PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of no-tillage sowing on soil properties and forage wheat and Italian ryegrass yields in winter fallow paddy fields
items: Effects of dietary fennel (Foeniculum vulgare Mill.) seed powder supplementation on growth performance, nutrient digestibility, small intestinal morphology, and carcass traits of broilers
items: Effect of salt stress in urban conditions on two Acer species with different sensitivity
items: Evaluation of effective quantum yields of photosystem II for CO2 leakage monitoring in carbon capture and storage sites
items: Monomorium (Hymenoptera: Formicidae) of the Arabian Peninsula with description of two new species, M. heggyi sp. n. and M. khalidi sp. n.
items: Biological effects of electron beam to target turning X-ray (EBTTX) on two freesia (Freesia hybrida) cultivars
items: Metabolic impact of weight variations in Icelandic horses
items: Arithmetic processing in children with dyscalculia: an event-related potential study
items: Clinical relevance assessment of animal preclinical research (RAA) tool: development and explanation
items: Exploring a model-based analysis of patient derived xenograft studies in oncology drug development

Effects of no-tillage sowing on soil properties and forage wheat and Italian ryegrass yields in winter fallow paddy fields
type: item
type: AcademicArticle
description: In South China, it is common practice for the late rice (Oryza sativa) that is planted during the summer in the paddy fields after harvest to be used for fallowing or to plant winter forage crops. The land is ploughed before early rice planting. Both forage wheat (Triticum aestivum) and Italian ryegrass (Lolium multiflorum) have relatively high nutritional value, and planting them in winter fallow paddy fields could potentially address food shortages and provide quality forage for livestock. In this study, we examined the effects of no-tillage sowing 5 days before rice harvest (NB5), no-tillage sowing 1 day after rice harvest (NA1), and conventional tillage sowing (CK) 1 day after rice harvest on forage wheat and Italian ryegrass soil properties, dry matter (DM), and crude protein (CP) yields. Soil and plant samples were collected after three months of crop growth. The results showed that the NB5 and NA1 soil bulk density (0-20 cm soil layer) tended to increase when compared to that of the CK field. The NA1 treatment increased the total soil nitrogen and organic matter content. The enzyme activities and total soil porosity in the no-tillage forage wheat and Italian ryegrass fields tended to decrease, while the no-tillage water content and soil capillary porosity tended to increase when compared to that of the CK field. Overall, planting year significantly influenced soil chemical properties (except for total nitrogen) and enzyme activity, but crop type had no significant effect on soil physical-chemical properties (except for capillary moisture capacity) and enzyme activity. Sowing methods had no significant effects on the crop DM and CP yields. The DM yield was affected by the interaction between planting year and sowing methods, or between sowing methods and crop type. No-tillage also increased the number of species and aboveground weed biomass. We concluded that the best sowing method for forage wheat and Italian ryegrass in winter fallow paddy fields was no-till…
format: application/pdf
format: text/html
creator: Liuxing Xu
creator: Guojian Tang
creator: Jing Tian
creator: Xiaoya Wang
creator: Jianguo Zhang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.10573
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: In South China, it is common practice for the late rice (Oryza sativa) that is planted during the summer in the paddy fields after harvest to be used for fallowing or to plant winter forage crops. The land is ploughed before early rice planting. Both forage wheat (Triticum aestivum) and Italian ryegrass (Lolium multiflorum) have relatively high nutritional value, and planting them in winter fallow paddy fields could potentially address food shortages and provide quality forage for livestock. In this study, we examined the effects of no-tillage sowing 5 days before rice harvest (NB5), no-tillage sowing 1 day after rice harvest (NA1), and conventional tillage sowing (CK) 1 day after rice harvest on forage wheat and Italian ryegrass soil properties, dry matter (DM), and crude protein (CP) yields. Soil and plant samples were collected after three months of crop growth. The results showed that the NB5 and NA1 soil bulk density (0-20 cm soil layer) tended to increase when compared to that of the CK field. The NA1 treatment increased the total soil nitrogen and organic matter content. The enzyme activities and total soil porosity in the no-tillage forage wheat and Italian ryegrass fields tended to decrease, while the no-tillage water content and soil capillary porosity tended to increase when compared to that of the CK field. Overall, planting year significantly influenced soil chemical properties (except for total nitrogen) and enzyme activity, but crop type had no significant effect on soil physical-chemical properties (except for capillary moisture capacity) and enzyme activity. Sowing methods had no significant effects on the crop DM and CP yields. The DM yield was affected by the interaction between planting year and sowing methods, or between sowing methods and crop type. No-tillage also increased the number of species and aboveground weed biomass. We concluded that the best sowing method for forage wheat and Italian ryegrass in winter fallow paddy fields was no-till…
bibliographic citation: Xu et al. (2021) Effects of no-tillage sowing on soil properties and forage wheat and Italian ryegrass yields in winter fallow paddy fields. PeerJ 9:e10573 https://doi.org/10.7717/peerj.10573
date submitted: 2020-05-06
date accepted: 2020-11-23
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Liuxing
author list: Agent
  family name: Tang
  given name: Guojian
author list: Agent
  family name: Tian
  given name: Jing
author list: Agent
  family name: Wang
  given name: Xiaoya
author list: Agent
  family name: Zhang
  given name: Jianguo
doi: 10.7717/peerj.10573
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Effects of dietary fennel (Foeniculum vulgare Mill.) seed powder supplementation on growth performance, nutrient digestibility, small intestinal morphology, and carcass traits of broilers
type: item
type: AcademicArticle
description: Background With the increasing demands in livestock and poultry breeding and the growing number of food-borne diseases, it is necessary to practice food safety and develop strategies to produce healthy livestock. Fennel (Foeniculum vulgare Mill.) has been used as an additive in poultry production by some researchers, but there are few studies on the systemic beneficial effects of dietary fennel seed powder supplementation on broilers. Therefore, this study aimed to investigate the effect of dietary fennel seed powder supplementation on feed intake, the apparent metabolic rate of nutrients, intestinal morphology, and carcass traits in Cobb broilers. Methods A single-factor experimental design was used. In total, 160 1-day-old Cobb broiler chicks were randomly assigned to four treatments, with four replicates each (n = 10/replicate). Broilers in the control (CN) group were fed a basal diet without fennel seed powder, and broilers in the treatment groups were fed a basal diet supplemented with 0.15% (LF), 0.30% (MF), or 0.45% (HF) fennel seed powder, respectively. Feeding trials lasted for 42 days under the conditions of ad libitum access to feed and water, and 24-h illumination. During the third and sixth weeks, digestive and metabolic assays were carried out. When the broilers were 42 days old, one chicken with a weight close to the average was selected from each repetition, euthanized by an intravenous injection of 5% sodium pentobarbital, and carcass traits were measured and intestinal samples were collected for morphological assessment. Results There was no significant difference in growth performance of broilers (P > 0.05). The breast muscle percentage, fat width and fat width index, breast muscle area, and breast muscle area index of broilers in the LF group were higher than those in other groups (P < 0.05). Jejunum weight and length were higher in MF than in CN and LF broilers (P < 0.05). Additionally, duodenal villi height, ileal villi height, and ileal wall t…
format: application/pdf
format: text/html
creator: Huihui Liu
creator: Jinlu Li
creator: Shuqin Lin
creator: Ting Liu
creator: Chen Zheng
subject: Food Science and Technology
subject: Zoology
description: doi:10.7717/peerj.10308
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background With the increasing demands in livestock and poultry breeding and the growing number of food-borne diseases, it is necessary to practice food safety and develop strategies to produce healthy livestock. Fennel (Foeniculum vulgare Mill.) has been used as an additive in poultry production by some researchers, but there are few studies on the systemic beneficial effects of dietary fennel seed powder supplementation on broilers. Therefore, this study aimed to investigate the effect of dietary fennel seed powder supplementation on feed intake, the apparent metabolic rate of nutrients, intestinal morphology, and carcass traits in Cobb broilers. Methods A single-factor experimental design was used. In total, 160 1-day-old Cobb broiler chicks were randomly assigned to four treatments, with four replicates each (n = 10/replicate). Broilers in the control (CN) group were fed a basal diet without fennel seed powder, and broilers in the treatment groups were fed a basal diet supplemented with 0.15% (LF), 0.30% (MF), or 0.45% (HF) fennel seed powder, respectively. Feeding trials lasted for 42 days under the conditions of ad libitum access to feed and water, and 24-h illumination. During the third and sixth weeks, digestive and metabolic assays were carried out. When the broilers were 42 days old, one chicken with a weight close to the average was selected from each repetition, euthanized by an intravenous injection of 5% sodium pentobarbital, and carcass traits were measured and intestinal samples were collected for morphological assessment. Results There was no significant difference in growth performance of broilers (P > 0.05). The breast muscle percentage, fat width and fat width index, breast muscle area, and breast muscle area index of broilers in the LF group were higher than those in other groups (P < 0.05). Jejunum weight and length were higher in MF than in CN and LF broilers (P < 0.05). Additionally, duodenal villi height, ileal villi height, and ileal wall t…
bibliographic citation: Liu et al. (2021) Effects of dietary fennel (Foeniculum vulgare Mill.) seed powder supplementation on growth performance, nutrient digestibility, small intestinal morphology, and carcass traits of broilers. PeerJ 9:e10308 https://doi.org/10.7717/peerj.10308
date submitted: 2020-07-28
date accepted: 2020-10-15
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Huihui
author list: Agent
  family name: Li
  given name: Jinlu
author list: Agent
  family name: Lin
  given name: Shuqin
author list: Agent
  family name: Liu
  given name: Ting
author list: Agent
  family name: Zheng
  given name: Chen
doi: 10.7717/peerj.10308
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: © 2021 Liu et al.
attribution name: Liu et al.

Effect of salt stress in urban conditions on two Acer species with different sensitivity
type: item
type: AcademicArticle
description: Background The benefits of trees in urban areas include the following: an increase in ecosystem health, an increase in human health, the mitigation of the effects of heat and drought at microclimate level, the storage and sequestration of carbon, and a reduction in air pollution and noise. These ecosystem services can be provided only by trees that are in good health. The main cause of salt stress in urban environments is the use of de-icing salts on the streets in winter. Salt stress is a complex process that includes changes in plants on the physiological, histological, cellular and molecular levels, leading to limitations in nutrient uptake, disrupting the ionic balance of trees and resulting in the death of roadside trees. In response to salinity, trees have developed a variety of defence mechanisms that allow them to minimize the effects of stress and maintain homeostasis. Methodology The reactions of two species Acer species: A. platanoides and A. campestre, which have different sensitivities to the unfavourable conditions of the urban environments (mainly salt stress), were investigated. The research included two experiments: a field experiment with city trees and a controlled pot experiment with young trees treated with increasing doses of salt. In both experiments, the following were performed: an assessment of the health condition of the trees and the content of macroelements as well as the Cl and Na in leaves and a qualitative and quantitative analysis of polyprenols. Results A. campestre had a more specific strategy than A. platanoides for dealing with Na and Cl, which resulted in undamaged leaves. Under the same conditions, A. platanoides leaves contained more Cl and Na and were severely damaged. The disruption of the ion balance due to salt stress was lower in A. campestre than in A. platanoides. Compared with A. platanoides, A. campestre synthesized more polyprenols in the field experiment. This ability was acquired during the process of acclimation, …
format: application/pdf
format: text/html
creator: Wojciech Dmuchowski
creator: Aneta Baczewska-Dąbrowska
creator: Dariusz Gozdowski
creator: Paulina Brągoszewska
creator: Barbara Gworek
creator: Irena Suwara
creator: Tadeusz Chojnacki
creator: Adam Jóźwiak
creator: Ewa Swiezewska
subject: Biochemistry
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.10577
publisher: PeerJ Inc.
rights: © 2021 Dmuchowski et al.
abstract: Background The benefits of trees in urban areas include the following: an increase in ecosystem health, an increase in human health, the mitigation of the effects of heat and drought at microclimate level, the storage and sequestration of carbon, and a reduction in air pollution and noise. These ecosystem services can be provided only by trees that are in good health. The main cause of salt stress in urban environments is the use of de-icing salts on the streets in winter. Salt stress is a complex process that includes changes in plants on the physiological, histological, cellular and molecular levels, leading to limitations in nutrient uptake, disrupting the ionic balance of trees and resulting in the death of roadside trees. In response to salinity, trees have developed a variety of defence mechanisms that allow them to minimize the effects of stress and maintain homeostasis. Methodology The reactions of two species Acer species: A. platanoides and A. campestre, which have different sensitivities to the unfavourable conditions of the urban environments (mainly salt stress), were investigated. The research included two experiments: a field experiment with city trees and a controlled pot experiment with young trees treated with increasing doses of salt. In both experiments, the following were performed: an assessment of the health condition of the trees and the content of macroelements as well as the Cl and Na in leaves and a qualitative and quantitative analysis of polyprenols. Results A. campestre had a more specific strategy than A. platanoides for dealing with Na and Cl, which resulted in undamaged leaves. Under the same conditions, A. platanoides leaves contained more Cl and Na and were severely damaged. The disruption of the ion balance due to salt stress was lower in A. campestre than in A. platanoides. Compared with A. platanoides, A. campestre synthesized more polyprenols in the field experiment. This ability was acquired during the process of acclimation, …
bibliographic citation: Dmuchowski et al. (2021) Effect of salt stress in urban conditions on two Acer species with different sensitivity. PeerJ 9:e10577 https://doi.org/10.7717/peerj.10577
date submitted: 2020-06-25
date accepted: 2020-11-24
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dmuchowski
  given name: Wojciech
author list: Agent
  family name: Baczewska-Dąbrowska
  given name: Aneta
author list: Agent
  family name: Gozdowski
  given name: Dariusz
author list: Agent
  family name: Brągoszewska
  given name: Paulina
author list: Agent
  family name: Gworek
  given name: Barbara
author list: Agent
  family name: Suwara
  given name: Irena
author list: Agent
  family name: Chojnacki
  given name: Tadeusz
author list: Agent
  family name: Jóźwiak
  given name: Adam
author list: Agent
  family name: Swiezewska
  given name: Ewa
doi: 10.7717/peerj.10577
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: ©2021 Dmuchowski et al.
attribution name: Dmuchowski et al.

Evaluation of effective quantum yields of photosystem II for CO2 leakage monitoring in carbon capture and storage sites
type: item
type: AcademicArticle
description: Vegetation monitoring can be used to detect CO2 leakage in carbon capture and storage (CCS) sites because it can monitor a large area at a relatively low cost. However, a rapidly responsive, sensitive, and cost-effective plant parameters must be suggested for vegetation monitoring to be practically utilized as a CCS management strategy. To screen the proper plant parameters for leakage monitoring, a greenhouse experiment was conducted by exposing kale (Brassica oleracea var. viridis), a sensitive plant, to 10%, 20%, and 40% soil CO2 concentrations. Water and water with CO2 stress treatments were also introduced to examine the parameters differentiating CO2 stress from water stresses. We tested the hypothesis that chlorophyl fluorescence parameters would be early and sensitive indicator to detect CO2 leakage. The results showed that the fluorescence parameters of effective quantum yield of photosystem II (Y(II)), detected the difference between CO2 treatments and control earlier than any other parameters, such as chlorophyl content, hyperspectral vegetation indices, and biomass. For systematic comparison among many parameters, we proposed an indicator evaluation score (IES) method based on four categories: CO2 specificity, early detection, field applicability, and cost. The IES results showed that fluorescence parameters (Y(II)) had the highest IES scores, and the parameters from spectral sensors (380–800 nm wavelength) had the second highest values. We suggest the IES system as a useful tool for evaluating new parameters in vegetation monitoring.
format: application/pdf
format: text/html
creator: Wenmei He
creator: Gayoung Yoo
creator: Youngryel Ryu
subject: Biophysics
subject: Ecology
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.10652
publisher: PeerJ Inc.
rights: © 2021 He et al.
abstract: Vegetation monitoring can be used to detect CO2 leakage in carbon capture and storage (CCS) sites because it can monitor a large area at a relatively low cost. However, a rapidly responsive, sensitive, and cost-effective plant parameters must be suggested for vegetation monitoring to be practically utilized as a CCS management strategy. To screen the proper plant parameters for leakage monitoring, a greenhouse experiment was conducted by exposing kale (Brassica oleracea var. viridis), a sensitive plant, to 10%, 20%, and 40% soil CO2 concentrations. Water and water with CO2 stress treatments were also introduced to examine the parameters differentiating CO2 stress from water stresses. We tested the hypothesis that chlorophyl fluorescence parameters would be early and sensitive indicator to detect CO2 leakage. The results showed that the fluorescence parameters of effective quantum yield of photosystem II (Y(II)), detected the difference between CO2 treatments and control earlier than any other parameters, such as chlorophyl content, hyperspectral vegetation indices, and biomass. For systematic comparison among many parameters, we proposed an indicator evaluation score (IES) method based on four categories: CO2 specificity, early detection, field applicability, and cost. The IES results showed that fluorescence parameters (Y(II)) had the highest IES scores, and the parameters from spectral sensors (380–800 nm wavelength) had the second highest values. We suggest the IES system as a useful tool for evaluating new parameters in vegetation monitoring.
bibliographic citation: He et al. (2021) Evaluation of effective quantum yields of photosystem II for CO2 leakage monitoring in carbon capture and storage sites. PeerJ 9:e10652 https://doi.org/10.7717/peerj.10652
date submitted: 2020-07-13
date accepted: 2020-12-04
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Wenmei
author list: Agent
  family name: Yoo
  given name: Gayoung
author list: Agent
  family name: Ryu
  given name: Youngryel
doi: 10.7717/peerj.10652
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: © 2021 He et al.
attribution name: He et al.

Monomorium (Hymenoptera: Formicidae) of the Arabian Peninsula with description of two new species, M. heggyi sp. n. and M. khalidi sp. n.
type: item
type: AcademicArticle
description: We present a revised and updated synoptic list of 44 Arabian Monomorium species, including two new species of the M. salomonis species-group: M. heggyi sp. n., and M. khalidi sp. n. We propose the following new synonyms: M. abeillei André (= M. wahibiense Collingwood & Agosti syn. n.); M. areniphilum Santschi (= M. fezzanense Collingwood & Agosti syn. n., = M. hemame Collingwood & Agosti syn. n. = M. marmule Collingwood & Agosti syn. n.); M. bicolor Emery (= M. phoenicum Santschi syn. n.); M. harithe Collingwood & Agosti (= M. najrane Collingwood & Agosti syn. n.); M. niloticum Emery (= M. matame Collingwood & Agosti syn. n.); and M. nitidiventre Emery (= M. yemene Collingwood & Agosti syn. n.). An illustrated key and distribution maps are presented for the treated species. Ecological and biological notes are given when available. The majority of Arabian Monomorium species (24) are endemic to the peninsula. All except one of the remaining species are more broadly ranging Afrotropical and Palearctic species, supporting the view of Arabia as a biogeographical crossroads between these two regions. Monomorium floricola (Jerdon), the sole species of Indomalayan origin, is recorded for the first time from the Arabian Peninsula.
format: application/pdf
format: text/html
creator: Mostafa R. Sharaf
creator: Amr A. Mohamed
creator: Brendon E. Boudinot
creator: James K. Wetterer
creator: Francisco Hita Garcia
creator: Hathal M. Al Dhafer
creator: Abdulrahman S. Aldawood
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10726
publisher: PeerJ Inc.
rights: © 2021 Sharaf et al.
abstract: We present a revised and updated synoptic list of 44 Arabian Monomorium species, including two new species of the M. salomonis species-group: M. heggyi sp. n., and M. khalidi sp. n. We propose the following new synonyms: M. abeillei André (= M. wahibiense Collingwood & Agosti syn. n.); M. areniphilum Santschi (= M. fezzanense Collingwood & Agosti syn. n., = M. hemame Collingwood & Agosti syn. n. = M. marmule Collingwood & Agosti syn. n.); M. bicolor Emery (= M. phoenicum Santschi syn. n.); M. harithe Collingwood & Agosti (= M. najrane Collingwood & Agosti syn. n.); M. niloticum Emery (= M. matame Collingwood & Agosti syn. n.); and M. nitidiventre Emery (= M. yemene Collingwood & Agosti syn. n.). An illustrated key and distribution maps are presented for the treated species. Ecological and biological notes are given when available. The majority of Arabian Monomorium species (24) are endemic to the peninsula. All except one of the remaining species are more broadly ranging Afrotropical and Palearctic species, supporting the view of Arabia as a biogeographical crossroads between these two regions. Monomorium floricola (Jerdon), the sole species of Indomalayan origin, is recorded for the first time from the Arabian Peninsula.
bibliographic citation: Sharaf et al. (2021) Monomorium (Hymenoptera: Formicidae) of the Arabian Peninsula with description of two new species, M. heggyi sp. n. and M. khalidi sp. n.. PeerJ 9:e10726 https://doi.org/10.7717/peerj.10726
date submitted: 2020-11-03
date accepted: 2020-12-16
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharaf
  given name: Mostafa R.
author list: Agent
  family name: Mohamed
  given name: Amr A.
author list: Agent
  family name: Boudinot
  given name: Brendon E.
author list: Agent
  family name: Wetterer
  given name: James K.
author list: Agent
  family name: Hita Garcia
  given name: Francisco
author list: Agent
  family name: Al Dhafer
  given name: Hathal M.
author list: Agent
  family name: Aldawood
  given name: Abdulrahman S.
doi: 10.7717/peerj.10726
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: © 2021 Sharaf et al.
attribution name: Sharaf et al.

Biological effects of electron beam to target turning X-ray (EBTTX) on two freesia (Freesia hybrida) cultivars
type: item
type: AcademicArticle
description: Electron beam to target turning X-ray (EBTTX) is an emerging irradiation technology that can potentially accelerate the breeding process of plants. The biological effects of EBTTX irradiation on the two freesia cultivars (the red freesia and the purple freesia) were investigated by establishing an irradiation-mediated mutation breeding protocol. The germination rate, survival rate, plant height, leaf number and area, root number and length of the two freesia cultivars decreased following different irradiation doses (25, 50, 75, and 100-Gy). A high irradiation dose exhibited stronger inhibition effects on these plant growth parameters, and the survival rate of the two freesia cultivars was 0.00% following the 100-Gy irradiation treatment. The median lethal dose (LD50) based on survival rates was 54.28-Gy for the red freesia and 60.11-Gy for the purple freesia. The flowering rate, flower number, and pollen vigor were significantly decreased by irradiation treatment. At 75-Gy irradiation, the flowering rate, flower number and pollen viability of the two varieties reached the minimum, exhibiting strong inhibitory effects. Meanwhile, 75-Gy irradiation significantly decreased the chlorophyll content and increased the malondialdehyde (MDA) content of the two freesia cultivars. Furthermore, as the irradiation dose increased, the changes in the micro-morphology of the leaf epidermis and pollen gradually increased according to a scanning electron microscope (SEM) analysis. These results are expected to provide useful information for the mutation breeding of different freesia cultivars and other flowering plants.
format: application/pdf
format: text/html
creator: Yi-rui Li
creator: Ling Liu
creator: Dan Wang
creator: Li Chen
creator: Hao Chen
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.10742
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Electron beam to target turning X-ray (EBTTX) is an emerging irradiation technology that can potentially accelerate the breeding process of plants. The biological effects of EBTTX irradiation on the two freesia cultivars (the red freesia and the purple freesia) were investigated by establishing an irradiation-mediated mutation breeding protocol. The germination rate, survival rate, plant height, leaf number and area, root number and length of the two freesia cultivars decreased following different irradiation doses (25, 50, 75, and 100-Gy). A high irradiation dose exhibited stronger inhibition effects on these plant growth parameters, and the survival rate of the two freesia cultivars was 0.00% following the 100-Gy irradiation treatment. The median lethal dose (LD50) based on survival rates was 54.28-Gy for the red freesia and 60.11-Gy for the purple freesia. The flowering rate, flower number, and pollen vigor were significantly decreased by irradiation treatment. At 75-Gy irradiation, the flowering rate, flower number and pollen viability of the two varieties reached the minimum, exhibiting strong inhibitory effects. Meanwhile, 75-Gy irradiation significantly decreased the chlorophyll content and increased the malondialdehyde (MDA) content of the two freesia cultivars. Furthermore, as the irradiation dose increased, the changes in the micro-morphology of the leaf epidermis and pollen gradually increased according to a scanning electron microscope (SEM) analysis. These results are expected to provide useful information for the mutation breeding of different freesia cultivars and other flowering plants.
bibliographic citation: Li et al. (2021) Biological effects of electron beam to target turning X-ray (EBTTX) on two freesia (Freesia hybrida) cultivars. PeerJ 9:e10742 https://doi.org/10.7717/peerj.10742
date submitted: 2020-10-27
date accepted: 2020-12-18
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yi-rui
author list: Agent
  family name: Liu
  given name: Ling
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Chen
  given name: Li
author list: Agent
  family name: Chen
  given name: Hao
doi: 10.7717/peerj.10742
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: ©2021 Li et al.
attribution name: Li et al.

Metabolic impact of weight variations in Icelandic horses
type: item
type: AcademicArticle
description: Background Insulin dysregulation (ID) is an equine endocrine disorder, which is often accompanied by obesity and various metabolic perturbations. The relationship between weight variations and fluctuations of the insulin response to oral glucose tests (OGT) as well as the metabolic impact of ID have been described previously. The present study seeks to characterize the concomitant metabolic impact of variations in the insulin response and bodyweight during repeated OGTs using a metabolomics approach. Methods Nineteen Icelandic horses were subjected to five OGTs over one year and their bodyweight, insulin and metabolic response were monitored. Analysis of metabolite concentrations depending on time (during the OGT), relative bodyweight (rWeight; defined as the bodyweight at one OGT divided by the mean bodyweight across all OGTs) and relative insulin response (rAUCins; defined accordingly from the area under the insulin curve during OGT) was performed using linear models. Additionally, the pathways significantly associated with time, rWeight and rAUCins were identified by rotation set testing. Results The results suggested that weight gain and worsening of ID activate distinct metabolic pathways. The metabolic profile associated with weight gain indicated an increased activation of arginase, while the pathways associated with time and rAUCins were consistent with the expected effect of glucose and insulin, respectively. Overall, more metabolites were significantly associated with rWeight than with rAUCins.
format: application/pdf
format: text/html
creator: Julien Delarocque
creator: Florian Frers
creator: Korinna Huber
creator: Klaus Jung
creator: Karsten Feige
creator: Tobias Warnken
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10764
publisher: PeerJ Inc.
rights: © 2021 Delarocque et al.
abstract: Background Insulin dysregulation (ID) is an equine endocrine disorder, which is often accompanied by obesity and various metabolic perturbations. The relationship between weight variations and fluctuations of the insulin response to oral glucose tests (OGT) as well as the metabolic impact of ID have been described previously. The present study seeks to characterize the concomitant metabolic impact of variations in the insulin response and bodyweight during repeated OGTs using a metabolomics approach. Methods Nineteen Icelandic horses were subjected to five OGTs over one year and their bodyweight, insulin and metabolic response were monitored. Analysis of metabolite concentrations depending on time (during the OGT), relative bodyweight (rWeight; defined as the bodyweight at one OGT divided by the mean bodyweight across all OGTs) and relative insulin response (rAUCins; defined accordingly from the area under the insulin curve during OGT) was performed using linear models. Additionally, the pathways significantly associated with time, rWeight and rAUCins were identified by rotation set testing. Results The results suggested that weight gain and worsening of ID activate distinct metabolic pathways. The metabolic profile associated with weight gain indicated an increased activation of arginase, while the pathways associated with time and rAUCins were consistent with the expected effect of glucose and insulin, respectively. Overall, more metabolites were significantly associated with rWeight than with rAUCins.
bibliographic citation: Delarocque et al. (2021) Metabolic impact of weight variations in Icelandic horses. PeerJ 9:e10764 https://doi.org/10.7717/peerj.10764
date submitted: 2020-09-08
date accepted: 2020-12-22
issued: 2021-01-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Delarocque
  given name: Julien
author list: Agent
  family name: Frers
  given name: Florian
author list: Agent
  family name: Huber
  given name: Korinna
author list: Agent
  family name: Jung
  given name: Klaus
author list: Agent
  family name: Feige
  given name: Karsten
author list: Agent
  family name: Warnken
  given name: Tobias
doi: 10.7717/peerj.10764
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-28
copyright: ©2021 Delarocque et al.
attribution name: Delarocque et al.

Arithmetic processing in children with dyscalculia: an event-related potential study
type: item
type: AcademicArticle
description: Introduction Dyscalculia is a specific learning disorder affecting the ability to learn certain math processes, such as arithmetic data recovery. The group of children with dyscalculia is very heterogeneous, in part due to variability in their working memory (WM) deficits. To assess the brain response to arithmetic data recovery, we applied an arithmetic verification task during an event-related potential (ERP) recording. Two effects have been reported: the N400 effect (higher negative amplitude for incongruent than for congruent condition), associated with arithmetic incongruency and caused by the arithmetic priming effect, and the LPC effect (higher positive amplitude for the incongruent compared to the congruent condition), associated with a reevaluation process and modulated by the plausibility of the presented condition. This study aimed to (a) compare arithmetic processing between children with dyscalculia and children with good academic performance (GAP) using ERPs during an addition verification task and (b) explore, among children with dyscalculia, the relationship between WM and ERP effects. Materials and Methods EEGs of 22 children with dyscalculia (DYS group) and 22 children with GAP (GAP group) were recorded during the performance of an addition verification task. ERPs synchronized with the probe stimulus were computed separately for the congruent and incongruent probes, and included only epochs with correct answers. Mixed 2-way ANOVAs for response times and correct answers were conducted. Comparisons between groups and correlation analyses using ERP amplitude data were carried out through multivariate nonparametric permutation tests. Results The GAP group obtained more correct answers than the DYS group. An arithmetic N400 effect was observed in the GAP group but not in the DYS group. Both groups displayed an LPC effect. The larger the LPC amplitude was, the higher the WM index. Two subgroups were found within the DYS group: one with an average WM inde…
format: application/pdf
format: text/html
creator: Sonia Y. Cárdenas
creator: Juan Silva-Pereyra
creator: Belén Prieto-Corona
creator: Susana A. Castro-Chavira
creator: Thalía Fernández
subject: Cognitive Disorders
subject: Pediatrics
description: doi:10.7717/peerj.10489
publisher: PeerJ Inc.
rights: © 2021 Cárdenas et al.
abstract: Introduction Dyscalculia is a specific learning disorder affecting the ability to learn certain math processes, such as arithmetic data recovery. The group of children with dyscalculia is very heterogeneous, in part due to variability in their working memory (WM) deficits. To assess the brain response to arithmetic data recovery, we applied an arithmetic verification task during an event-related potential (ERP) recording. Two effects have been reported: the N400 effect (higher negative amplitude for incongruent than for congruent condition), associated with arithmetic incongruency and caused by the arithmetic priming effect, and the LPC effect (higher positive amplitude for the incongruent compared to the congruent condition), associated with a reevaluation process and modulated by the plausibility of the presented condition. This study aimed to (a) compare arithmetic processing between children with dyscalculia and children with good academic performance (GAP) using ERPs during an addition verification task and (b) explore, among children with dyscalculia, the relationship between WM and ERP effects. Materials and Methods EEGs of 22 children with dyscalculia (DYS group) and 22 children with GAP (GAP group) were recorded during the performance of an addition verification task. ERPs synchronized with the probe stimulus were computed separately for the congruent and incongruent probes, and included only epochs with correct answers. Mixed 2-way ANOVAs for response times and correct answers were conducted. Comparisons between groups and correlation analyses using ERP amplitude data were carried out through multivariate nonparametric permutation tests. Results The GAP group obtained more correct answers than the DYS group. An arithmetic N400 effect was observed in the GAP group but not in the DYS group. Both groups displayed an LPC effect. The larger the LPC amplitude was, the higher the WM index. Two subgroups were found within the DYS group: one with an average WM inde…
bibliographic citation: Cárdenas et al. (2021) Arithmetic processing in children with dyscalculia: an event-related potential study. PeerJ 9:e10489 https://doi.org/10.7717/peerj.10489
date submitted: 2019-09-04
date accepted: 2020-11-13
issued: 2021-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cárdenas
  given name: Sonia Y.
author list: Agent
  family name: Silva-Pereyra
  given name: Juan
author list: Agent
  family name: Prieto-Corona
  given name: Belén
author list: Agent
  family name: Castro-Chavira
  given name: Susana A.
author list: Agent
  family name: Fernández
  given name: Thalía
doi: 10.7717/peerj.10489
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-27
copyright: © 2021 Cárdenas et al.
attribution name: Cárdenas et al.

Clinical relevance assessment of animal preclinical research (RAA) tool: development and explanation
type: item
type: AcademicArticle
description: Background Only a small proportion of preclinical research (research performed in animal models prior to clinical trials in humans) translates into clinical benefit in humans. Possible reasons for the lack of translation of the results observed in preclinical research into human clinical benefit include the design, conduct, and reporting of preclinical studies. There is currently no formal domain-based assessment of the clinical relevance of preclinical research. To address this issue, we have developed a tool for the assessment of the clinical relevance of preclinical studies, with the intention of assessing the likelihood that therapeutic preclinical findings can be translated into improvement in the management of human diseases. Methods We searched the EQUATOR network for guidelines that describe the design, conduct, and reporting of preclinical research. We searched the references of these guidelines to identify further relevant publications and developed a set of domains and signalling questions. We then conducted a modified Delphi-consensus to refine and develop the tool. The Delphi panel members included specialists in evidence-based (preclinical) medicine specialists, methodologists, preclinical animal researchers, a veterinarian, and clinical researchers. A total of 20 Delphi-panel members completed the first round and 17 members from five countries completed all three rounds. Results This tool has eight domains (construct validity, external validity, risk of bias, experimental design and data analysis plan, reproducibility and replicability of methods and results in the same model, research integrity, and research transparency) and a total of 28 signalling questions and provides a framework for researchers, journal editors, grant funders, and regulatory authorities to assess the potential clinical relevance of preclinical animal research. Conclusion We have developed a tool to assess the clinical relevance of preclinical studies. This tool is currently bei…
format: application/pdf
format: text/html
creator: Kurinchi S. Gurusamy
creator: David Moher
creator: Marilena Loizidou
creator: Irfan Ahmed
creator: Marc T. Avey
creator: Carly C. Barron
creator: Brian Davidson
creator: Miriam Dwek
creator: Christian Gluud
creator: Gavin Jell
creator: Kiran Katakam
creator: Joshua Montroy
creator: Timothy D. McHugh
creator: Nicola J. Osborne
creator: Merel Ritskes-Hoitinga
creator: Kees van Laarhoven
creator: Jan Vollert
creator: Manoj Lalu
subject: Clinical Trials
subject: Drugs and Devices
subject: Evidence Based Medicine
subject: Science and Medical Education
description: doi:10.7717/peerj.10673
publisher: PeerJ Inc.
rights: © 2021
abstract: Background Only a small proportion of preclinical research (research performed in animal models prior to clinical trials in humans) translates into clinical benefit in humans. Possible reasons for the lack of translation of the results observed in preclinical research into human clinical benefit include the design, conduct, and reporting of preclinical studies. There is currently no formal domain-based assessment of the clinical relevance of preclinical research. To address this issue, we have developed a tool for the assessment of the clinical relevance of preclinical studies, with the intention of assessing the likelihood that therapeutic preclinical findings can be translated into improvement in the management of human diseases. Methods We searched the EQUATOR network for guidelines that describe the design, conduct, and reporting of preclinical research. We searched the references of these guidelines to identify further relevant publications and developed a set of domains and signalling questions. We then conducted a modified Delphi-consensus to refine and develop the tool. The Delphi panel members included specialists in evidence-based (preclinical) medicine specialists, methodologists, preclinical animal researchers, a veterinarian, and clinical researchers. A total of 20 Delphi-panel members completed the first round and 17 members from five countries completed all three rounds. Results This tool has eight domains (construct validity, external validity, risk of bias, experimental design and data analysis plan, reproducibility and replicability of methods and results in the same model, research integrity, and research transparency) and a total of 28 signalling questions and provides a framework for researchers, journal editors, grant funders, and regulatory authorities to assess the potential clinical relevance of preclinical animal research. Conclusion We have developed a tool to assess the clinical relevance of preclinical studies. This tool is currently bei…
bibliographic citation: Gurusamy et al. (2021) Clinical relevance assessment of animal preclinical research (RAA) tool: development and explanation. PeerJ 9:e10673 https://doi.org/10.7717/peerj.10673
date submitted: 2020-06-16
date accepted: 2020-12-09
issued: 2021-01-27
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Gurusamy
  given name: Kurinchi S.
author list: Agent
  family name: Moher
  given name: David
author list: Agent
  family name: Loizidou
  given name: Marilena
author list: Agent
  family name: Ahmed
  given name: Irfan
author list: Agent
  family name: Avey
  given name: Marc T.
author list: Agent
  family name: Barron
  given name: Carly C.
author list: Agent
  family name: Davidson
  given name: Brian
author list: Agent
  family name: Dwek
  given name: Miriam
author list: Agent
  family name: Gluud
  given name: Christian
author list: Agent
  family name: Jell
  given name: Gavin
author list: Agent
  family name: Katakam
  given name: Kiran
author list: Agent
  family name: Montroy
  given name: Joshua
author list: Agent
  family name: McHugh
  given name: Timothy D.
author list: Agent
  family name: Osborne
  given name: Nicola J.
author list: Agent
  family name: Ritskes-Hoitinga
  given name: Merel
author list: Agent
  family name: van Laarhoven
  given name: Kees
author list: Agent
  family name: Vollert
  given name: Jan
author list: Agent
  family name: Lalu
  given name: Manoj
doi: 10.7717/peerj.10673
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-27

Exploring a model-based analysis of patient derived xenograft studies in oncology drug development
type: item
type: AcademicArticle
description: Purpose To assess whether a model-based analysis increased statistical power over an analysis of final day volumes and provide insights into more efficient patient derived xenograft (PDX) study designs. Methods Tumour xenograft time-series data was extracted from a public PDX drug treatment database. For all 2-arm studies the percent tumour growth inhibition (TGI) at day 14, 21 and 28 was calculated. Treatment effect was analysed using an un-paired, two-tailed t-test (empirical) and a model-based analysis, likelihood ratio-test (LRT). In addition, a simulation study was performed to assess the difference in power between the two data-analysis approaches for PDX or standard cell-line derived xenografts (CDX). Results The model-based analysis had greater statistical power than the empirical approach within the PDX data-set. The model-based approach was able to detect TGI values as low as 25% whereas the empirical approach required at least 50% TGI. The simulation study confirmed the findings and highlighted that CDX studies require fewer animals than PDX studies which show the equivalent level of TGI. Conclusions The study conducted adds to the growing literature which has shown that a model-based analysis of xenograft data improves statistical power over the common empirical approach. The analysis conducted showed that a model-based approach, based on the first mathematical model of tumour growth, was able to detect smaller size of effect compared to the empirical approach which is common of such studies. A model-based analysis should allow studies to reduce animal use and experiment length providing effective insights into compound anti-tumour activity.
format: application/pdf
format: text/html
creator: Jake Dickinson
creator: Marcel de Matas
creator: Paul A. Dickinson
creator: Hitesh B. Mistry
subject: Drugs and Devices
subject: Computational Science
subject: Data Science
subject: Pharmacology
subject: Oncology
description: doi:10.7717/peerj.10681
publisher: PeerJ Inc.
rights: © 2021 Dickinson et al.
abstract: Purpose To assess whether a model-based analysis increased statistical power over an analysis of final day volumes and provide insights into more efficient patient derived xenograft (PDX) study designs. Methods Tumour xenograft time-series data was extracted from a public PDX drug treatment database. For all 2-arm studies the percent tumour growth inhibition (TGI) at day 14, 21 and 28 was calculated. Treatment effect was analysed using an un-paired, two-tailed t-test (empirical) and a model-based analysis, likelihood ratio-test (LRT). In addition, a simulation study was performed to assess the difference in power between the two data-analysis approaches for PDX or standard cell-line derived xenografts (CDX). Results The model-based analysis had greater statistical power than the empirical approach within the PDX data-set. The model-based approach was able to detect TGI values as low as 25% whereas the empirical approach required at least 50% TGI. The simulation study confirmed the findings and highlighted that CDX studies require fewer animals than PDX studies which show the equivalent level of TGI. Conclusions The study conducted adds to the growing literature which has shown that a model-based analysis of xenograft data improves statistical power over the common empirical approach. The analysis conducted showed that a model-based approach, based on the first mathematical model of tumour growth, was able to detect smaller size of effect compared to the empirical approach which is common of such studies. A model-based analysis should allow studies to reduce animal use and experiment length providing effective insights into compound anti-tumour activity.
bibliographic citation: Dickinson et al. (2021) Exploring a model-based analysis of patient derived xenograft studies in oncology drug development. PeerJ 9:e10681 https://doi.org/10.7717/peerj.10681
date submitted: 2020-10-08
date accepted: 2020-12-09
issued: 2021-01-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dickinson
  given name: Jake
author list: Agent
  family name: de Matas
  given name: Marcel
author list: Agent
  family name: Dickinson
  given name: Paul A.
author list: Agent
  family name: Mistry
  given name: Hitesh B.
doi: 10.7717/peerj.10681
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-27
copyright: ©2021 Dickinson et al.
attribution name: Dickinson et al.

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