PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bird-window collisions: Mitigation efficacy and risk factors across two years
items: Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli
items: Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia
items: Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum)
items: A new HSI denoising method via interpolated block matching 3D and guided filter
items: Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication
items: MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions
items: Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan
items: Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study
items: ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review

Bird-window collisions: Mitigation efficacy and risk factors across two years
type: item
type: AcademicArticle
description: Background Research on bird-window collision mitigation is needed to prevent up to a billion bird fatalities yearly in the U.S. At the University of Utah campus (Salt Lake City, Utah, USA), past research documented collisions, especially for Cedar Waxwings (Bombycilla cedrorum) drawn to fruiting ornamental pears in winter. Mirrored windows, which have a metallic coating that turns window exteriors into mirrors, had frequent collisions, which were mitigated when Feather Friendly®bird deterrent markers were applied. Bird-friendly windows–ORNILUX®ultraviolet (UV) and fritted windows–also reduced collisions when data were collected across fall and winter. Extending this prior research, we evaluated additional mitigation and tested the replicability of effects for pear trees, mirrored windows, and bird-friendly windows across two years. Methods Using published data from eight buildings monitored for collisions in year 1 (Fall and Winter, 2019–2020), we added another year of monitoring, Fall and Winter, 2020–2021. Between years, Feather Friendly®mitigation markers were added to collision-prone areas of two buildings, including both mirrored and transparent windows. Results The two buildings that received new Feather Friendly®mitigation had significantly fewer collisions post-mitigation. Control areas also had nonsignificant decline in collisions. The interaction of area (mitigation vs. control) by time (year 1 vs. 2) was significant, based on generalized estimating equations (GEE). The total yearly collisions across all eight buildings declined from 39 to 23. A second GEE analysis of all 8 buildings showed that mirrored windows, pear trees, and bird-friendly windows were each significant when analyzed separately. The best-fit model showed more collisions for mirrored windows and fewer collisions for bird-friendly windows. We found pear tree proximity to be related to more collisions in winter than fall. In addition, pear trees showed reduced collisions from year 1 to 2, c…
format: application/pdf
format: text/html
creator: Barbara B. Brown
creator: Sabrina Santos
creator: Natalia Ocampo-Peñuela
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.11867
publisher: PeerJ Inc.
rights: © 2021 Brown et al.
abstract: Background Research on bird-window collision mitigation is needed to prevent up to a billion bird fatalities yearly in the U.S. At the University of Utah campus (Salt Lake City, Utah, USA), past research documented collisions, especially for Cedar Waxwings (Bombycilla cedrorum) drawn to fruiting ornamental pears in winter. Mirrored windows, which have a metallic coating that turns window exteriors into mirrors, had frequent collisions, which were mitigated when Feather Friendly®bird deterrent markers were applied. Bird-friendly windows–ORNILUX®ultraviolet (UV) and fritted windows–also reduced collisions when data were collected across fall and winter. Extending this prior research, we evaluated additional mitigation and tested the replicability of effects for pear trees, mirrored windows, and bird-friendly windows across two years. Methods Using published data from eight buildings monitored for collisions in year 1 (Fall and Winter, 2019–2020), we added another year of monitoring, Fall and Winter, 2020–2021. Between years, Feather Friendly®mitigation markers were added to collision-prone areas of two buildings, including both mirrored and transparent windows. Results The two buildings that received new Feather Friendly®mitigation had significantly fewer collisions post-mitigation. Control areas also had nonsignificant decline in collisions. The interaction of area (mitigation vs. control) by time (year 1 vs. 2) was significant, based on generalized estimating equations (GEE). The total yearly collisions across all eight buildings declined from 39 to 23. A second GEE analysis of all 8 buildings showed that mirrored windows, pear trees, and bird-friendly windows were each significant when analyzed separately. The best-fit model showed more collisions for mirrored windows and fewer collisions for bird-friendly windows. We found pear tree proximity to be related to more collisions in winter than fall. In addition, pear trees showed reduced collisions from year 1 to 2, c…
bibliographic citation: Brown et al. (2021) Bird-window collisions: Mitigation efficacy and risk factors across two years. PeerJ 9:e11867 https://doi.org/10.7717/peerj.11867
date submitted: 2021-05-10
date accepted: 2021-07-05
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Barbara B.
author list: Agent
  family name: Santos
  given name: Sabrina
author list: Agent
  family name: Ocampo-Peñuela
  given name: Natalia
doi: 10.7717/peerj.11867
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Brown et al.
attribution name: Brown et al.

Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli
type: item
type: AcademicArticle
description: Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quant…
format: application/pdf
format: text/html
creator: Keiji Nakamura
creator: Chikashi Tokuda
creator: Hideyuki Arimitsu
creator: Yoshiki Etoh
creator: Mitsuhiro Hamasaki
creator: Yuichiro Deguchi
creator: Itsuki Taniguchi
creator: Yasuhiro Gotoh
creator: Yoshitoshi Ogura
creator: Tetsuya Hayashi
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.11871
publisher: PeerJ Inc.
rights: © 2021 Nakamura et al.
abstract: Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quant…
bibliographic citation: Nakamura et al. (2021) Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli. PeerJ 9:e11871 https://doi.org/10.7717/peerj.11871
date submitted: 2021-04-20
date accepted: 2021-07-06
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakamura
  given name: Keiji
author list: Agent
  family name: Tokuda
  given name: Chikashi
author list: Agent
  family name: Arimitsu
  given name: Hideyuki
author list: Agent
  family name: Etoh
  given name: Yoshiki
author list: Agent
  family name: Hamasaki
  given name: Mitsuhiro
author list: Agent
  family name: Deguchi
  given name: Yuichiro
author list: Agent
  family name: Taniguchi
  given name: Itsuki
author list: Agent
  family name: Gotoh
  given name: Yasuhiro
author list: Agent
  family name: Ogura
  given name: Yoshitoshi
author list: Agent
  family name: Hayashi
  given name: Tetsuya
doi: 10.7717/peerj.11871
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: © 2021 Nakamura et al.
attribution name: Nakamura et al.

Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia
type: item
type: AcademicArticle
description: This study aimed to reveal the habitat variables that determine the distribution and abundance of the land snail Pollicaria elephas in limestone habitats in Perak, Malaysia. Seventeen plots were selected on a limestone hill to determine the effect of environmental variables on the abundance of this land snail. The environmental variables we considered included habitat (canopy cover and leaf litter thickness), topography (elevation, aspect, ruggedness, and slope), microclimate (soil temperature, air temperature, and humidity), and vegetation (abundance of respective vascular plant species). The correlation analyses suggested that the snails’ abundance was positively correlated with the abundance of the four vascular plant species: Diospyros toposia var. toposoides, Croton cascarilloides, Kibatalia laurifolia, and Mallotus peltatus. Plots with lower soil temperatures had more snails than plots with higher soil temperatures. Our results show that plots in the southern part of the limestone hill, in which P. elephas were absent, were similar in habitat, topography, microclimate, and vegetation to the plots in the northern part of the limestone hill, where specimens were mostly present. The absence of this species in suitable habitats may be due to their low dispersal ability rather than adverse environmental conditions.
format: application/pdf
format: text/html
creator: Thor-Seng Liew
creator: Chee-Chean Phung
creator: Mohamad Afandi Mat Said
creator: Pui Kiat Hoo
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11886
publisher: PeerJ Inc.
rights: © 2021 Liew et al.
abstract: This study aimed to reveal the habitat variables that determine the distribution and abundance of the land snail Pollicaria elephas in limestone habitats in Perak, Malaysia. Seventeen plots were selected on a limestone hill to determine the effect of environmental variables on the abundance of this land snail. The environmental variables we considered included habitat (canopy cover and leaf litter thickness), topography (elevation, aspect, ruggedness, and slope), microclimate (soil temperature, air temperature, and humidity), and vegetation (abundance of respective vascular plant species). The correlation analyses suggested that the snails’ abundance was positively correlated with the abundance of the four vascular plant species: Diospyros toposia var. toposoides, Croton cascarilloides, Kibatalia laurifolia, and Mallotus peltatus. Plots with lower soil temperatures had more snails than plots with higher soil temperatures. Our results show that plots in the southern part of the limestone hill, in which P. elephas were absent, were similar in habitat, topography, microclimate, and vegetation to the plots in the northern part of the limestone hill, where specimens were mostly present. The absence of this species in suitable habitats may be due to their low dispersal ability rather than adverse environmental conditions.
bibliographic citation: Liew et al. (2021) Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia. PeerJ 9:e11886 https://doi.org/10.7717/peerj.11886
date submitted: 2020-09-28
date accepted: 2021-07-09
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Phung
  given name: Chee-Chean
author list: Agent
  family name: Mat Said
  given name: Mohamad Afandi
author list: Agent
  family name: Hoo
  given name: Pui Kiat
doi: 10.7717/peerj.11886
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Liew et al.
attribution name: Liew et al.

Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum)
type: item
type: AcademicArticle
description: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density…
format: application/pdf
format: text/html
creator: Kennedy Judith Grant
creator: Lisa DeVetter
creator: Andony Melathopoulos
subject: Agricultural Science
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.11634
publisher: PeerJ Inc.
rights: © 2021 Grant et al.
abstract: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density…
bibliographic citation: Grant et al. (2021) Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum). PeerJ 9:e11634 https://doi.org/10.7717/peerj.11634
date submitted: 2021-02-11
date accepted: 2021-05-27
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grant
  given name: Kennedy Judith
author list: Agent
  family name: DeVetter
  given name: Lisa
author list: Agent
  family name: Melathopoulos
  given name: Andony
doi: 10.7717/peerj.11634
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Grant et al.
attribution name: Grant et al.

A new HSI denoising method via interpolated block matching 3D and guided filter
type: item
type: AcademicArticle
description: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs.
format: application/pdf
format: text/html
creator: Ping Xu
creator: Bingqiang Chen
creator: Jingcheng Zhang
creator: Lingyun Xue
creator: Lei Zhu
subject: Computational Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11642
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs.
bibliographic citation: Xu et al. (2021) A new HSI denoising method via interpolated block matching 3D and guided filter. PeerJ 9:e11642 https://doi.org/10.7717/peerj.11642
date submitted: 2019-01-17
date accepted: 2021-05-28
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Ping
author list: Agent
  family name: Chen
  given name: Bingqiang
author list: Agent
  family name: Zhang
  given name: Jingcheng
author list: Agent
  family name: Xue
  given name: Lingyun
author list: Agent
  family name: Zhu
  given name: Lei
doi: 10.7717/peerj.11642
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication
type: item
type: AcademicArticle
description: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
format: application/pdf
format: text/html
creator: Susana Marcela Simancas-Giraldo
creator: Nan Xiang
creator: Meghan Moger Kennedy
creator: Rassil Nafeh
creator: Edoardo Zelli
creator: Christian Wild
subject: Marine Biology
subject: Climate Change Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11663
publisher: PeerJ Inc.
rights: © 2021 Simancas-Giraldo et al.
abstract: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
bibliographic citation: Simancas-Giraldo et al. (2021) Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication. PeerJ 9:e11663 https://doi.org/10.7717/peerj.11663
date submitted: 2020-12-09
date accepted: 2021-06-01
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simancas-Giraldo
  given name: Susana Marcela
author list: Agent
  family name: Xiang
  given name: Nan
author list: Agent
  family name: Kennedy
  given name: Meghan Moger
author list: Agent
  family name: Nafeh
  given name: Rassil
author list: Agent
  family name: Zelli
  given name: Edoardo
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.11663
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Simancas-Giraldo et al.
attribution name: Simancas-Giraldo et al.

MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions
type: item
type: AcademicArticle
description: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.
format: application/pdf
format: text/html
creator: Xiaoying Wang
creator: Eva Cheng
creator: Ian S. Burnett
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Science
subject: Freshwater Biology
description: doi:10.7717/peerj.11750
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.
bibliographic citation: Wang et al. (2021) MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions. PeerJ 9:e11750 https://doi.org/10.7717/peerj.11750
date submitted: 2020-11-25
date accepted: 2021-06-19
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoying
author list: Agent
  family name: Cheng
  given name: Eva
author list: Agent
  family name: Burnett
  given name: Ian S.
doi: 10.7717/peerj.11750
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan
type: item
type: AcademicArticle
description: Background International and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan. Methods A total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires. Results On the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months post…
format: application/pdf
format: text/html
creator: Keiko Nanishi
creator: Joseph Green
creator: Hiroko Hongo
subject: Nursing
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.11779
publisher: PeerJ Inc.
rights: © 2021 Nanishi et al.
abstract: Background International and national organizations recommend exclusive breastfeeding for the first 6 months of life, but many women stop earlier. Lay and professional persons can support mothers’ efforts to overcome breastfeeding difficulties. Considering breastfeeding support to comprise emotional support, practical help, and information offered to women who desire to breastfeed (by professionals, family members, and others), we developed and tested a scale to measure it in Japan. Methods A total of 31 items were generated by literature review and from the authors’ clinical experiences. Those items were tested with 243 mothers who visited public health centers in Tokyo for their infant’s health check-up 3 months after birth. Breastfeeding support and infant feeding status were then assessed 5 months after birth. All the data were collected by using self-administered questionnaires. Results On the basis of the results of factor analysis, the number of items was reduced to 11. There were three factors: support from breastfeeding peers and from people in specifically named healthcare professions, practical help, and support from people the mother can rely on to help meet emotional needs and address breastfeeding concerns. Internal-consistency reliability (alpha) of scores on the 11-item scale was 0.83 when measured 3 months postpartum and 0.85 when measured 5 months postpartum. Higher scores on the 11-item scale 3 months postpartum were associated with more breastfeeding exclusivity both at that time (Kruskal–Wallis test, chi-squared = 14.871, df = 3, n = 211, p = 0.002, eta-squared = 0.071) and also 5 months postpartum (Kruskal–Wallis test, chi-squared = 8.556, df = 3, n = 159, p = 0.036, eta-squared = 0.054). Further, the area under the Receiver Operating Characteristic curve was 0.73 (95% CI [0.57–0.88]), which indicates that scores on the 11-item scale 3 months postpartum may be useful to predict which mothers will be less exclusive in breastfeeding 5 months post…
bibliographic citation: Nanishi et al. (2021) Development of the breastfeeding support scale to measure breastfeeding support from lay and professional persons, and its predictive validity in Japan. PeerJ 9:e11779 https://doi.org/10.7717/peerj.11779
date submitted: 2020-12-16
date accepted: 2021-06-24
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Nanishi
  given name: Keiko
author list: Agent
  family name: Green
  given name: Joseph
author list: Agent
  family name: Hongo
  given name: Hiroko
doi: 10.7717/peerj.11779
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: © 2021 Nanishi et al.
attribution name: Nanishi et al.

Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study
type: item
type: AcademicArticle
description: Background The relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly. Methods A case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected. Results Our study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001).
format: application/pdf
format: text/html
creator: Yunfang Zhou
creator: Zhenyu Ma
creator: Cun-Xian Jia
creator: Liang Zhou
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.11801
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Background The relationship between impulsivity and suicide is inconsistent in different populations. Hence, the relationship between impulsivity and suicide still needs to be studied among the elderly population. The present study intends to explore the relationship between impulsivity and suicide among the rural Chinese elderly. Methods A case-control psychological autopsy study was conducted from February 1, 2014 to December 18, 2015 among rural residents over the age of 60 who died by suicide. The sample consisted of 242 suicides as the case group and 242 living individuals as the control group. Data on demographic characteristics, impulsivity, previous history of suicide attempts, social support, negative life events, and suicidal behavior were collected. Results Our study found that impulsivity increased the risk of suicide. The case group showed a higher Barratt Impulsiveness Scale score compared with the control group (p < 0.001), which indicates that impulsivity was higher among the elderly suicides. In addition, regression analyses show that impulsivity (odds ratio: 1.03, 95% confidence interval: 1.01–1.06) is an independent risk factor of suicide, after controlling for the effects of marital status, education, family annual income, being left behind, social support, and negative life events. Finally, compared with elderly who do not have a history of attempted suicide, elderly with a history of attempted suicide showed higher impulsivity (p = 0.001).
bibliographic citation: Zhou et al. (2021) Relationship between impulsivity and suicide among the rural elderly in China: a case-control psychological autopsy study. PeerJ 9:e11801 https://doi.org/10.7717/peerj.11801
date submitted: 2020-07-24
date accepted: 2021-06-26
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yunfang
author list: Agent
  family name: Ma
  given name: Zhenyu
author list: Agent
  family name: Jia
  given name: Cun-Xian
author list: Agent
  family name: Zhou
  given name: Liang
doi: 10.7717/peerj.11801
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review
type: item
type: AcademicArticle
description: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker…
format: application/pdf
format: text/html
creator: Richard Dormatey
creator: Chao Sun
creator: Kazim Ali
creator: Sajid Fiaz
creator: Derong Xu
creator: Alejandro Calderón-Urrea
creator: Zhenzhen Bi
creator: Junlian Zhang
creator: Jiangping Bai
subject: Agricultural Science
subject: Biotechnology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.11809
publisher: PeerJ Inc.
rights: © 2021 Dormatey et al.
abstract: Antibiotic and herbicide resistance genes are the most common marker genes for plant transformation to improve crop yield and food quality. However, there is public concern about the use of resistance marker genes in food crops due to the risk of potential gene flow from transgenic plants to compatible weedy relatives, leading to the possible development of “superweeds” and antibiotic resistance. Several selectable marker genes such as aph, nptII, aaC3, aadA, pat, bar, epsp and gat, which have been synthesized to generate transgenic plants by genetic transformation, have shown some limitations. These marker genes, which confer antibiotic or herbicide resistance and are introduced into crops along with economically valuable genes, have three main problems: selective agents have negative effects on plant cell proliferation and differentiation, uncertainty about the environmental effects of many selectable marker genes, and difficulty in performing recurrent transformations with the same selectable marker to pyramid desired genes. Recently, a simple, novel, and affordable method was presented for plant cells to convert non-metabolizable phosphite (Phi) to an important phosphate (Pi) for developing cells by gene expression encoding a phosphite oxidoreductase (PTXD) enzyme. The ptxD gene, in combination with a selection medium containing Phi as the sole phosphorus (P) source, can serve as an effective and efficient system for selecting transformed cells. The selection system adds nutrients to transgenic plants without potential risks to the environment. The ptxD/Phi system has been shown to be a promising transgenic selection system with several advantages in cost and safety compared to other antibiotic-based selection systems. In this review, we have summarized the development of selection markers for genetic transformation and the potential use of the ptxD/Phi scheme as an alternative selection marker system to minimize the future use of antibiotic and herbicide marker…
bibliographic citation: Dormatey et al. (2021) ptxD/Phi as alternative selectable marker system for genetic transformation for bio-safety concerns: a review. PeerJ 9:e11809 https://doi.org/10.7717/peerj.11809
date submitted: 2020-12-15
date accepted: 2021-06-27
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dormatey
  given name: Richard
author list: Agent
  family name: Sun
  given name: Chao
author list: Agent
  family name: Ali
  given name: Kazim
author list: Agent
  family name: Fiaz
  given name: Sajid
author list: Agent
  family name: Xu
  given name: Derong
author list: Agent
  family name: Calderón-Urrea
  given name: Alejandro
author list: Agent
  family name: Bi
  given name: Zhenzhen
author list: Agent
  family name: Zhang
  given name: Junlian
author list: Agent
  family name: Bai
  given name: Jiangping
doi: 10.7717/peerj.11809
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Dormatey et al.
attribution name: Dormatey et al.

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