PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
items: Auditory processing in the zebra finch midbrain: single unit responses and effect of rearing experience
items: The effects of humic substances on DNA isolation from soils
items: Effectiveness of non-lethal predator deterrents to reduce livestock losses to leopard attacks within a multiple-use landscape of the Himalayan region
items: A cross-sectional assessment of the relationship between sedative medication and anticholinergic medication use and the movement behaviour of older adults living in residential aged care
items: Disentangling biological variability and taphonomy: shape analysis of the limb long bones of the sauropodomorph dinosaur Plateosaurus
items: Morphological changes in the lower Lancang River due to extensive human activities
items: The rule-based insensitivity effect: a systematic review
items: Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma
items: Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy
type: item
type: AcademicArticle
description: We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival.
format: application/pdf
format: text/html
creator: Shanliang Zhong
creator: Huanwen Chen
creator: Sujin Yang
creator: Jifeng Feng
creator: Siying Zhou
subject: Bioinformatics
subject: Oncology
subject: Women’s Health
subject: Computational Science
description: doi:10.7717/peerj.9621
publisher: PeerJ Inc.
rights: © 2020 Zhong et al.
abstract: We aimed to identify prognostic signature based on autophagy-related genes (ARGs) for breast cancer patients. The datasets of breast cancer were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Least absolute shrinkage and selection operator (LASSO) Cox regression was conducted to construct multiple-ARG risk signature. In total, 32 ARGs were identified as differentially expressed between tumors and adjacent normal tissues based on TCGA. Six ARGs (IFNG, TP63, PPP1R15A, PTK6, EIF4EBP1 and NKX2-3) with non-zero coefficient were selected from the 32 ARGs using LASSO regression. The 6-ARG signature divided patients into high-and low-risk group. Survival analysis indicated that low-risk group had longer survival time than high-risk group. We further validated the 6-ARG signature using dataset from GEO and found similar results. We analyzed the associations between ARGs and breast cancer survival in TCGA and nine GEO datasets, and obtained 170 ARGs with significant associations. EIF4EBP1, FOS and FAS were the top three ARGs with highest numbers of significant associations. EIF4EBP1 may be a key ARG which had a higher expression level in patients with more malignant molecular subtypes and higher grade breast cancer. In conclusion, our 6-ARG signature was of significance in predicting of overall survival of patients with breast cancer. EIF4EBP1 may be a key ARG associated with breast cancer survival.
bibliographic citation: Zhong et al. (2020) Identification and validation of prognostic signature for breast cancer based on genes potentially involved in autophagy. PeerJ 8:e9621 https://doi.org/10.7717/peerj.9621
date submitted: 2020-04-21
date accepted: 2020-07-07
issued: 2020-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Shanliang
author list: Agent
  family name: Chen
  given name: Huanwen
author list: Agent
  family name: Yang
  given name: Sujin
author list: Agent
  family name: Feng
  given name: Jifeng
author list: Agent
  family name: Zhou
  given name: Siying
doi: 10.7717/peerj.9621
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-27
copyright: © 2020 Zhong et al.
attribution name: Zhong et al.

Auditory processing in the zebra finch midbrain: single unit responses and effect of rearing experience
type: item
type: AcademicArticle
description: In birds the auditory system plays a key role in providing the sensory input used to discriminate between conspecific and heterospecific vocal signals. In those species that are known to learn their vocalizations, for example, songbirds, it is generally considered that this ability arises and is manifest in the forebrain, although there is no a priori reason why brainstem components of the auditory system could not also play an important part. To test this assumption, we used groups of normal reared and cross-fostered zebra finches that had previously been shown in behavioural experiments to reduce their preference for conspecific songs subsequent to cross fostering experience with Bengalese finches, a related species with a distinctly different song. The question we asked, therefore, is whether this experiential change also changes the bias in favour of conspecific song displayed by auditory midbrain units of normally raised zebra finches. By recording the responses of single units in MLd to a variety of zebra finch and Bengalese finch songs in both normally reared and cross-fostered zebra finches, we provide a positive answer to this question. That is, the difference in response to conspecific and heterospecific songs seen in normal reared zebra finches is reduced following cross-fostering. In birds the virtual absence of mammalian-like cortical projections upon auditory brainstem nuclei argues against the interpretation that MLd units change, as observed in the present experiments, as a result of top-down influences on sensory processing. Instead, it appears that MLd units can be influenced significantly by sensory inputs arising directly from a change in auditory experience during development.
format: application/pdf
format: text/html
creator: Priscilla Logerot
creator: Paul F. Smith
creator: Martin Wild
creator: M. Fabiana Kubke
subject: Animal Behavior
subject: Neuroscience
subject: Zoology
description: doi:10.7717/peerj.9363
publisher: PeerJ Inc.
rights: © 2020 Logerot et al.
abstract: In birds the auditory system plays a key role in providing the sensory input used to discriminate between conspecific and heterospecific vocal signals. In those species that are known to learn their vocalizations, for example, songbirds, it is generally considered that this ability arises and is manifest in the forebrain, although there is no a priori reason why brainstem components of the auditory system could not also play an important part. To test this assumption, we used groups of normal reared and cross-fostered zebra finches that had previously been shown in behavioural experiments to reduce their preference for conspecific songs subsequent to cross fostering experience with Bengalese finches, a related species with a distinctly different song. The question we asked, therefore, is whether this experiential change also changes the bias in favour of conspecific song displayed by auditory midbrain units of normally raised zebra finches. By recording the responses of single units in MLd to a variety of zebra finch and Bengalese finch songs in both normally reared and cross-fostered zebra finches, we provide a positive answer to this question. That is, the difference in response to conspecific and heterospecific songs seen in normal reared zebra finches is reduced following cross-fostering. In birds the virtual absence of mammalian-like cortical projections upon auditory brainstem nuclei argues against the interpretation that MLd units change, as observed in the present experiments, as a result of top-down influences on sensory processing. Instead, it appears that MLd units can be influenced significantly by sensory inputs arising directly from a change in auditory experience during development.
bibliographic citation: Logerot et al. (2020) Auditory processing in the zebra finch midbrain: single unit responses and effect of rearing experience. PeerJ 8:e9363 https://doi.org/10.7717/peerj.9363
date submitted: 2019-09-05
date accepted: 2020-05-26
issued: 2020-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Logerot
  given name: Priscilla
author list: Agent
  family name: Smith
  given name: Paul F.
author list: Agent
  family name: Wild
  given name: Martin
author list: Agent
  family name: Kubke
  given name: M. Fabiana
doi: 10.7717/peerj.9363
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-24
copyright: © 2020 Logerot et al.
attribution name: Logerot et al.

The effects of humic substances on DNA isolation from soils
type: item
type: AcademicArticle
description: Background Humic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions. Methods The research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. Results Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
format: application/pdf
format: text/html
creator: Ewa Wnuk
creator: Adam Waśko
creator: Anna Walkiewicz
creator: Piotr Bartmiński
creator: Romualda Bejger
creator: Lilla Mielnik
creator: Andrzej Bieganowski
subject: Biotechnology
subject: Genomics
subject: Microbiology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.9378
publisher: PeerJ Inc.
rights: © 2020 Wnuk et al.
abstract: Background Humic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions. Methods The research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV–Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. Results Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
bibliographic citation: Wnuk et al. (2020) The effects of humic substances on DNA isolation from soils. PeerJ 8:e9378 https://doi.org/10.7717/peerj.9378
date submitted: 2020-01-29
date accepted: 2020-05-28
issued: 2020-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wnuk
  given name: Ewa
author list: Agent
  family name: Waśko
  given name: Adam
author list: Agent
  family name: Walkiewicz
  given name: Anna
author list: Agent
  family name: Bartmiński
  given name: Piotr
author list: Agent
  family name: Bejger
  given name: Romualda
author list: Agent
  family name: Mielnik
  given name: Lilla
author list: Agent
  family name: Bieganowski
  given name: Andrzej
doi: 10.7717/peerj.9378
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-24
copyright: © 2020 Wnuk et al.
attribution name: Wnuk et al.

Effectiveness of non-lethal predator deterrents to reduce livestock losses to leopard attacks within a multiple-use landscape of the Himalayan region
type: item
type: AcademicArticle
description: Lethal measures are widely adopted by local communities and governments to manage human-wildlife conflicts. Such measures lead to large scale decline of carnivore populations globally with trophic cascades on ecosystems and questionable impacts on human-wildlife conflicts. Mitigating human-carnivore conflicts through non-lethal measures will protect endangered predators and secure livelihoods. However, information on the effectiveness of such measures are extremely limited and hence cannot be applied in developing scientific evidence. Further to develop human-carnivore coexistence models, it is important for local community members, biologists and wildlife managers to actively participate in conservation programs. We evaluated the response of a non-lethal visual deterrent (i.e. fox lights) to deter leopard attacks on livestock within a multiple-use landscape of western Himalaya through community engagement. We monitored 16 experimental sites and 17 control sites within 27 villages and recorded data on livestock depredation by leopards between April 2018 to April 2019. A multivariate analysis was conducted to determine the influence of landscape predictors and animal husbandry practices on livestock depredation by leopards within the vicinity of human settlements. We found that visual deterrents discouraged common leopards to predate on livestock (cows and goats). We also demonstrated that community based conservation initiatives are successful in mitigating human-carnivore conflicts within large semi-natural landscapes. We suggest developing site specific coexistence strategies and adopting non-lethal measures to safeguard carnivores, livestock and humans within shared landscapes.
format: application/pdf
format: text/html
creator: Dipanjan Naha
creator: Pooja Chaudhary
creator: Gaurav Sonker
creator: Sambandam Sathyakumar
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.9544
publisher: PeerJ Inc.
rights: © 2020 Naha et al.
abstract: Lethal measures are widely adopted by local communities and governments to manage human-wildlife conflicts. Such measures lead to large scale decline of carnivore populations globally with trophic cascades on ecosystems and questionable impacts on human-wildlife conflicts. Mitigating human-carnivore conflicts through non-lethal measures will protect endangered predators and secure livelihoods. However, information on the effectiveness of such measures are extremely limited and hence cannot be applied in developing scientific evidence. Further to develop human-carnivore coexistence models, it is important for local community members, biologists and wildlife managers to actively participate in conservation programs. We evaluated the response of a non-lethal visual deterrent (i.e. fox lights) to deter leopard attacks on livestock within a multiple-use landscape of western Himalaya through community engagement. We monitored 16 experimental sites and 17 control sites within 27 villages and recorded data on livestock depredation by leopards between April 2018 to April 2019. A multivariate analysis was conducted to determine the influence of landscape predictors and animal husbandry practices on livestock depredation by leopards within the vicinity of human settlements. We found that visual deterrents discouraged common leopards to predate on livestock (cows and goats). We also demonstrated that community based conservation initiatives are successful in mitigating human-carnivore conflicts within large semi-natural landscapes. We suggest developing site specific coexistence strategies and adopting non-lethal measures to safeguard carnivores, livestock and humans within shared landscapes.
bibliographic citation: Naha et al. (2020) Effectiveness of non-lethal predator deterrents to reduce livestock losses to leopard attacks within a multiple-use landscape of the Himalayan region. PeerJ 8:e9544 https://doi.org/10.7717/peerj.9544
date submitted: 2020-05-06
date accepted: 2020-06-24
issued: 2020-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naha
  given name: Dipanjan
author list: Agent
  family name: Chaudhary
  given name: Pooja
author list: Agent
  family name: Sonker
  given name: Gaurav
author list: Agent
  family name: Sathyakumar
  given name: Sambandam
doi: 10.7717/peerj.9544
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-24
copyright: ©2020 Naha et al.
attribution name: Naha et al.

A cross-sectional assessment of the relationship between sedative medication and anticholinergic medication use and the movement behaviour of older adults living in residential aged care
type: item
type: AcademicArticle
description: Objectives Medications with anticholinergic or sedative effects are frequently used by older people but can increase risk of falls and adverse events; however, less is known about their effect on movement behaviour. Here we examine the cross-sectional association between medication use and movement behaviour in older adults living in residential aged care. Materials and Methods Twenty-eight older adults living in residential aged care in metropolitan Australia participated. Medication data were collected from participants’ medical charts and sedative load and anticholinergic burden were determined. Seven-day movement behaviour was objectively assessed by a wrist-worn triaxial accelerometer. Raw accelerations were converted to sleep, sedentary time, and time in light, moderate, and moderate-to-vigorous physical activity. To explore the relationship between medication and movement behaviour, Spearman’s Rho correlations were conducted, as the data were not normally distributed. Results Analyses indicated that while anticholinergic burden was not associated with movement behaviour, sedative load was negatively correlated with a number of variables, accounting for 14% variance in moderate-to-vigorous physical activity (MVPA), and 17% in the bout length of MVPA (p < .02). Conclusion The findings of this study showed a negative association between sedative load, due to medicines, and an individual’s movement behaviour. The impact of this could be a reduction in the ability of this population to maintain or improve their functional mobility, which may overshadow any benefits of the medicine in some circumstances.
format: application/pdf
format: text/html
creator: Gaynor Parfitt
creator: Dannielle Post
creator: Lisa Kalisch Ellett
creator: Renly Lim
creator: Alison Penington
creator: Megan Corlis
creator: Elizabeth Roughead
subject: Cognitive Disorders
subject: Geriatrics
subject: Pharmacology
subject: Public Health
description: doi:10.7717/peerj.9605
publisher: PeerJ Inc.
rights: © 2020 Parfitt et al.
abstract: Objectives Medications with anticholinergic or sedative effects are frequently used by older people but can increase risk of falls and adverse events; however, less is known about their effect on movement behaviour. Here we examine the cross-sectional association between medication use and movement behaviour in older adults living in residential aged care. Materials and Methods Twenty-eight older adults living in residential aged care in metropolitan Australia participated. Medication data were collected from participants’ medical charts and sedative load and anticholinergic burden were determined. Seven-day movement behaviour was objectively assessed by a wrist-worn triaxial accelerometer. Raw accelerations were converted to sleep, sedentary time, and time in light, moderate, and moderate-to-vigorous physical activity. To explore the relationship between medication and movement behaviour, Spearman’s Rho correlations were conducted, as the data were not normally distributed. Results Analyses indicated that while anticholinergic burden was not associated with movement behaviour, sedative load was negatively correlated with a number of variables, accounting for 14% variance in moderate-to-vigorous physical activity (MVPA), and 17% in the bout length of MVPA (p < .02). Conclusion The findings of this study showed a negative association between sedative load, due to medicines, and an individual’s movement behaviour. The impact of this could be a reduction in the ability of this population to maintain or improve their functional mobility, which may overshadow any benefits of the medicine in some circumstances.
bibliographic citation: Parfitt et al. (2020) A cross-sectional assessment of the relationship between sedative medication and anticholinergic medication use and the movement behaviour of older adults living in residential aged care. PeerJ 8:e9605 https://doi.org/10.7717/peerj.9605
date submitted: 2020-04-03
date accepted: 2020-07-04
issued: 2020-07-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parfitt
  given name: Gaynor
author list: Agent
  family name: Post
  given name: Dannielle
author list: Agent
  family name: Kalisch Ellett
  given name: Lisa
author list: Agent
  family name: Lim
  given name: Renly
author list: Agent
  family name: Penington
  given name: Alison
author list: Agent
  family name: Corlis
  given name: Megan
author list: Agent
  family name: Roughead
  given name: Elizabeth
doi: 10.7717/peerj.9605
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-24
copyright: ©2020 Parfitt et al.
attribution name: Parfitt et al.

Disentangling biological variability and taphonomy: shape analysis of the limb long bones of the sauropodomorph dinosaur Plateosaurus
type: item
type: AcademicArticle
description: Sauropodomorph dinosaurs constitute a well-studied clade of dinosaurs, notably because of the acquisition of gigantism within this group. The genus Plateosaurus is one of the best-known sauropodomorphs, with numerous remains from various localities. Its tumultuous taxonomic history suggests the relevance of addressing its intrageneric shape variability, mixed with taphonomic modifications of the original bone shape. Here we investigate quantitatively the morphological variation of Plateosaurus occurring at the genus level by studying the shape variation of a sample of limb long bones. By means of 3D geometric morphometrics, the analysis of the uncorrelated variation permits separation of the variation estimated as obviously taphonomically influenced from the more biologically plausible variation. Beyond the dominant taphonomic signal, our approach permits interpretation of the most biologically plausible features, even on anatomical parts influenced by taphonomic deformations. Those features are thus found on a quantitative basis from the variation of samples containing fossil specimens, by taking the impact of taphonomy into account, which is paramount in order to avoid making biologically ambiguous interpretations.
format: application/pdf
format: text/html
creator: Rémi Lefebvre
creator: Ronan Allain
creator: Alexandra Houssaye
creator: Raphaël Cornette
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.9359
publisher: PeerJ Inc.
rights: © 2020 Lefebvre et al.
abstract: Sauropodomorph dinosaurs constitute a well-studied clade of dinosaurs, notably because of the acquisition of gigantism within this group. The genus Plateosaurus is one of the best-known sauropodomorphs, with numerous remains from various localities. Its tumultuous taxonomic history suggests the relevance of addressing its intrageneric shape variability, mixed with taphonomic modifications of the original bone shape. Here we investigate quantitatively the morphological variation of Plateosaurus occurring at the genus level by studying the shape variation of a sample of limb long bones. By means of 3D geometric morphometrics, the analysis of the uncorrelated variation permits separation of the variation estimated as obviously taphonomically influenced from the more biologically plausible variation. Beyond the dominant taphonomic signal, our approach permits interpretation of the most biologically plausible features, even on anatomical parts influenced by taphonomic deformations. Those features are thus found on a quantitative basis from the variation of samples containing fossil specimens, by taking the impact of taphonomy into account, which is paramount in order to avoid making biologically ambiguous interpretations.
bibliographic citation: Lefebvre et al. (2020) Disentangling biological variability and taphonomy: shape analysis of the limb long bones of the sauropodomorph dinosaur Plateosaurus. PeerJ 8:e9359 https://doi.org/10.7717/peerj.9359
date submitted: 2019-12-23
date accepted: 2020-05-25
issued: 2020-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lefebvre
  given name: Rémi
author list: Agent
  family name: Allain
  given name: Ronan
author list: Agent
  family name: Houssaye
  given name: Alexandra
author list: Agent
  family name: Cornette
  given name: Raphaël
doi: 10.7717/peerj.9359
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-23
copyright: © 2020 Lefebvre et al.
attribution name: Lefebvre et al.

Morphological changes in the lower Lancang River due to extensive human activities
type: item
type: AcademicArticle
description: Background Morphological changes in river beds determine the risk for soil erosion within floodplain areas. At present, little is known about river morphological changes in high-altitude mountainous area influenced by extensive human activities. The study has important reference value for clarifying the morphological changes of mountainous rivers due to extensive human activities. Methods Based on the long-term multi-source remote sensing image data, we analyzed morphological changes in the lower Lancang River (LCR) in Southwest China at regional and local scales, and determined their influencing factors. Visual interpretation is used to extract the information and unify the interpretation standards of various localities, mainly including water bodies, sandbars, shorelines and beaches. Based on high-resolution remote sensing images, we analyzed the planforms, erosion and accretion conditions in Jinghongba (JHB) reach and Ganlanba (GLB) reach. Results Our results showed that: (1) during 1993–2016, the planforms of Jinghongba and Ganlanba in the wide valley of the lower LCR changed significantly, (2) In the interval 1993 to 2016, the JHB reach exhibited extensive erosion, with the right bank more eroded seriously than the left bank, and an erosion area of 0.36 km2. The erosion area of the GLB reach was 0.33 km2, with accretion area of 0.61 km2. The right bank was dominated by erosion, while the left bank by sedimentation; (3) Morphological changes in JHB and GLB reches were the result of the combined effects of cascade hydropower development, river regulation, and sand-mining in the river. The results improved the understanding of riverbed evolution, and could help guide sediment management in mountainous areas influenced by extensive human activities.
format: application/pdf
format: text/html
creator: Peijia Wang
creator: Kaidao Fu
creator: Jiangcheng Huang
creator: Xingwu Duan
creator: Zaizhi Yang
subject: Ecosystem Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.9471
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Morphological changes in river beds determine the risk for soil erosion within floodplain areas. At present, little is known about river morphological changes in high-altitude mountainous area influenced by extensive human activities. The study has important reference value for clarifying the morphological changes of mountainous rivers due to extensive human activities. Methods Based on the long-term multi-source remote sensing image data, we analyzed morphological changes in the lower Lancang River (LCR) in Southwest China at regional and local scales, and determined their influencing factors. Visual interpretation is used to extract the information and unify the interpretation standards of various localities, mainly including water bodies, sandbars, shorelines and beaches. Based on high-resolution remote sensing images, we analyzed the planforms, erosion and accretion conditions in Jinghongba (JHB) reach and Ganlanba (GLB) reach. Results Our results showed that: (1) during 1993–2016, the planforms of Jinghongba and Ganlanba in the wide valley of the lower LCR changed significantly, (2) In the interval 1993 to 2016, the JHB reach exhibited extensive erosion, with the right bank more eroded seriously than the left bank, and an erosion area of 0.36 km2. The erosion area of the GLB reach was 0.33 km2, with accretion area of 0.61 km2. The right bank was dominated by erosion, while the left bank by sedimentation; (3) Morphological changes in JHB and GLB reches were the result of the combined effects of cascade hydropower development, river regulation, and sand-mining in the river. The results improved the understanding of riverbed evolution, and could help guide sediment management in mountainous areas influenced by extensive human activities.
bibliographic citation: Wang et al. (2020) Morphological changes in the lower Lancang River due to extensive human activities. PeerJ 8:e9471 https://doi.org/10.7717/peerj.9471
date submitted: 2020-03-11
date accepted: 2020-06-11
issued: 2020-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Peijia
author list: Agent
  family name: Fu
  given name: Kaidao
author list: Agent
  family name: Huang
  given name: Jiangcheng
author list: Agent
  family name: Duan
  given name: Xingwu
author list: Agent
  family name: Yang
  given name: Zaizhi
doi: 10.7717/peerj.9471
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-23
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The rule-based insensitivity effect: a systematic review
type: item
type: AcademicArticle
description: Background Adherence to inaccurate rules has been viewed as a characteristic of human rule-following (i.e., the rule-based insensitivity effect; RBIE) and has been thought to be exacerbated in individuals suffering from clinical conditions. This review intended to systematically examine these claims in adult populations. Methodology We screened 1464 records which resulted in 21 studies that were deemed eligible for inclusion. Each of these studies was examined to determine: (1) if there is evidence for the RBIE in adults and (2) if this effect is larger in those suffering from psychological problems compared to their non-suffering counterparts. In addition, we investigated how (3) different operationalizations of the RBIE, and (4) the external validity and risks of bias of the experimental work investigating this effect, might influence the conclusions that can be drawn from the current systematic review. Results (1) Out of the 20 studies that were relevant for examining if evidence exists for the RBIE in adults, only 11 were eligible for vote counting. Results showed that after the contingency change, the rule groups were more inclined to demonstrate behavior that was reinforced before the change, compared to their non-instructed counterparts. Critically, however, none of these studies examined if their no-instructions group was an adequate comparison group. As a result, this made it difficult to determine whether the effects that were observed in the rule groups could be attributed to the rules or instructions that were manipulated in those experiments. (2) The single study that was relevant for examining if adults suffering from psychological problems demonstrated larger levels of the RBIE, compared to their non-clinical counterparts, was not eligible for vote counting. As a result, no conclusions could be drawn about the extent to which psychological problems moderated the RBIE in that study. (3) Similar procedures and tasks have been used to examine the RBIE, b…
format: application/pdf
format: text/html
creator: Ama Kissi
creator: Colin Harte
creator: Sean Hughes
creator: Jan De Houwer
creator: Geert Crombez
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9496
publisher: PeerJ Inc.
rights: © 2020 Kissi et al.
abstract: Background Adherence to inaccurate rules has been viewed as a characteristic of human rule-following (i.e., the rule-based insensitivity effect; RBIE) and has been thought to be exacerbated in individuals suffering from clinical conditions. This review intended to systematically examine these claims in adult populations. Methodology We screened 1464 records which resulted in 21 studies that were deemed eligible for inclusion. Each of these studies was examined to determine: (1) if there is evidence for the RBIE in adults and (2) if this effect is larger in those suffering from psychological problems compared to their non-suffering counterparts. In addition, we investigated how (3) different operationalizations of the RBIE, and (4) the external validity and risks of bias of the experimental work investigating this effect, might influence the conclusions that can be drawn from the current systematic review. Results (1) Out of the 20 studies that were relevant for examining if evidence exists for the RBIE in adults, only 11 were eligible for vote counting. Results showed that after the contingency change, the rule groups were more inclined to demonstrate behavior that was reinforced before the change, compared to their non-instructed counterparts. Critically, however, none of these studies examined if their no-instructions group was an adequate comparison group. As a result, this made it difficult to determine whether the effects that were observed in the rule groups could be attributed to the rules or instructions that were manipulated in those experiments. (2) The single study that was relevant for examining if adults suffering from psychological problems demonstrated larger levels of the RBIE, compared to their non-clinical counterparts, was not eligible for vote counting. As a result, no conclusions could be drawn about the extent to which psychological problems moderated the RBIE in that study. (3) Similar procedures and tasks have been used to examine the RBIE, b…
bibliographic citation: Kissi et al. (2020) The rule-based insensitivity effect: a systematic review. PeerJ 8:e9496 https://doi.org/10.7717/peerj.9496
date submitted: 2020-01-27
date accepted: 2020-06-17
issued: 2020-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kissi
  given name: Ama
author list: Agent
  family name: Harte
  given name: Colin
author list: Agent
  family name: Hughes
  given name: Sean
author list: Agent
  family name: De Houwer
  given name: Jan
author list: Agent
  family name: Crombez
  given name: Geert
doi: 10.7717/peerj.9496
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-23
copyright: ©2020 Kissi et al.
attribution name: Kissi et al.

Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Prognostic genes in the tumor microenvironment play an important role in immune biological processes and the response of cancer to immunotherapy. Thus, we aimed to assess new biomarkers that are associated with immune/stromal cells in lung adenocarcinomas (LUAD) using the ESTIMATE algorithm, which also significantly affects the prognosis of cancer. Methods The RNA sequencing (RNA-Seq) and clinical data of LUAD were downloaded from the the Cancer Genome Atlas (TCGA ). The immune and stromal scores were calculated for each sample using the ESTIMATE algorithm. The LUAD gene chip expression profile data and the clinical data (GSE37745, GSE11969, and GSE50081) were downloaded from the Gene Expression Omnibus (GEO) for subsequent validation analysis. Differentially expressed genes were calculated between high and low score groups. Univariate Cox regression analysis was performed on differentially expressed genes (DEGs) between the two groups to obtain initial prognosis genes. These were verified by three independent LUAD cohorts from the GEO database. Multivariate Cox regression was used to identify overall survival-related DEGs. UALCAN and the Human Protein Atlas were used to analyze the mRNA /protein expression levels of the target genes. Immune cell infiltration was evaluated using the Tumor Immune Estimation Resource (TIMER) and CIBERSORT methods, and stromal cell infiltration was assessed using xCell. Results In this study, immune scores and stromal scores are significantly associated with the clinical characteristics of LUAD, including T stage, M stage, pathological stage, and overall survival time. 530 DEGs (18 upregulated and 512 downregulated) were found to coexist in the difference analysis with the immune scores and stromal scores subgroup. Univariate Cox regression analysis showed that 286 of the 530 DEGs were survival-related genes (p < 0.05). Of the 286 genes initially identified, nine prognosis-related genes (CSF2RB, ITK, FLT3, CD79A, CCR4, CCR6,…
format: application/pdf
format: text/html
creator: Zhan-yu Xu
creator: Mengli Zhao
creator: Wenjie Chen
creator: Kun Li
creator: Fanglu Qin
creator: Wei-wei Xiang
creator: Yu Sun
creator: Jiangbo Wei
creator: Li-qiang Yuan
creator: Shi-kang Li
creator: Sheng-hua Lin
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
subject: Data Science
description: doi:10.7717/peerj.9530
publisher: PeerJ Inc.
rights: © 2020 Xu et al.
abstract: Background Prognostic genes in the tumor microenvironment play an important role in immune biological processes and the response of cancer to immunotherapy. Thus, we aimed to assess new biomarkers that are associated with immune/stromal cells in lung adenocarcinomas (LUAD) using the ESTIMATE algorithm, which also significantly affects the prognosis of cancer. Methods The RNA sequencing (RNA-Seq) and clinical data of LUAD were downloaded from the the Cancer Genome Atlas (TCGA ). The immune and stromal scores were calculated for each sample using the ESTIMATE algorithm. The LUAD gene chip expression profile data and the clinical data (GSE37745, GSE11969, and GSE50081) were downloaded from the Gene Expression Omnibus (GEO) for subsequent validation analysis. Differentially expressed genes were calculated between high and low score groups. Univariate Cox regression analysis was performed on differentially expressed genes (DEGs) between the two groups to obtain initial prognosis genes. These were verified by three independent LUAD cohorts from the GEO database. Multivariate Cox regression was used to identify overall survival-related DEGs. UALCAN and the Human Protein Atlas were used to analyze the mRNA /protein expression levels of the target genes. Immune cell infiltration was evaluated using the Tumor Immune Estimation Resource (TIMER) and CIBERSORT methods, and stromal cell infiltration was assessed using xCell. Results In this study, immune scores and stromal scores are significantly associated with the clinical characteristics of LUAD, including T stage, M stage, pathological stage, and overall survival time. 530 DEGs (18 upregulated and 512 downregulated) were found to coexist in the difference analysis with the immune scores and stromal scores subgroup. Univariate Cox regression analysis showed that 286 of the 530 DEGs were survival-related genes (p < 0.05). Of the 286 genes initially identified, nine prognosis-related genes (CSF2RB, ITK, FLT3, CD79A, CCR4, CCR6,…
bibliographic citation: Xu et al. (2020) Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma. PeerJ 8:e9530 https://doi.org/10.7717/peerj.9530
date submitted: 2020-01-22
date accepted: 2020-06-22
issued: 2020-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Zhan-yu
author list: Agent
  family name: Zhao
  given name: Mengli
author list: Agent
  family name: Chen
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Kun
author list: Agent
  family name: Qin
  given name: Fanglu
author list: Agent
  family name: Xiang
  given name: Wei-wei
author list: Agent
  family name: Sun
  given name: Yu
author list: Agent
  family name: Wei
  given name: Jiangbo
author list: Agent
  family name: Yuan
  given name: Li-qiang
author list: Agent
  family name: Li
  given name: Shi-kang
author list: Agent
  family name: Lin
  given name: Sheng-hua
doi: 10.7717/peerj.9530
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-23
copyright: ©2020 Xu et al.
attribution name: Xu et al.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)
type: item
type: AcademicArticle
description: Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323–25,369 bp each) separated by a large single-copy (LSC) region (86,510–86,716 bp) and a small single-copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among to…
format: application/pdf
format: text/html
creator: Furrukh Mehmood
creator: Abdullah
creator: Zartasha Ubaid
creator: Iram Shahzadi
creator: Ibrar Ahmed
creator: Mohammad Tahir Waheed
creator: Peter Poczai
creator: Bushra Mirza
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.9552
publisher: PeerJ Inc.
rights: © 2020 Mehmood et al.
abstract: Species of the genus Nicotiana (Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species: N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323–25,369 bp each) separated by a large single-copy (LSC) region (86,510–86,716 bp) and a small single-copy (SSC) region (18,441–18,555 bp). Comparative analyses of Nicotiana plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. Relaxed molecular clock analyses estimated the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among to…
bibliographic citation: Mehmood et al. (2020) Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica). PeerJ 8:e9552 https://doi.org/10.7717/peerj.9552
date submitted: 2020-01-20
date accepted: 2020-06-24
issued: 2020-07-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mehmood
  given name: Furrukh
author list: Agent
  family name: Abdullah
author list: Agent
  family name: Ubaid
  given name: Zartasha
author list: Agent
  family name: Shahzadi
  given name: Iram
author list: Agent
  family name: Ahmed
  given name: Ibrar
author list: Agent
  family name: Waheed
  given name: Mohammad Tahir
author list: Agent
  family name: Poczai
  given name: Peter
author list: Agent
  family name: Mirza
  given name: Bushra
doi: 10.7717/peerj.9552
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-23
copyright: ©2020 Mehmood et al.
attribution name: Mehmood et al.

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