommend a suite of measures for assessment and monitoring that take into account response time to disturbance and account for different levels of eelgrass organizational response (from physiological to community).
format: application/pdf
format: text/html
creator: Nakia Cullain
creator: Reba McIver
creator: Allison L. Schmidt
creator: Inka Milewski
creator: Heike K. Lotze
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.5630
publisher: PeerJ Inc.
rights: © 2018 Cullain et al.
abstract: Eelgrass (Zostera marina) has been designated an Ecologically Significant Species in Atlantic Canada. The development and rapid expansion of netpen finfish aquaculture into sensitive coastal habitats has raised concerns about the impacts of finfish aquaculture on eelgrass habitats. To date, no studies have been done in Atlantic Canada to examine these impacts or to identify potential monitoring variables that would aid in the development of specific conservation and management objectives. As a first step in addressing this gap, we examined differences in environmental variables, eelgrass bed structure and macroinfauna communities at increasing distances from a finfish farm in Port Mouton Bay, a reference site in adjacent Port Joli Bay, and published survey results from other sites without finfish farms along the Atlantic Coast of Nova Scotia. Drawing on research done elsewhere and our results, we then identified possible metrics for assessing and monitoring local impacts of finfish aquaculture on eelgrass habitats. Our results suggest some nutrient and organic enrichment, higher epiphyte loads, lower eelgrass cover and biomass, and lower macroinfauna biomass closer to the farm. Moreover, community structure significantly differed between sites with some species increasing and others decreasing closer to the farm. Changes in the macroinfauna community could be linked to observed differences in environmental and eelgrass bed variables. These results provide new insights into the potential impacts of finfish aquaculture on eelgrass habitats in Atlantic Canada. We recommend a suite of measures for assessment and monitoring that take into account response time to disturbance and account for different levels of eelgrass organizational response (from physiological to community).
bibliographic citation: Cullain et al. (2018) Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada. PeerJ 6:e5630 https://doi.org/10.7717/peerj.5630
date submitted: 2018-03-27
date accepted: 2018-08-22
issued: 2018-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cullain
  given name: Nakia
author list: Agent
  family name: McIver
  given name: Reba
author list: Agent
  family name: Schmidt
  given name: Allison L.
author list: Agent
  family name: Milewski
  given name: Inka
author list: Agent
  family name: Lotze
  given name: Heike K.
doi: 10.7717/peerj.5630
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-05
copyright: ©2018 Cullain et al.
attribution name: Cullain et al.

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