PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Master regulator genes and their impact on major diseases
items: Increased photosynthesis and grain yields in maize grown with less irrigation water combined with density adjustment in semiarid regions
items: Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia
items: Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin
items: The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians
items: Neighbourhood socioeconomic characteristics and blood pressure among Jamaican youth: a pooled analysis of data from observational studies
items: Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies
items: A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction
items: Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring
items: Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children

Master regulator genes and their impact on major diseases
type: item
type: AcademicArticle
description: Master regulator genes (MRGs) have become a hot topic in recent decades. They not only affect the development of tissue and organ systems but also play a role in other signal pathways by regulating additional MRGs. Because a MRG can regulate the concurrent expression of several genes, its mutation often leads to major diseases. Moreover, the occurrence of many tumors and cardiovascular and nervous system diseases are closely related to MRG changes. With the development in omics technology, an increasing amount of investigations will be directed toward MRGs because their regulation involves all aspects of an organism’s development. This review focuses on the definition and classification of MRGs as well as their influence on disease regulation.
format: application/pdf
format: text/html
creator: Wanwan Cai
creator: Wanbang Zhou
creator: Zhe Han
creator: Junrong Lei
creator: Jian Zhuang
creator: Ping Zhu
creator: Xiushan Wu
creator: Wuzhou Yuan
subject: Molecular Biology
subject: Clinical Trials
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.9952
publisher: PeerJ Inc.
rights: © 2020 Cai et al.
abstract: Master regulator genes (MRGs) have become a hot topic in recent decades. They not only affect the development of tissue and organ systems but also play a role in other signal pathways by regulating additional MRGs. Because a MRG can regulate the concurrent expression of several genes, its mutation often leads to major diseases. Moreover, the occurrence of many tumors and cardiovascular and nervous system diseases are closely related to MRG changes. With the development in omics technology, an increasing amount of investigations will be directed toward MRGs because their regulation involves all aspects of an organism’s development. This review focuses on the definition and classification of MRGs as well as their influence on disease regulation.
bibliographic citation: Cai et al. (2020) Master regulator genes and their impact on major diseases. PeerJ 8:e9952 https://doi.org/10.7717/peerj.9952
date submitted: 2020-06-16
date accepted: 2020-08-25
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Wanwan
author list: Agent
  family name: Zhou
  given name: Wanbang
author list: Agent
  family name: Han
  given name: Zhe
author list: Agent
  family name: Lei
  given name: Junrong
author list: Agent
  family name: Zhuang
  given name: Jian
author list: Agent
  family name: Zhu
  given name: Ping
author list: Agent
  family name: Wu
  given name: Xiushan
author list: Agent
  family name: Yuan
  given name: Wuzhou
doi: 10.7717/peerj.9952
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Cai et al.
attribution name: Cai et al.

Increased photosynthesis and grain yields in maize grown with less irrigation water combined with density adjustment in semiarid regions
type: item
type: AcademicArticle
description: In order to design a water-saving and high-yield maize planting model suitable for semiarid areas, we conducted trials by combining supplementary irrigation with different planting densities. Three planting densities (L: 52,500, M: 75,000, and H: 97,500 plants ha–1) and four supplementary irrigation modes (NI: no irrigation; IV: 375 m3 ha–1 during the 11-leaf stage; IS: 375 m3 ha–1 in the silking stage; and IVS: 375 m3 ha–1 during both stages) were tested. The irrigation treatments significantly increased the leaf relative water content, but the high planting density significantly decreased the relative water content during the silking and filling stages. After supplementary irrigation during the 11-leaf stage, IV and IVS significantly increased the photosynthetic capacity, but decreased the leaf water use efficiency. IS and IVS significantly increased the photosynthetic capacity after supplementary irrigation in the silking stage over two years. During the filling stage, IV, IS, and IVS increased the two-year average net photosynthetic rate by 17.0%, 27.2%, and 30.3%, respectively. The intercellular CO2 concentration increased as the density increased, whereas the stomatal conductance, transpiration rate, net photosynthetic rate, and leaf water use efficiency decreased, and the high planting density significantly reduced the leaf photosynthetic capacity. The highest grain yield was obtained using the IVS treatment under the medium planting density, but it did not differ significantly from that with the IS treatment. Furthermore, the IVS treatment used two times more water than the IS treatment. Thus, the medium planting density combined with supplementary irrigation during the silking stage was identified as a suitable water-saving planting model to improve the photosynthetic capacity and grain yield, and to cope with drought and water shortages in semiarid regions.
format: application/pdf
format: text/html
creator: Donghua Liu
creator: Qianmin Jia
creator: Juan Li
creator: Peng Zhang
creator: Xiaolong Ren
creator: Zhikuan Jia
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9959
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: In order to design a water-saving and high-yield maize planting model suitable for semiarid areas, we conducted trials by combining supplementary irrigation with different planting densities. Three planting densities (L: 52,500, M: 75,000, and H: 97,500 plants ha–1) and four supplementary irrigation modes (NI: no irrigation; IV: 375 m3 ha–1 during the 11-leaf stage; IS: 375 m3 ha–1 in the silking stage; and IVS: 375 m3 ha–1 during both stages) were tested. The irrigation treatments significantly increased the leaf relative water content, but the high planting density significantly decreased the relative water content during the silking and filling stages. After supplementary irrigation during the 11-leaf stage, IV and IVS significantly increased the photosynthetic capacity, but decreased the leaf water use efficiency. IS and IVS significantly increased the photosynthetic capacity after supplementary irrigation in the silking stage over two years. During the filling stage, IV, IS, and IVS increased the two-year average net photosynthetic rate by 17.0%, 27.2%, and 30.3%, respectively. The intercellular CO2 concentration increased as the density increased, whereas the stomatal conductance, transpiration rate, net photosynthetic rate, and leaf water use efficiency decreased, and the high planting density significantly reduced the leaf photosynthetic capacity. The highest grain yield was obtained using the IVS treatment under the medium planting density, but it did not differ significantly from that with the IS treatment. Furthermore, the IVS treatment used two times more water than the IS treatment. Thus, the medium planting density combined with supplementary irrigation during the silking stage was identified as a suitable water-saving planting model to improve the photosynthetic capacity and grain yield, and to cope with drought and water shortages in semiarid regions.
bibliographic citation: Liu et al. (2020) Increased photosynthesis and grain yields in maize grown with less irrigation water combined with density adjustment in semiarid regions. PeerJ 8:e9959 https://doi.org/10.7717/peerj.9959
date submitted: 2020-02-19
date accepted: 2020-08-25
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Donghua
author list: Agent
  family name: Jia
  given name: Qianmin
author list: Agent
  family name: Li
  given name: Juan
author list: Agent
  family name: Zhang
  given name: Peng
author list: Agent
  family name: Ren
  given name: Xiaolong
author list: Agent
  family name: Jia
  given name: Zhikuan
doi: 10.7717/peerj.9959
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia
type: item
type: AcademicArticle
description: Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type…
format: application/pdf
format: text/html
creator: José J. Nuñez
creator: Elkin Y. Suárez-Villota
creator: Camila A. Quercia
creator: Angel P. Olivares
creator: Jack W. Sites Jr
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.9980
publisher: PeerJ Inc.
rights: © 2020 Nuñez et al.
abstract: Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type…
bibliographic citation: Nuñez et al. (2020) Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia. PeerJ 8:e9980 https://doi.org/10.7717/peerj.9980
date submitted: 2020-03-24
date accepted: 2020-08-27
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nuñez
  given name: José J.
author list: Agent
  family name: Suárez-Villota
  given name: Elkin Y.
author list: Agent
  family name: Quercia
  given name: Camila A.
author list: Agent
  family name: Olivares
  given name: Angel P.
author list: Agent
  family name: Sites Jr
  given name: Jack W.
doi: 10.7717/peerj.9980
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Nuñez et al.
attribution name: Nuñez et al.

Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin
type: item
type: AcademicArticle
description: Background Camellia oleifera is an important oil-yielding woody plant native to China. Tea oil extracted from the seeds is rich in health-beneficial compounds. Huajin is a high-yielding elite variety of C. oleifera, with large fruits and remarkable resilience, widely cultivated in southern China; however, its seedling quality tends to be uneven. At present, techniques such as grafting, and cuttings are primarily adopted to propagate C. oleifera. These approaches are susceptible to environmental constraints owing to the long growth period, resulting in the lack of C. oleifera seedlings. Methods to make the cultivation more economical are warranted; this can be facilitated by tissue culture technology to provide good-quality seedlings in a short time. Methods In vitro cultured plantlets of C. oleifera Huajin were exposed to red light (RL), blue light (BL), red:blue light at a 4:1 ratio (R4:B1), and red:blue light at a 1:4 ratio (R1:B4); white light (WL) was used as the control treatment. To investigate the influence of light spectral quality on the proliferation coefficient, photosynthetic pigments, soluble proteins, plant height, leaf shape, Rubisco enzyme activity, and stomata and leaf anatomical features. Results The highest proliferation coefficient was observed under combined red and blue (4:1) light. In addition, this treatment resulted in the second highest chlorophyll content, the thickest palisade and spongy tissues, and consequently, the thickest leaves. The same treatment resulted in the second highest stomatal density, albeit concomitantly with the smallest average stomatal length and width. Discussion These results indicate that high-quality propagation of Huajin shoots can be achieved by culturing the plants in vitro under a combination of red and blue (4:1) lights. Previous studies have shown that red and blue lights improve rooting and transplanting rates of tissue culture seedlings. Hence, future research should focus on the effect of light quality on…
format: application/pdf
format: text/html
creator: Chaoyin He
creator: Yanling Zeng
creator: Yuzhong Fu
creator: Jiahao Wu
creator: Qin Liang
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.10016
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Background Camellia oleifera is an important oil-yielding woody plant native to China. Tea oil extracted from the seeds is rich in health-beneficial compounds. Huajin is a high-yielding elite variety of C. oleifera, with large fruits and remarkable resilience, widely cultivated in southern China; however, its seedling quality tends to be uneven. At present, techniques such as grafting, and cuttings are primarily adopted to propagate C. oleifera. These approaches are susceptible to environmental constraints owing to the long growth period, resulting in the lack of C. oleifera seedlings. Methods to make the cultivation more economical are warranted; this can be facilitated by tissue culture technology to provide good-quality seedlings in a short time. Methods In vitro cultured plantlets of C. oleifera Huajin were exposed to red light (RL), blue light (BL), red:blue light at a 4:1 ratio (R4:B1), and red:blue light at a 1:4 ratio (R1:B4); white light (WL) was used as the control treatment. To investigate the influence of light spectral quality on the proliferation coefficient, photosynthetic pigments, soluble proteins, plant height, leaf shape, Rubisco enzyme activity, and stomata and leaf anatomical features. Results The highest proliferation coefficient was observed under combined red and blue (4:1) light. In addition, this treatment resulted in the second highest chlorophyll content, the thickest palisade and spongy tissues, and consequently, the thickest leaves. The same treatment resulted in the second highest stomatal density, albeit concomitantly with the smallest average stomatal length and width. Discussion These results indicate that high-quality propagation of Huajin shoots can be achieved by culturing the plants in vitro under a combination of red and blue (4:1) lights. Previous studies have shown that red and blue lights improve rooting and transplanting rates of tissue culture seedlings. Hence, future research should focus on the effect of light quality on…
bibliographic citation: He et al. (2020) Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin. PeerJ 8:e10016 https://doi.org/10.7717/peerj.10016
date submitted: 2020-02-21
date accepted: 2020-09-01
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Chaoyin
author list: Agent
  family name: Zeng
  given name: Yanling
author list: Agent
  family name: Fu
  given name: Yuzhong
author list: Agent
  family name: Wu
  given name: Jiahao
author list: Agent
  family name: Liang
  given name: Qin
doi: 10.7717/peerj.10016
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 He et al.
attribution name: He et al.

The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians
type: item
type: AcademicArticle
description: The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.
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format: text/html
creator: Jana Bozáňová
creator: Zuzana Čiamporová Zat’ovičová
creator: Fedor Čiampor Jr
creator: Tomasz Mamos
creator: Michał Grabowski
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.10039
publisher: PeerJ Inc.
rights: © 2020 Bozáňová et al.
abstract: The Western Carpathians are a particularly interesting part of the Carpathian Arc. According to recent molecular data upon aquatic and terrestrial taxa, this mountain area is an important biodiversity hotspot of Europe. Moreover, the W Carpathians include rich systems of karst springs inhabited by specific fauna, where molecular diversity and phylogeographic patterns are yet to be fully explored. Our study aims to compare population genetic structure and molecular diversity of two related and commonly co-occurring riffle beetles, Elmis aenea (PWJ Müller, 1806) and Limnius perrisi (Dufour, 1843) in the springs and streams of the W Carpathians using the mitochondrial DNA barcoding fragment of the cytochrome c oxidase subunit I gene (COI). The relatively stable thermal and chemical conditions of springs throughout unfavourable climatic settings make these highly specific lotic systems potentially ideal for a long-term survival of some aquatic biota. Populations of both elmid species were relatively homogeneous genetically, with a single dominant haplotype. However, we revealed that E. aenea significantly dominated in the springs, while L. perrisi preferred streams. Relative isolation of the springs and their stable conditions were reflected in significantly higher molecular diversity of the E. aenea population in comparison to L. perrisi. The results of Bayesian Skyline Plot analysis also indicated the exceptional position of springs regarding maintaining the population size of E. aenea. On the other hand, it seems that streams in the W Carpathians provide more effective dispersal channels for L. perrisi, whose population expanded much earlier compared to E. aenea. Present study points out that different demographic histories of these two closely related elmid species are manifested by their different habitat preference and molecular diversity.
bibliographic citation: Bozáňová et al. (2020) The tale of springs and streams: how different aquatic ecosystems impacted the mtDNA population structure of two riffle beetles in the Western Carpathians. PeerJ 8:e10039 https://doi.org/10.7717/peerj.10039
date submitted: 2020-06-02
date accepted: 2020-09-04
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bozáňová
  given name: Jana
author list: Agent
  family name: Čiamporová Zat’ovičová
  given name: Zuzana
author list: Agent
  family name: Čiampor Jr
  given name: Fedor
author list: Agent
  family name: Mamos
  given name: Tomasz
author list: Agent
  family name: Grabowski
  given name: Michał
doi: 10.7717/peerj.10039
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Bozáňová et al.
attribution name: Bozáňová et al.

Neighbourhood socioeconomic characteristics and blood pressure among Jamaican youth: a pooled analysis of data from observational studies
type: item
type: AcademicArticle
description: Introduction Neighbourhood characteristics are associated with several diseases, but few studies have investigated the association between neighbourhood and health in Jamaica. We evaluated the relationship between neighbourhood socioeconomic status (SES) and blood pressure (BP) among youth, 15–24 years old, in Jamaica. Methods A pooled analysis was conducted using data from three studies (two national surveys and a birth cohort), conducted between 2005–2008, with individual level BP, anthropometric and demographic data, and household SES. Data on neighbourhood SES were obtained from the Mona Geo-Informatics Institute. Neighbourhood was defined using community boundaries from the Social Development Commission in Jamaica. Community characteristics (poverty, unemployment, dependency ratio, population density, house size, and proportion with tertiary education) were combined into SES scores using principal component analysis (PCA). Multivariable analyses were computed using mixed effects multilevel models. Results Analyses included 2,556 participants (1,446 females; 1,110 males; mean age 17.9 years) from 306 communities. PCA yielded two neighbourhood SES variables; the first, PCA-SES1, loaded highly positive for tertiary education and larger house size (higher value = higher SES); while the second, PCA-SES2, loaded highly positive for unemployment and population density (higher value = lower SES). Among males, PCA-SES1 was inversely associated with systolic BP (β-1.48 [95%CI −2.11, −0.84] mmHg, p < 0.001, for each standard deviation unit increase in PCA-SES1 score) in multivariable model accounting for age, household SES, study, BMI, fasting glucose, physical activity and diet. PCA-SES1 was not significantly associated with systolic BP among females (β −0.48 [−1.62, 0.66], p = 0.410) in a similar model. Associations for PCA-SES2 was assessed using linear splines to account for non-linear effects. The were no significant associations between systolic BP and PCA-SES2 amon…
format: application/pdf
format: text/html
creator: Trevor S. Ferguson
creator: Novie O.M. Younger-Coleman
creator: Jasneth Mullings
creator: Damian Francis
creator: Lisa-Gaye Greene
creator: Parris Lyew-Ayee
creator: Rainford Wilks
subject: Cardiology
subject: Epidemiology
subject: Internal Medicine
subject: Public Health
description: doi:10.7717/peerj.10058
publisher: PeerJ Inc.
rights: © 2020 Ferguson et al.
abstract: Introduction Neighbourhood characteristics are associated with several diseases, but few studies have investigated the association between neighbourhood and health in Jamaica. We evaluated the relationship between neighbourhood socioeconomic status (SES) and blood pressure (BP) among youth, 15–24 years old, in Jamaica. Methods A pooled analysis was conducted using data from three studies (two national surveys and a birth cohort), conducted between 2005–2008, with individual level BP, anthropometric and demographic data, and household SES. Data on neighbourhood SES were obtained from the Mona Geo-Informatics Institute. Neighbourhood was defined using community boundaries from the Social Development Commission in Jamaica. Community characteristics (poverty, unemployment, dependency ratio, population density, house size, and proportion with tertiary education) were combined into SES scores using principal component analysis (PCA). Multivariable analyses were computed using mixed effects multilevel models. Results Analyses included 2,556 participants (1,446 females; 1,110 males; mean age 17.9 years) from 306 communities. PCA yielded two neighbourhood SES variables; the first, PCA-SES1, loaded highly positive for tertiary education and larger house size (higher value = higher SES); while the second, PCA-SES2, loaded highly positive for unemployment and population density (higher value = lower SES). Among males, PCA-SES1 was inversely associated with systolic BP (β-1.48 [95%CI −2.11, −0.84] mmHg, p < 0.001, for each standard deviation unit increase in PCA-SES1 score) in multivariable model accounting for age, household SES, study, BMI, fasting glucose, physical activity and diet. PCA-SES1 was not significantly associated with systolic BP among females (β −0.48 [−1.62, 0.66], p = 0.410) in a similar model. Associations for PCA-SES2 was assessed using linear splines to account for non-linear effects. The were no significant associations between systolic BP and PCA-SES2 amon…
bibliographic citation: Ferguson et al. (2020) Neighbourhood socioeconomic characteristics and blood pressure among Jamaican youth: a pooled analysis of data from observational studies. PeerJ 8:e10058 https://doi.org/10.7717/peerj.10058
date submitted: 2019-10-22
date accepted: 2020-09-07
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferguson
  given name: Trevor S.
author list: Agent
  family name: Younger-Coleman
  given name: Novie O.M.
author list: Agent
  family name: Mullings
  given name: Jasneth
author list: Agent
  family name: Francis
  given name: Damian
author list: Agent
  family name: Greene
  given name: Lisa-Gaye
author list: Agent
  family name: Lyew-Ayee
  given name: Parris
author list: Agent
  family name: Wilks
  given name: Rainford
doi: 10.7717/peerj.10058
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Ferguson et al.
attribution name: Ferguson et al.

Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies
type: item
type: AcademicArticle
description: Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
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creator: Iván Prieto-Potin
creator: Nerea Carvajal
creator: Jenifer Plaza-Sánchez
creator: Rebeca Manso
creator: Carmen Laura Aúz-Alexandre
creator: Cristina Chamizo
creator: Sandra Zazo
creator: Almudena López-Sánchez
creator: Socorro María Rodríguez-Pinilla
creator: Laura Camacho
creator: Raquel Longarón
creator: Beatriz Bellosillo
creator: Rosa Somoza
creator: Javier Hernández-Losa
creator: Víctor Manuel Fernández-Soria
creator: Ricardo Ramos-Ruiz
creator: Ion Cristóbal
creator: Jesús García-Foncillas
creator: Federico Rojo
subject: Molecular Biology
subject: Hematology
subject: Oncology
subject: Pathology
subject: Medical Genetics
description: doi:10.7717/peerj.10069
publisher: PeerJ Inc.
rights: © 2020 Prieto-Potin et al.
abstract: Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
bibliographic citation: Prieto-Potin et al. (2020) Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ 8:e10069 https://doi.org/10.7717/peerj.10069
date submitted: 2020-07-02
date accepted: 2020-09-09
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prieto-Potin
  given name: Iván
author list: Agent
  family name: Carvajal
  given name: Nerea
author list: Agent
  family name: Plaza-Sánchez
  given name: Jenifer
author list: Agent
  family name: Manso
  given name: Rebeca
author list: Agent
  family name: Aúz-Alexandre
  given name: Carmen Laura
author list: Agent
  family name: Chamizo
  given name: Cristina
author list: Agent
  family name: Zazo
  given name: Sandra
author list: Agent
  family name: López-Sánchez
  given name: Almudena
author list: Agent
  family name: Rodríguez-Pinilla
  given name: Socorro María
author list: Agent
  family name: Camacho
  given name: Laura
author list: Agent
  family name: Longarón
  given name: Raquel
author list: Agent
  family name: Bellosillo
  given name: Beatriz
author list: Agent
  family name: Somoza
  given name: Rosa
author list: Agent
  family name: Hernández-Losa
  given name: Javier
author list: Agent
  family name: Fernández-Soria
  given name: Víctor Manuel
author list: Agent
  family name: Ramos-Ruiz
  given name: Ricardo
author list: Agent
  family name: Cristóbal
  given name: Ion
author list: Agent
  family name: García-Foncillas
  given name: Jesús
author list: Agent
  family name: Rojo
  given name: Federico
doi: 10.7717/peerj.10069
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Prieto-Potin et al.
attribution name: Prieto-Potin et al.

A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction
type: item
type: AcademicArticle
description: Cerebral edema (CE) is a non-specific pathological swelling of the brain secondary to any type of neurological injury. The real-time monitoring of focal CE mostly found in early stage is of great significance to reduce mortality and disability. Magnetic Induction Phase Shift (MIPS) is expected to achieve non-invasive continuous monitoring of CE. However, most existing MIPS sensors are made of hard materials which makes it difficult to accurately retrieve CE information. In this article, we designed a conformal two-coil structure and a single-coil structure, and studied their sensitivity map using finite element method (FEM). After that, the conformal MIPS sensor that is preferable for local CE monitoring was fabricated by flexible printed circuit (FPC). Next, physical experiments were conducted to investigate its performance on different levels of simulated CE solution volume, measurement distance, and bending. Subsequently, 14 rabbits were chosen to establish CE model and another three rabbits were selected as controls. The 24-hour MIPS real-time monitoring experiments was carried out to verify that the feasibility. Results showed a gentler attenuation trend of the conformal two-coil structure, compared with the single-coil structure. In addition, the novel flexible conformal MIPS sensor has a characteristic of being robust to bending according to the physical experiments. The results of animal experiments showed that the sensor can be used for CE monitoring. It can be concluded that this flexible conformal MIPS sensor is desirable for local focusing measurement of CE and subsequent multidimensional information extraction for predicting model. Also, it enables a much more comfortable environment for long-time bedside monitoring.
format: application/pdf
format: text/html
creator: Jingbo Chen
creator: Gen Li
creator: Mingsheng Chen
creator: Gui Jin
creator: Shuanglin Zhao
creator: Zelin Bai
creator: Jun Yang
creator: Huayou Liang
creator: Jia Xu
creator: Jian Sun
creator: Mingxin Qin
subject: Bioengineering
subject: Biophysics
subject: Neurology
subject: Computational Science
description: doi:10.7717/peerj.10079
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Cerebral edema (CE) is a non-specific pathological swelling of the brain secondary to any type of neurological injury. The real-time monitoring of focal CE mostly found in early stage is of great significance to reduce mortality and disability. Magnetic Induction Phase Shift (MIPS) is expected to achieve non-invasive continuous monitoring of CE. However, most existing MIPS sensors are made of hard materials which makes it difficult to accurately retrieve CE information. In this article, we designed a conformal two-coil structure and a single-coil structure, and studied their sensitivity map using finite element method (FEM). After that, the conformal MIPS sensor that is preferable for local CE monitoring was fabricated by flexible printed circuit (FPC). Next, physical experiments were conducted to investigate its performance on different levels of simulated CE solution volume, measurement distance, and bending. Subsequently, 14 rabbits were chosen to establish CE model and another three rabbits were selected as controls. The 24-hour MIPS real-time monitoring experiments was carried out to verify that the feasibility. Results showed a gentler attenuation trend of the conformal two-coil structure, compared with the single-coil structure. In addition, the novel flexible conformal MIPS sensor has a characteristic of being robust to bending according to the physical experiments. The results of animal experiments showed that the sensor can be used for CE monitoring. It can be concluded that this flexible conformal MIPS sensor is desirable for local focusing measurement of CE and subsequent multidimensional information extraction for predicting model. Also, it enables a much more comfortable environment for long-time bedside monitoring.
bibliographic citation: Chen et al. (2020) A noninvasive flexible conformal sensor for accurate real-time monitoring of local cerebral edema based on electromagnetic induction. PeerJ 8:e10079 https://doi.org/10.7717/peerj.10079
date submitted: 2020-06-02
date accepted: 2020-09-11
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jingbo
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Chen
  given name: Mingsheng
author list: Agent
  family name: Jin
  given name: Gui
author list: Agent
  family name: Zhao
  given name: Shuanglin
author list: Agent
  family name: Bai
  given name: Zelin
author list: Agent
  family name: Yang
  given name: Jun
author list: Agent
  family name: Liang
  given name: Huayou
author list: Agent
  family name: Xu
  given name: Jia
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Qin
  given name: Mingxin
doi: 10.7717/peerj.10079
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Chen et al.
attribution name: Chen et al.

Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring
type: item
type: AcademicArticle
description: The social context of social species such as sheep can modify their physiological and behavioural responses to stressors, through social buffering and social facilitation. Social buffering can lead to amelioration of stress, while social facilitation can lead to stress responses in an observer animal in the presence of a conspecific in distress. The current study investigated twin lambs undergoing ring castration, grouped either homogeneously with a castrated lamb (actor), or heterogeneously with a non-castrated lamb (observer) to examine the impact of social grouping on behavioural responses. Each lamb was scored for two classes of behaviour: pain-related behaviours and postures that are putatively related to the response to castration; and attentional behaviours directed at its twin. Thus, each lamb participated in the experiment as an actor exhibiting pain-related behaviours and postures, and as an observer of its twin. When behaviours of lambs were assessed as actors, there was a significant (P < 0.05) effect of castration but no significant effect of social grouping on expression of pain-related behaviours. When behaviours of lambs were assessed as observers, homogeneous grouping of castrated lambs increased attention towards the other twin in comparison to non-castrated lambs grouped homogeneously or lambs grouped heterogeneously (P < 0.01). Non-castrated lambs grouped homogeneously demonstrated significantly lower numbers of head direction changes (P < 0.001) and lower number of ear posture changes (P < 0.05) than heterogeneously grouped or castrated lambs. This study indicates that social attention between twin lambs is not clearly dependent on pain status of the actor lamb. It suggests that in order for the observer lamb to provide significant attention to the actor lamb displaying pain-related behaviour, the observer lamb also needs to be experiencing pain concurrently. Furthermore, there is some evidence that the presence of pain-related behaviours can le…
format: application/pdf
format: text/html
creator: Andrew Inhyuk Cho
creator: Caroline Lee
creator: Alison Small
subject: Agricultural Science
subject: Animal Behavior
subject: Veterinary Medicine
subject: Ethical Issues
description: doi:10.7717/peerj.10081
publisher: PeerJ Inc.
rights: © 2020 Cho et al.
abstract: The social context of social species such as sheep can modify their physiological and behavioural responses to stressors, through social buffering and social facilitation. Social buffering can lead to amelioration of stress, while social facilitation can lead to stress responses in an observer animal in the presence of a conspecific in distress. The current study investigated twin lambs undergoing ring castration, grouped either homogeneously with a castrated lamb (actor), or heterogeneously with a non-castrated lamb (observer) to examine the impact of social grouping on behavioural responses. Each lamb was scored for two classes of behaviour: pain-related behaviours and postures that are putatively related to the response to castration; and attentional behaviours directed at its twin. Thus, each lamb participated in the experiment as an actor exhibiting pain-related behaviours and postures, and as an observer of its twin. When behaviours of lambs were assessed as actors, there was a significant (P < 0.05) effect of castration but no significant effect of social grouping on expression of pain-related behaviours. When behaviours of lambs were assessed as observers, homogeneous grouping of castrated lambs increased attention towards the other twin in comparison to non-castrated lambs grouped homogeneously or lambs grouped heterogeneously (P < 0.01). Non-castrated lambs grouped homogeneously demonstrated significantly lower numbers of head direction changes (P < 0.001) and lower number of ear posture changes (P < 0.05) than heterogeneously grouped or castrated lambs. This study indicates that social attention between twin lambs is not clearly dependent on pain status of the actor lamb. It suggests that in order for the observer lamb to provide significant attention to the actor lamb displaying pain-related behaviour, the observer lamb also needs to be experiencing pain concurrently. Furthermore, there is some evidence that the presence of pain-related behaviours can le…
bibliographic citation: Cho et al. (2020) Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring. PeerJ 8:e10081 https://doi.org/10.7717/peerj.10081
date submitted: 2020-04-23
date accepted: 2020-09-11
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Andrew Inhyuk
author list: Agent
  family name: Lee
  given name: Caroline
author list: Agent
  family name: Small
  given name: Alison
doi: 10.7717/peerj.10081
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: © 2020 Cho et al.
attribution name: Cho et al.

Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children
type: item
type: AcademicArticle
description: Several studies have tried to establish the factors that underlie mathematical ability across development. Among them, spatial and motor abilities might play a relevant role, but no studies jointly contemplate both types of abilities to account for mathematical performance. The present study was designed to observe the roles of spatial and motor skills in mathematical performance. A total of 305 children aged between 6 and 8 years took part in this study. A generalized linear regression model with mathematical performance as a dependent variable was performed. Results revealed that Block design (as a visuospatial reasoning measure) accounted for mathematical performance, especially among 6- and 7-year-olds but not in 8-year-olds. After controlling for the effect of the block design, mental rotation and manual dexterity predicted mathematical performance. These findings highlight the role of underlying cognitive (spatial) and motor abilities in supporting mathematical achievement in primary school children.
format: application/pdf
format: text/html
creator: Laura M. Fernández-Méndez
creator: María José Contreras
creator: Irene Cristina Mammarella
creator: Tommaso Feraco
creator: Chiara Meneghetti
subject: Psychiatry and Psychology
subject: Science and Medical Education
description: doi:10.7717/peerj.10095
publisher: PeerJ Inc.
rights: © 2020 Fernández-Méndez et al.
abstract: Several studies have tried to establish the factors that underlie mathematical ability across development. Among them, spatial and motor abilities might play a relevant role, but no studies jointly contemplate both types of abilities to account for mathematical performance. The present study was designed to observe the roles of spatial and motor skills in mathematical performance. A total of 305 children aged between 6 and 8 years took part in this study. A generalized linear regression model with mathematical performance as a dependent variable was performed. Results revealed that Block design (as a visuospatial reasoning measure) accounted for mathematical performance, especially among 6- and 7-year-olds but not in 8-year-olds. After controlling for the effect of the block design, mental rotation and manual dexterity predicted mathematical performance. These findings highlight the role of underlying cognitive (spatial) and motor abilities in supporting mathematical achievement in primary school children.
bibliographic citation: Fernández-Méndez et al. (2020) Mathematical achievement: the role of spatial and motor skills in 6–8 year-old children. PeerJ 8:e10095 https://doi.org/10.7717/peerj.10095
date submitted: 2020-04-29
date accepted: 2020-09-14
issued: 2020-10-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernández-Méndez
  given name: Laura M.
author list: Agent
  family name: Contreras
  given name: María José
author list: Agent
  family name: Mammarella
  given name: Irene Cristina
author list: Agent
  family name: Feraco
  given name: Tommaso
author list: Agent
  family name: Meneghetti
  given name: Chiara
doi: 10.7717/peerj.10095
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-06
copyright: ©2020 Fernández-Méndez et al.
attribution name: Fernández-Méndez et al.

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