PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: URMAP, an ultra-fast read mapper
items: Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea
items: Biofilm modelling on the contact lenses and comparison of the in vitro activities of multipurpose lens solutions and antibiotics
items: A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands
items: A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil
items: Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau
items: Modelling of climate change impact on flow conditions in the lowland anastomosing river
items: Feasibility of a smartphone app to enhance physical activity in progressive MS: a pilot randomized controlled pilot trial over three months
items: Longitudinal relationships between changes in body composition and changes in selected metabolic risk factors (abdominal obesity and blood pressure) among South African adolescents
items: Marsupial and monotreme milk—a review of its nutrient and immune properties

URMAP, an ultra-fast read mapper
type: item
type: AcademicArticle
description: Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map and may therefore pose an unrealistically easy challenge to read mappers and variant callers.
format: application/pdf
format: text/html
creator: Robert Edgar
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.9338
publisher: PeerJ Inc.
rights: © 2020 Edgar
abstract: Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map and may therefore pose an unrealistically easy challenge to read mappers and variant callers.
bibliographic citation: Edgar (2020) URMAP, an ultra-fast read mapper. PeerJ 8:e9338 https://doi.org/10.7717/peerj.9338
date submitted: 2020-02-26
date accepted: 2020-05-20
issued: 2020-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Edgar
  given name: Robert
doi: 10.7717/peerj.9338
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-24
copyright: ©2020 Edgar
attribution name: Edgar

Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea
type: item
type: AcademicArticle
description: Climate, which sets broad limits for migrating species, is considered a key filter to species migration between contrasting marine environments. The Southeast Mediterranean Sea (SEMS) is one of the regions where ocean temperatures are rising the fastest under recent climate change. Also, it is the most vulnerable marine region to species introductions. Here, we explore the factors which enabled the colonization of the endemic Red Sea octocoral Melithaea erythraea (Ehrenberg, 1834) along the SEMS coast, using sclerite oxygen and carbon stable isotope composition (δ18OSC and δ13CSC), morphology, and crystallography. The unique conditions presented by the SEMS include a greater temperature range (∼15 °C) and ultra-oligotrophy, and these are reflected by the lower δ13CSCvalues. This is indicative of a larger metabolic carbon intake during calcification, as well as an increase in crystal size, a decrease of octocoral wart density and thickness of the migrating octocoral sclerites compared to the Red Sea samples. This suggests increased stress conditions, affecting sclerite deposition of the SEMS migrating octocoral. The δ18Osc range of the migrating M. erythraea indicates a preference for warm water sclerite deposition, similar to the native depositional temperature range of 21–28 °C. These findings are associated with the observed increase of minimum temperatures in winter for this region, at a rate of 0.35 ± 0.27 °C decade−1 over the last 30 years, and thus the region is becoming more hospitable to the Indo-Pacific M. erythraea. This study shows a clear case study of “tropicalization” of the Mediterranean Sea due to recent warming.
format: application/pdf
format: text/html
creator: Michal Grossowicz
creator: Or M. Bialik
creator: Eli Shemesh
creator: Dan Tchernov
creator: Hubert B. Vonhof
creator: Guy Sisma-Ventura
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
subject: Biogeochemistry
subject: Population Biology
description: doi:10.7717/peerj.9355
publisher: PeerJ Inc.
rights: © 2020 Grossowicz et al.
abstract: Climate, which sets broad limits for migrating species, is considered a key filter to species migration between contrasting marine environments. The Southeast Mediterranean Sea (SEMS) is one of the regions where ocean temperatures are rising the fastest under recent climate change. Also, it is the most vulnerable marine region to species introductions. Here, we explore the factors which enabled the colonization of the endemic Red Sea octocoral Melithaea erythraea (Ehrenberg, 1834) along the SEMS coast, using sclerite oxygen and carbon stable isotope composition (δ18OSC and δ13CSC), morphology, and crystallography. The unique conditions presented by the SEMS include a greater temperature range (∼15 °C) and ultra-oligotrophy, and these are reflected by the lower δ13CSCvalues. This is indicative of a larger metabolic carbon intake during calcification, as well as an increase in crystal size, a decrease of octocoral wart density and thickness of the migrating octocoral sclerites compared to the Red Sea samples. This suggests increased stress conditions, affecting sclerite deposition of the SEMS migrating octocoral. The δ18Osc range of the migrating M. erythraea indicates a preference for warm water sclerite deposition, similar to the native depositional temperature range of 21–28 °C. These findings are associated with the observed increase of minimum temperatures in winter for this region, at a rate of 0.35 ± 0.27 °C decade−1 over the last 30 years, and thus the region is becoming more hospitable to the Indo-Pacific M. erythraea. This study shows a clear case study of “tropicalization” of the Mediterranean Sea due to recent warming.
bibliographic citation: Grossowicz et al. (2020) Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea. PeerJ 8:e9355 https://doi.org/10.7717/peerj.9355
date submitted: 2020-02-21
date accepted: 2020-05-24
issued: 2020-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grossowicz
  given name: Michal
author list: Agent
  family name: Bialik
  given name: Or M.
author list: Agent
  family name: Shemesh
  given name: Eli
author list: Agent
  family name: Tchernov
  given name: Dan
author list: Agent
  family name: Vonhof
  given name: Hubert B.
author list: Agent
  family name: Sisma-Ventura
  given name: Guy
doi: 10.7717/peerj.9355
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-24
copyright: ©2020 Grossowicz et al.
attribution name: Grossowicz et al.

Biofilm modelling on the contact lenses and comparison of the in vitro activities of multipurpose lens solutions and antibiotics
type: item
type: AcademicArticle
description: During the contact lens (CL) usage, microbial adhesion and biofilm formation are crucial threats for eye health due to the development of mature biofilms on CL surfaces associated with serious eye infections such as keratitis. For CL related eye infections, multi drug resistant Pseudomonas aeruginosa or Staphylococcus aureus (especially MRSA) and Candida albicans are the most common infectious bacteria and yeast, respectively. In this study, CL biofilm models were created by comparing them to reveal the differences on specific conditions. Then the anti-biofilm activities of some commercially available multipurpose CL solutions (MPSs) and antibiotic eye drops against mature biofilms of S. aureus, P. aeruginosa, and C. albicans standard and clinical strains were determined by the time killing curve (TKC) method at 6, 24 and 48 h. According to the biofilm formation models, the optimal biofilms occurred in a mixture of bovine serum albumin (20% v/v) and lysozyme (2 g/L) diluted in PBS at 37 °C for 24 h, without shaking. When we compared the CL types under the same conditions, the strongest biofilms according to their cell density, were formed on Pure Vision ≥ Softens 38 > Acuve 2 ∼ Softens Toric CLs. When we compared the used CLs with the new ones, a significant increase at the density of biofilms on the used CLs was observed. The most active MPS against P. aeruginosa and S. aureus biofilms at 24 h was Opti-Free followed by Bio-True and Renu according to the TKC analyses. In addition, the most active MPS against C. albicans was Renu followed by Opti-Free and Bio-True at 48 h. None of the MPSs showed 3 Log bactericidal/fungicidal activity, except for Opti-Free against S. aureus and P. aeruginosa biofilms during 6 h contact time. Moreover, all studied antibiotic eye drops were active against S. aureus and P. aeruginosa biofilms on CLs at 6 h and 24 h either directly or as 1/10 concentration, respectively. According to the results of the study, anti-biofilm activities of M…
format: application/pdf
format: text/html
creator: Sibel Dosler
creator: Mayram Hacioglu
creator: Fatima Nur Yilmaz
creator: Ozlem Oyardi
subject: Microbiology
subject: Ophthalmology
description: doi:10.7717/peerj.9419
publisher: PeerJ Inc.
rights: © 2020 Dosler et al.
abstract: During the contact lens (CL) usage, microbial adhesion and biofilm formation are crucial threats for eye health due to the development of mature biofilms on CL surfaces associated with serious eye infections such as keratitis. For CL related eye infections, multi drug resistant Pseudomonas aeruginosa or Staphylococcus aureus (especially MRSA) and Candida albicans are the most common infectious bacteria and yeast, respectively. In this study, CL biofilm models were created by comparing them to reveal the differences on specific conditions. Then the anti-biofilm activities of some commercially available multipurpose CL solutions (MPSs) and antibiotic eye drops against mature biofilms of S. aureus, P. aeruginosa, and C. albicans standard and clinical strains were determined by the time killing curve (TKC) method at 6, 24 and 48 h. According to the biofilm formation models, the optimal biofilms occurred in a mixture of bovine serum albumin (20% v/v) and lysozyme (2 g/L) diluted in PBS at 37 °C for 24 h, without shaking. When we compared the CL types under the same conditions, the strongest biofilms according to their cell density, were formed on Pure Vision ≥ Softens 38 > Acuve 2 ∼ Softens Toric CLs. When we compared the used CLs with the new ones, a significant increase at the density of biofilms on the used CLs was observed. The most active MPS against P. aeruginosa and S. aureus biofilms at 24 h was Opti-Free followed by Bio-True and Renu according to the TKC analyses. In addition, the most active MPS against C. albicans was Renu followed by Opti-Free and Bio-True at 48 h. None of the MPSs showed 3 Log bactericidal/fungicidal activity, except for Opti-Free against S. aureus and P. aeruginosa biofilms during 6 h contact time. Moreover, all studied antibiotic eye drops were active against S. aureus and P. aeruginosa biofilms on CLs at 6 h and 24 h either directly or as 1/10 concentration, respectively. According to the results of the study, anti-biofilm activities of M…
bibliographic citation: Dosler et al. (2020) Biofilm modelling on the contact lenses and comparison of the in vitro activities of multipurpose lens solutions and antibiotics. PeerJ 8:e9419 https://doi.org/10.7717/peerj.9419
date submitted: 2019-05-31
date accepted: 2020-06-03
issued: 2020-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dosler
  given name: Sibel
author list: Agent
  family name: Hacioglu
  given name: Mayram
author list: Agent
  family name: Yilmaz
  given name: Fatima Nur
author list: Agent
  family name: Oyardi
  given name: Ozlem
doi: 10.7717/peerj.9419
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-24
copyright: ©2020 Dosler et al.
attribution name: Dosler et al.

A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands
type: item
type: AcademicArticle
description: We describe a new, medium-sized species of terrestrial frog of the genus Phrynopus from a single locality in the central Andes of Peru (Departamento de Huánuco) at 3,730 meters of elevation. Phylogenetic analyses supported Phrynopus remotum sp. nov. as an independent lineage, sister to most of its congeners. The new species is morphologically distinguishable by the presence of small tubercles on upper eyelids and heels, an areolate venter, and the absence of dorsolateral folds or ridges. This species inhabits the highlands adjacent to the Marañón Dry valley. The only sympatric amphibian species recorded is the marsupial frog Gastrotheca peruana.
format: application/pdf
format: text/html
creator: Germán Chávez
creator: Luis Alberto García Ayachi
creator: Alessandro Catenazzi
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9433
publisher: PeerJ Inc.
rights: © 2020 Chávez et al.
abstract: We describe a new, medium-sized species of terrestrial frog of the genus Phrynopus from a single locality in the central Andes of Peru (Departamento de Huánuco) at 3,730 meters of elevation. Phylogenetic analyses supported Phrynopus remotum sp. nov. as an independent lineage, sister to most of its congeners. The new species is morphologically distinguishable by the presence of small tubercles on upper eyelids and heels, an areolate venter, and the absence of dorsolateral folds or ridges. This species inhabits the highlands adjacent to the Marañón Dry valley. The only sympatric amphibian species recorded is the marsupial frog Gastrotheca peruana.
bibliographic citation: Chávez et al. (2020) A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands. PeerJ 8:e9433 https://doi.org/10.7717/peerj.9433
date submitted: 2020-04-13
date accepted: 2020-06-06
issued: 2020-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chávez
  given name: Germán
author list: Agent
  family name: García Ayachi
  given name: Luis Alberto
author list: Agent
  family name: Catenazzi
  given name: Alessandro
doi: 10.7717/peerj.9433
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-24
copyright: ©2020 Chávez et al.
attribution name: Chávez et al.

A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil
type: item
type: AcademicArticle
description: The known diversity of treefrogs of the genus Phyllodytes has rapidly increased in recent years, currently comprising 14 species. Recent field work in the Atlantic Rainforest of the state of Bahia lead to the discovery of a new large species of Phyllodytes which is herein described based on multiple evidence including morphological, acoustical and genetic data. Phyllodytes sp. nov. is one of the largest species within the genus and presents immaculate yellowish dorsum and limbs. The advertisement call of the species is composed of 7–31 notes (half pulsed/pulsatile-half harmonic) with frequency-modulated harmonics. Phyllodytes sp. nov. has a karyotype of 2n = 22 chromosomes, as also found in other species of the genus. Genetic distance values of the 16S mitochondrial rRNA among Phyllodytes sp. nov. and its congeners range between 6.4 to 10.2%. The description of another new species for this state reinforces the need for further taxonomic work with Phyllodytes in this region that has been revealed as a priority area for research and conservation of this genus.
format: application/pdf
format: text/html
creator: Iuri R. Dias
creator: Gabriel Novaes-e-Fagundes
creator: Antonio Mollo Neto
creator: Juliana Zina
creator: Caroline Garcia
creator: Renato Sousa Recoder
creator: Francisco Dal Vechio
creator: Miguel Trefaut Rodrigues
creator: Mirco Solé
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8642
publisher: PeerJ Inc.
rights: © 2020 Dias et al.
abstract: The known diversity of treefrogs of the genus Phyllodytes has rapidly increased in recent years, currently comprising 14 species. Recent field work in the Atlantic Rainforest of the state of Bahia lead to the discovery of a new large species of Phyllodytes which is herein described based on multiple evidence including morphological, acoustical and genetic data. Phyllodytes sp. nov. is one of the largest species within the genus and presents immaculate yellowish dorsum and limbs. The advertisement call of the species is composed of 7–31 notes (half pulsed/pulsatile-half harmonic) with frequency-modulated harmonics. Phyllodytes sp. nov. has a karyotype of 2n = 22 chromosomes, as also found in other species of the genus. Genetic distance values of the 16S mitochondrial rRNA among Phyllodytes sp. nov. and its congeners range between 6.4 to 10.2%. The description of another new species for this state reinforces the need for further taxonomic work with Phyllodytes in this region that has been revealed as a priority area for research and conservation of this genus.
bibliographic citation: Dias et al. (2020) A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil. PeerJ 8:e8642 https://doi.org/10.7717/peerj.8642
date submitted: 2019-09-18
date accepted: 2020-01-27
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dias
  given name: Iuri R.
author list: Agent
  family name: Novaes-e-Fagundes
  given name: Gabriel
author list: Agent
  family name: Neto
  given name: Antonio Mollo
author list: Agent
  family name: Zina
  given name: Juliana
author list: Agent
  family name: Garcia
  given name: Caroline
author list: Agent
  family name: Recoder
  given name: Renato Sousa
author list: Agent
  family name: Vechio
  given name: Francisco Dal
author list: Agent
  family name: Rodrigues
  given name: Miguel Trefaut
author list: Agent
  family name: Solé
  given name: Mirco
doi: 10.7717/peerj.8642
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: ©2020 Dias et al.
attribution name: Dias et al.

Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau
type: item
type: AcademicArticle
description: Background Stoichiometric relations drive powerful constraints in several fundamental ecosystem processes. However, limited studies have been conducted on the ecological stoichiometry of plants after the change of community composition induced by Stellera chamaejasme removal in alpine grassland in the Qinghai–Tibetan Plateau. Methods We investigated the effects of S. chamaejasme removal on ecological stoichiometry by estimating the C:N:P stoichiometry in species, functional group and community levels of the ecosystem. The interactions between different species, functional groups and correlation with soil nutrient, responding to S. chamaejasme removal were also analyzed. Results For the plants that became dominant after S. chamaejasme removal (SR), N content decreased and their C:N increased. S. chamaejasme removal significantly affected the nutrient stoichiometry of different functional groups. Specifically, Gramineae in the SR sites had decreased N content and N:P, and increased C:N; however, forbs had increased N content, C:P and N:P and decreased P content and C:N. At the community level, N content was lower and C:N higher in SR communities compared to CK. The N content of the plant community was positively correlated with soil total N content. S. chamaejasme removal could change the nutrient balance from species level, to functional group level, and to community level. Thus, supplementary measures might be cooperated with S. chamaejasme removal for the recovery of S. chamaejasme-dominated degraded grassland. These results provide insight into the role of S. chamaejasme in ecological protection and conservation, and the conclusions from this study could be used to develop effective and sustainable measures for S. chamaejasme control in the Qinghai–Tibetan Plateau.
format: application/pdf
format: text/html
creator: Meiling Song
creator: Yuqin Wang
creator: Gensheng Bao
creator: Hongsheng Wang
creator: Yali Yin
creator: Xiuzhang Li
creator: Chunping Zhang
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
description: doi:10.7717/peerj.9239
publisher: PeerJ Inc.
rights: © 2020 Song et al.
abstract: Background Stoichiometric relations drive powerful constraints in several fundamental ecosystem processes. However, limited studies have been conducted on the ecological stoichiometry of plants after the change of community composition induced by Stellera chamaejasme removal in alpine grassland in the Qinghai–Tibetan Plateau. Methods We investigated the effects of S. chamaejasme removal on ecological stoichiometry by estimating the C:N:P stoichiometry in species, functional group and community levels of the ecosystem. The interactions between different species, functional groups and correlation with soil nutrient, responding to S. chamaejasme removal were also analyzed. Results For the plants that became dominant after S. chamaejasme removal (SR), N content decreased and their C:N increased. S. chamaejasme removal significantly affected the nutrient stoichiometry of different functional groups. Specifically, Gramineae in the SR sites had decreased N content and N:P, and increased C:N; however, forbs had increased N content, C:P and N:P and decreased P content and C:N. At the community level, N content was lower and C:N higher in SR communities compared to CK. The N content of the plant community was positively correlated with soil total N content. S. chamaejasme removal could change the nutrient balance from species level, to functional group level, and to community level. Thus, supplementary measures might be cooperated with S. chamaejasme removal for the recovery of S. chamaejasme-dominated degraded grassland. These results provide insight into the role of S. chamaejasme in ecological protection and conservation, and the conclusions from this study could be used to develop effective and sustainable measures for S. chamaejasme control in the Qinghai–Tibetan Plateau.
bibliographic citation: Song et al. (2020) Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau. PeerJ 8:e9239 https://doi.org/10.7717/peerj.9239
date submitted: 2019-11-14
date accepted: 2020-05-05
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Meiling
author list: Agent
  family name: Wang
  given name: Yuqin
author list: Agent
  family name: Bao
  given name: Gensheng
author list: Agent
  family name: Wang
  given name: Hongsheng
author list: Agent
  family name: Yin
  given name: Yali
author list: Agent
  family name: Li
  given name: Xiuzhang
author list: Agent
  family name: Zhang
  given name: Chunping
doi: 10.7717/peerj.9239
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Song et al.
attribution name: Song et al.

Modelling of climate change impact on flow conditions in the lowland anastomosing river
type: item
type: AcademicArticle
description: The progressive degradation of freshwater ecosystems worldwide requires action to be taken for their conservation. Nowadays, protection strategies need to step beyond the traditional approach of managing protected areas as they have to deal with the protection or recovery of natural flow regimes disrupted by the effects of future climate conditions. Climate change affects the hydrosphere at catchment scale altering hydrological processes which in turn impact hydrodynamics at the river reach scale. Therefore, conservation strategies should consider mathematical models, which allow for an improved understanding of ecosystem functions and their interactions across different spatial and temporal scales. This study focuses on an anastomosing river system in north-eastern Poland, where in recent decades a significant loss of the anabranches has been observed. The objective was to assess the impact of projected climate change on average flow conditions in the anastomosing section of the Narew River. The Soil and Water Assessment Tool (SWAT software) for the Narew catchment was coupled with the HEC-RAS one-dimensional unsteady flow model. The study looked into projected changes for two future time horizons 2021–2050 and 2071–2100 under the Representative Concentration Pathway 4.5 using an ensemble of nine EURO-CORDEX model scenarios. Results show that low flow conditions in the anastomosing section of the Narew National Park will remain relatively stable in 2021–2050 compared to current conditions and will slightly increase in 2071–2100. Duration of low flows, although projected to decrease on an annual basis, will increase for August–October, when the loss on anastomoses was found to be the most intense. Hydraulic modeling indicated extremely low flow velocities in the anastomosing arm (<0.1 m/s) nowadays and under future projections which is preferable for in-stream vegetation development and their gradual sedimentation and closure.
format: application/pdf
format: text/html
creator: Paweł Marcinkowski
creator: Dorota Mirosław-Świątek
subject: Climate Change Biology
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9275
publisher: PeerJ Inc.
rights: © 2020 Marcinkowski and Mirosław-Świątek
abstract: The progressive degradation of freshwater ecosystems worldwide requires action to be taken for their conservation. Nowadays, protection strategies need to step beyond the traditional approach of managing protected areas as they have to deal with the protection or recovery of natural flow regimes disrupted by the effects of future climate conditions. Climate change affects the hydrosphere at catchment scale altering hydrological processes which in turn impact hydrodynamics at the river reach scale. Therefore, conservation strategies should consider mathematical models, which allow for an improved understanding of ecosystem functions and their interactions across different spatial and temporal scales. This study focuses on an anastomosing river system in north-eastern Poland, where in recent decades a significant loss of the anabranches has been observed. The objective was to assess the impact of projected climate change on average flow conditions in the anastomosing section of the Narew River. The Soil and Water Assessment Tool (SWAT software) for the Narew catchment was coupled with the HEC-RAS one-dimensional unsteady flow model. The study looked into projected changes for two future time horizons 2021–2050 and 2071–2100 under the Representative Concentration Pathway 4.5 using an ensemble of nine EURO-CORDEX model scenarios. Results show that low flow conditions in the anastomosing section of the Narew National Park will remain relatively stable in 2021–2050 compared to current conditions and will slightly increase in 2071–2100. Duration of low flows, although projected to decrease on an annual basis, will increase for August–October, when the loss on anastomoses was found to be the most intense. Hydraulic modeling indicated extremely low flow velocities in the anastomosing arm (<0.1 m/s) nowadays and under future projections which is preferable for in-stream vegetation development and their gradual sedimentation and closure.
bibliographic citation: Marcinkowski et al. (2020) Modelling of climate change impact on flow conditions in the lowland anastomosing river. PeerJ 8:e9275 https://doi.org/10.7717/peerj.9275
date submitted: 2019-12-11
date accepted: 2020-05-11
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marcinkowski
  given name: Paweł
author list: Agent
  family name: Mirosław-Świątek
  given name: Dorota
doi: 10.7717/peerj.9275
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Marcinkowski and Mirosław-Świątek
attribution name: Marcinkowski and Mirosław-Świątek

Feasibility of a smartphone app to enhance physical activity in progressive MS: a pilot randomized controlled pilot trial over three months
type: item
type: AcademicArticle
description: Background People with chronic progressive multiple sclerosis (CPMS) have limited options in medical treatment. Enhancing physical activity (PA) might promote neuroregeneration in multiple sclerosis (MS) and positively influence disability, thus providing an alternative to medical treatment. Previous studies indicate that evidence-based patient information (EBPI) is essential for inducing behavioral change, e.g. enhancing PA. Objective To investigate feasibility of a smartphone app providing EBPI about the benefit of PA and a simple activity feedback to enhance PA in people with CPMS in a pilot randomized controlled trial over 3 months. Methods Thirty-eight people with CPMS (mean age 51 years, median Expanded Disability Status Scale 4.0) were 1:1 randomized into either a control group (n = 20) or an intervention group (n = 18). The intervention group received access to a multimedia EBPI app including activity feedback, texts, figures and videos. In the control group, participants received a leaflet with unspecific information about exercising in general. The EPBI itself was designed based on a systematic review. At baseline and after 3 months, all participants underwent clinical performance tests, filled in questionnaires and received an activity monitor (Actigraph®) for 7 days. The primary endpoint was the rate of responders defined as participants with a 20% increase of physical acitivity (time of moderate or vigiorous PA—MVPA) or 20% increase of the number of steps, both assessed with the activity monitor. As secondary endpoints, we compared accelerometry, performance and questionnaires adjusted for baseline measurments between the groups (ANCOVA). Moreover, we used questionnaires to compare knowledge about exercise (activity requiring physical effort, carried out to improve or improve health and fitness) in MS, usability of the app in general and motivation towards a more active lifestyle after 3 months in both groups. Results The groups showed significant diffe…
format: application/pdf
format: text/html
creator: Navina N. Nasseri
creator: Eghbal Ghezelbash
creator: Yuyang Zhai
creator: Stefan Patra
creator: Karin Riemann-Lorenz
creator: Christoph Heesen
creator: Anne C. Rahn
creator: Jan-Patrick Stellmann
subject: Clinical Trials
subject: Neurology
description: doi:10.7717/peerj.9303
publisher: PeerJ Inc.
rights: © 2020 Nasseri et al.
abstract: Background People with chronic progressive multiple sclerosis (CPMS) have limited options in medical treatment. Enhancing physical activity (PA) might promote neuroregeneration in multiple sclerosis (MS) and positively influence disability, thus providing an alternative to medical treatment. Previous studies indicate that evidence-based patient information (EBPI) is essential for inducing behavioral change, e.g. enhancing PA. Objective To investigate feasibility of a smartphone app providing EBPI about the benefit of PA and a simple activity feedback to enhance PA in people with CPMS in a pilot randomized controlled trial over 3 months. Methods Thirty-eight people with CPMS (mean age 51 years, median Expanded Disability Status Scale 4.0) were 1:1 randomized into either a control group (n = 20) or an intervention group (n = 18). The intervention group received access to a multimedia EBPI app including activity feedback, texts, figures and videos. In the control group, participants received a leaflet with unspecific information about exercising in general. The EPBI itself was designed based on a systematic review. At baseline and after 3 months, all participants underwent clinical performance tests, filled in questionnaires and received an activity monitor (Actigraph®) for 7 days. The primary endpoint was the rate of responders defined as participants with a 20% increase of physical acitivity (time of moderate or vigiorous PA—MVPA) or 20% increase of the number of steps, both assessed with the activity monitor. As secondary endpoints, we compared accelerometry, performance and questionnaires adjusted for baseline measurments between the groups (ANCOVA). Moreover, we used questionnaires to compare knowledge about exercise (activity requiring physical effort, carried out to improve or improve health and fitness) in MS, usability of the app in general and motivation towards a more active lifestyle after 3 months in both groups. Results The groups showed significant diffe…
bibliographic citation: Nasseri et al. (2020) Feasibility of a smartphone app to enhance physical activity in progressive MS: a pilot randomized controlled pilot trial over three months. PeerJ 8:e9303 https://doi.org/10.7717/peerj.9303
date submitted: 2019-10-21
date accepted: 2020-05-15
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nasseri
  given name: Navina N.
author list: Agent
  family name: Ghezelbash
  given name: Eghbal
author list: Agent
  family name: Zhai
  given name: Yuyang
author list: Agent
  family name: Patra
  given name: Stefan
author list: Agent
  family name: Riemann-Lorenz
  given name: Karin
author list: Agent
  family name: Heesen
  given name: Christoph
author list: Agent
  family name: Rahn
  given name: Anne C.
author list: Agent
  family name: Stellmann
  given name: Jan-Patrick
doi: 10.7717/peerj.9303
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: © 2020 Nasseri et al.
attribution name: Nasseri et al.

Longitudinal relationships between changes in body composition and changes in selected metabolic risk factors (abdominal obesity and blood pressure) among South African adolescents
type: item
type: AcademicArticle
description: Background Incidence of childhood high blood pressure (BP) is increasing worldwide. This study examined the longitudinal relationship between changes in body composition (i.e. body mass index (BMI), waist circumference (WC) and percentage body fat) and selected metabolic risk factors (abdominal obesity and BP) among adolescents from the Tlokwe municipality in the North West Province of South Africa. Method One hundred and eight-six adolescents (81 boys and 105 girls) aged 14 to 16 years participated in the study. Body composition was measured following the International Society of the Advancement of Kinanthropometry standard procedures. BMI, abdominal obesity using WC measurement, and resting BP were determined. Analysis of variance (ANOVA) for repeated measures was calculated to determine changes in anthropometric measures and body composition as well as changes in BP. Additionally, Univariate analysis of variance with repeated measures and participants as a random sample was applied. Diastolic BP (DBP) and systolic BP (SBP) were used as dependent variables and sex, age, BMI, WC, and waist-to-height ratio as independent variables. Results Significant changes were found for stature, BMI, body mass, WC, SBP, and DBP. BMI for the total group was significant and positively related to abdominal obesity in 2012 (r = 0.55; p < 0.01) and in 2013 (r = 0.77; p < 0.01) and to SBP (r = 0.26; p < 0.05) in 2012 and (r = 0.17; p = 0.43) in 2013. BMI among the boys was significantly and positively related to abdominal obesity in 2012 (r = 0.83; p < 0.01) and 2013 (r = 0.91; p < 0.01). For the girls, BMI was significantly and positively related to abdominal obesity (r = 0.49; p < 0.01) and to SBP (r = 0.32; p = 0.05) in 2012. Boys with a higher WC in 2012 had significantly increased DBP (p < 0.05). Boys measured in 2012 with greater WC and BMI show a significant increase in SBP. Conclusions BMI was positively related to BP and abdominal obesity over time. Relatively high BMI and ab…
format: application/pdf
format: text/html
creator: Vincent Masocha
creator: Makama Andries Monyeki
creator: Stanisław H. Czyż
subject: Pediatrics
subject: Public Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.9331
publisher: PeerJ Inc.
rights: © 2020 Masocha et al.
abstract: Background Incidence of childhood high blood pressure (BP) is increasing worldwide. This study examined the longitudinal relationship between changes in body composition (i.e. body mass index (BMI), waist circumference (WC) and percentage body fat) and selected metabolic risk factors (abdominal obesity and BP) among adolescents from the Tlokwe municipality in the North West Province of South Africa. Method One hundred and eight-six adolescents (81 boys and 105 girls) aged 14 to 16 years participated in the study. Body composition was measured following the International Society of the Advancement of Kinanthropometry standard procedures. BMI, abdominal obesity using WC measurement, and resting BP were determined. Analysis of variance (ANOVA) for repeated measures was calculated to determine changes in anthropometric measures and body composition as well as changes in BP. Additionally, Univariate analysis of variance with repeated measures and participants as a random sample was applied. Diastolic BP (DBP) and systolic BP (SBP) were used as dependent variables and sex, age, BMI, WC, and waist-to-height ratio as independent variables. Results Significant changes were found for stature, BMI, body mass, WC, SBP, and DBP. BMI for the total group was significant and positively related to abdominal obesity in 2012 (r = 0.55; p < 0.01) and in 2013 (r = 0.77; p < 0.01) and to SBP (r = 0.26; p < 0.05) in 2012 and (r = 0.17; p = 0.43) in 2013. BMI among the boys was significantly and positively related to abdominal obesity in 2012 (r = 0.83; p < 0.01) and 2013 (r = 0.91; p < 0.01). For the girls, BMI was significantly and positively related to abdominal obesity (r = 0.49; p < 0.01) and to SBP (r = 0.32; p = 0.05) in 2012. Boys with a higher WC in 2012 had significantly increased DBP (p < 0.05). Boys measured in 2012 with greater WC and BMI show a significant increase in SBP. Conclusions BMI was positively related to BP and abdominal obesity over time. Relatively high BMI and ab…
bibliographic citation: Masocha et al. (2020) Longitudinal relationships between changes in body composition and changes in selected metabolic risk factors (abdominal obesity and blood pressure) among South African adolescents. PeerJ 8:e9331 https://doi.org/10.7717/peerj.9331
date submitted: 2020-01-28
date accepted: 2020-05-19
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masocha
  given name: Vincent
author list: Agent
  family name: Monyeki
  given name: Makama Andries
author list: Agent
  family name: Czyż
  given name: Stanisław H.
doi: 10.7717/peerj.9331
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23
copyright: ©2020 Masocha et al.
attribution name: Masocha et al.

Marsupial and monotreme milk—a review of its nutrient and immune properties
type: item
type: AcademicArticle
description: All mammals are characterized by the ability of females to produce milk. Marsupial (metatherian) and monotreme (prototherian) young are born in a highly altricial state and rely on their mother’s milk for the first part of their life. Here we review the role and importance of milk in marsupial and monotreme development. Milk is the primary source of sustenance for young marsupials and monotremes and its composition varies at different stages of development. We applied nutritional geometry techniques to a limited number of species with values available to analyze changes in macronutrient composition of milk at different stages. Macronutrient energy composition of marsupial milk varies between species and changes concentration during the course of lactation. As well as nourishment, marsupial and monotreme milk supplies growth and immune factors. Neonates are unable to mount a specific immune response shortly after birth and therefore rely on immunoglobulins, immunological cells and other immunologically important molecules transferred through milk. Milk is also essential to the development of the maternal-young bond and is achieved through feedback systems and odor preferences in eutherian mammals. However, we have much to learn about the role of milk in marsupial and monotreme mother-young bonding. Further research is warranted in gaining a better understanding of the role of milk as a source of nutrition, developmental factors and immunity, in a broader range of marsupial species, and monotremes.
format: application/pdf
format: text/html
creator: Hayley J. Stannard
creator: Robert D. Miller
creator: Julie M. Old
subject: Biochemistry
subject: Zoology
subject: Immunology
subject: Nutrition
description: doi:10.7717/peerj.9335
publisher: PeerJ Inc.
rights: © 2020
abstract: All mammals are characterized by the ability of females to produce milk. Marsupial (metatherian) and monotreme (prototherian) young are born in a highly altricial state and rely on their mother’s milk for the first part of their life. Here we review the role and importance of milk in marsupial and monotreme development. Milk is the primary source of sustenance for young marsupials and monotremes and its composition varies at different stages of development. We applied nutritional geometry techniques to a limited number of species with values available to analyze changes in macronutrient composition of milk at different stages. Macronutrient energy composition of marsupial milk varies between species and changes concentration during the course of lactation. As well as nourishment, marsupial and monotreme milk supplies growth and immune factors. Neonates are unable to mount a specific immune response shortly after birth and therefore rely on immunoglobulins, immunological cells and other immunologically important molecules transferred through milk. Milk is also essential to the development of the maternal-young bond and is achieved through feedback systems and odor preferences in eutherian mammals. However, we have much to learn about the role of milk in marsupial and monotreme mother-young bonding. Further research is warranted in gaining a better understanding of the role of milk as a source of nutrition, developmental factors and immunity, in a broader range of marsupial species, and monotremes.
bibliographic citation: Stannard et al. (2020) Marsupial and monotreme milk—a review of its nutrient and immune properties. PeerJ 8:e9335 https://doi.org/10.7717/peerj.9335
date submitted: 2020-03-30
date accepted: 2020-05-20
issued: 2020-06-23
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Stannard
  given name: Hayley J.
author list: Agent
  family name: Miller
  given name: Robert D.
author list: Agent
  family name: Old
  given name: Julie M.
doi: 10.7717/peerj.9335
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-23

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