PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean
items: Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia
items: Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach
items: Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion
items: Optimising sampling of fish assemblages on intertidal reefs using remote underwater video
items: Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico
items: Valence moderates the effect of stimulus-hand proximity on conflict processing and gaze-cueing
items: A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis
items: https://peerj.com/articles/15357
items: Prediction study of prognostic nutrition index on the quality of life of patients with cervical cancer undergoing radiotherapy and chemotherapy

Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean
type: item
type: AcademicArticle
description: Background Ceriantharia is a subclass of the phylum Cnidaria, which comprises tube-dwelling marine invertebrates. This subclass is composed of three families, including Arachnactidae, with two known genera. Currently, the genus Arachnanthus has five valid species recorded from Australia, the Mediterranean Sea and both the Southern and Northern Pacific Ocean. However, at the moment, there is no record of organisms of this family from the South Atlantic Ocean. Besides that, the life cycle of any species of the genus Arachnanthus is known. The present study describes a new species of the genus Arachnanthus and its life cycle, based on specimens from Uruguay and South of Brazil. Methods Larvae were collected by plankton net in Rio Grande—Brazil and the development and external morphology of these specimens were observed in the laboratory during two years, and subsequently described. Additionally, nine adult ceriantharians correspondent to the larvae from Rio Grande were collected in Uruguay and their external and internal anatomies, and cnidome were described. Results Arachnanthus errans sp. nov. exhibited a free-swimming, short-lived cerinula larvae that spent short-time on the plankton. The larva developed into small and translucent polyps with a short actinopharynx, one pair of mesenteries attached to a siphonoglyph, and a medium first pair of metamesenteries. Further, the adult polyp displayed an unprecedented locomotion behavior in Ceriantharia that is first reported here, it can crawl under and in between the sediment.
format: application/pdf
format: text/html
creator: Celine S.S. Lopes
creator: Fabrizio Scarabino
creator: Alvar Carranza
creator: Ricardo González Muñoz
creator: André C. Morandini
creator: Renato Mitsuo Nagata
creator: Sérgio Nascimento Stampar
subject: Biodiversity
subject: Developmental Biology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15290
publisher: PeerJ Inc.
rights: © 2023 S S Lopes et al.
abstract: Background Ceriantharia is a subclass of the phylum Cnidaria, which comprises tube-dwelling marine invertebrates. This subclass is composed of three families, including Arachnactidae, with two known genera. Currently, the genus Arachnanthus has five valid species recorded from Australia, the Mediterranean Sea and both the Southern and Northern Pacific Ocean. However, at the moment, there is no record of organisms of this family from the South Atlantic Ocean. Besides that, the life cycle of any species of the genus Arachnanthus is known. The present study describes a new species of the genus Arachnanthus and its life cycle, based on specimens from Uruguay and South of Brazil. Methods Larvae were collected by plankton net in Rio Grande—Brazil and the development and external morphology of these specimens were observed in the laboratory during two years, and subsequently described. Additionally, nine adult ceriantharians correspondent to the larvae from Rio Grande were collected in Uruguay and their external and internal anatomies, and cnidome were described. Results Arachnanthus errans sp. nov. exhibited a free-swimming, short-lived cerinula larvae that spent short-time on the plankton. The larva developed into small and translucent polyps with a short actinopharynx, one pair of mesenteries attached to a siphonoglyph, and a medium first pair of metamesenteries. Further, the adult polyp displayed an unprecedented locomotion behavior in Ceriantharia that is first reported here, it can crawl under and in between the sediment.
bibliographic citation: S.S. Lopes et al. (2023) Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean. PeerJ 11:e15290 https://doi.org/10.7717/peerj.15290
date submitted: 2023-01-27
date accepted: 2023-04-04
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: S.S. Lopes
  given name: Celine
author list: Agent
  family name: Scarabino
  given name: Fabrizio
author list: Agent
  family name: Carranza
  given name: Alvar
author list: Agent
  family name: González Muñoz
  given name: Ricardo
author list: Agent
  family name: C. Morandini
  given name: André
author list: Agent
  family name: Nagata
  given name: Renato Mitsuo
author list: Agent
  family name: Nascimento Stampar
  given name: Sérgio
doi: 10.7717/peerj.15290
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 S S Lopes et al.
attribution name: S S Lopes et al.

Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia
type: item
type: AcademicArticle
description: The use of wild plants is considered to be an eco-friendly and promising natural resource. In sandy desert habitats, Leptadenia pyrotechnica flourishes as a xerophytic shrub with high biomass production. As a dominant shrub in the arid sand dune habitats of Saudi Arabia, Leptadenia pyrotechnica (Forssk.) Decne (Asclepiadaceae) is one of the most common xerophytes; the many medicinal uses of this plant include treating allergies, productive coughs, abortions, diabetes, stomach disorders, fevers, kidney disorders, and stones. In such a distribution, morpho-anatomical characteristics, among other adaptive traits, play an important role. This study aims to characterize some morpho-anatomical adaptations of L. pyrotechnica in two stressful habitats: the hyper-arid inland sand dunes of the Empty Quarter (EQ) and the arid coastal sand dunes of Jazan. A morpho-anatomical analysis of plant stems and roots from both habitats was conducted using light microscopy (LM) and scanning electron microscopy (SEM). The outcomes indicated similar characteristics, a low surface-to-volume ratio (S/V), a thin boundary layer (δbl), an epidermis with many layers of hypodermis, bundles of sclerenchymatous cells around vascular tissue, and storage starch grains in ray parenchyma between xylem conduits. On the other hand, the L. pyrotechnica stem from the hyper-arid habitat of the Empty Quarter revealed more encrypted stomata, more elongated palisade cells, less calcium oxalate crystals with low Ca percentage, and a high vulnerability index of xylem vessels compared with the same traits of the stem from the Jazan coastal sand dunes habitat. Roots of L. pyrotechnica from both habitats revealed similar features of general anatomy. However, differences in specific anatomical traits were observed, especially in xylem vessel characters. The vulnerability index of root xylem vessels from the Empty Quarter habitat was more than that from the Jazan coastal sand dunes habitat. Furthermore, vestured bord…
format: application/pdf
format: text/html
creator: Najla A. Al Shaye
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15320
publisher: PeerJ Inc.
rights: © 2023 Al Shaye
abstract: The use of wild plants is considered to be an eco-friendly and promising natural resource. In sandy desert habitats, Leptadenia pyrotechnica flourishes as a xerophytic shrub with high biomass production. As a dominant shrub in the arid sand dune habitats of Saudi Arabia, Leptadenia pyrotechnica (Forssk.) Decne (Asclepiadaceae) is one of the most common xerophytes; the many medicinal uses of this plant include treating allergies, productive coughs, abortions, diabetes, stomach disorders, fevers, kidney disorders, and stones. In such a distribution, morpho-anatomical characteristics, among other adaptive traits, play an important role. This study aims to characterize some morpho-anatomical adaptations of L. pyrotechnica in two stressful habitats: the hyper-arid inland sand dunes of the Empty Quarter (EQ) and the arid coastal sand dunes of Jazan. A morpho-anatomical analysis of plant stems and roots from both habitats was conducted using light microscopy (LM) and scanning electron microscopy (SEM). The outcomes indicated similar characteristics, a low surface-to-volume ratio (S/V), a thin boundary layer (δbl), an epidermis with many layers of hypodermis, bundles of sclerenchymatous cells around vascular tissue, and storage starch grains in ray parenchyma between xylem conduits. On the other hand, the L. pyrotechnica stem from the hyper-arid habitat of the Empty Quarter revealed more encrypted stomata, more elongated palisade cells, less calcium oxalate crystals with low Ca percentage, and a high vulnerability index of xylem vessels compared with the same traits of the stem from the Jazan coastal sand dunes habitat. Roots of L. pyrotechnica from both habitats revealed similar features of general anatomy. However, differences in specific anatomical traits were observed, especially in xylem vessel characters. The vulnerability index of root xylem vessels from the Empty Quarter habitat was more than that from the Jazan coastal sand dunes habitat. Furthermore, vestured bord…
bibliographic citation: Al Shaye (2023) Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia. PeerJ 11:e15320 https://doi.org/10.7717/peerj.15320
date submitted: 2023-01-18
date accepted: 2023-04-10
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Shaye
  given name: Najla A.
doi: 10.7717/peerj.15320
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Al Shaye
attribution name: Al Shaye

Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach
type: item
type: AcademicArticle
description: Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample’s contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
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creator: Caroline Chimeno
creator: Björn Rulik
creator: Alessandro Manfrin
creator: Gregor Kalinkat
creator: Franz Hölker
creator: Viktor Baranov
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.15336
publisher: PeerJ Inc.
rights: © 2023 Chimeno et al.
abstract: Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample’s contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
bibliographic citation: Chimeno et al. (2023) Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach. PeerJ 11:e15336 https://doi.org/10.7717/peerj.15336
date submitted: 2023-01-10
date accepted: 2023-04-11
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chimeno
  given name: Caroline
author list: Agent
  family name: Rulik
  given name: Björn
author list: Agent
  family name: Manfrin
  given name: Alessandro
author list: Agent
  family name: Kalinkat
  given name: Gregor
author list: Agent
  family name: Hölker
  given name: Franz
author list: Agent
  family name: Baranov
  given name: Viktor
doi: 10.7717/peerj.15336
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Chimeno et al.
attribution name: Chimeno et al.

Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion
type: item
type: AcademicArticle
description: Background The effects of FBXO43 on hepatocellular carcinoma (HCC) and its clinical significance have not yet been determined. This study aims to determine the clinical significance of FBXO43 in HCC and its impact on the biological functions of HCC cells. Methods Data from TCGA database were downloaded to investigate the expression of FBXO43 in HCC and its correlation with prognosis and immune infiltration. Immunohistochemical staining images of FBXO43 in HCC were acquired from the HPA website. HCC cells (BEL-7404 and SMMC-7721) were transfected with the lentivirus targeting FBXO43 to decrease FBXO43 expression in HCC cells. Western blotting assay was conducted to evaluate the expression level of FBXO43 protein. MTT assay was used to detect the proliferation of HCC cells. The migration and invasion of HCC cells were investigated by performing scratch wound-healing and Transwell invasion assays, respectively. Results In comparison to normal tissues, FBXO43 is overexpressed in HCC tissue, and high FBXO43 expression is linked to late T stage, TNM stage and tumor grade. Elevated FBXO43 expression is a risk factor for HCC. In patients with high FBXO43 expression, the overall survival, disease-specific survival, progression-free survival and disease-free survival are poorer. The proliferation, migration and invasion of HCC cells are significantly attenuated in FBXO43 knockdown cells. Also, TCGA data analysis reveals that FBXO43 exhibits a positive correlation with immunosuppression of HCC. Conclusion FBXO43 is overexpressed in HCC, and is linked to late tumor stage, worse prognosis and tumor immunosuppression. FBXO43 knockdown restrains the proliferation, migration and invasion of HCC.
format: application/pdf
format: text/html
creator: Rulan Ma
creator: Wenbo Liu
creator: Tuanhe Sun
creator: Chengxue Dang
creator: Kang Li
subject: Bioinformatics
subject: Cell Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.15373
publisher: PeerJ Inc.
rights: © 2023 Ma et al.
abstract: Background The effects of FBXO43 on hepatocellular carcinoma (HCC) and its clinical significance have not yet been determined. This study aims to determine the clinical significance of FBXO43 in HCC and its impact on the biological functions of HCC cells. Methods Data from TCGA database were downloaded to investigate the expression of FBXO43 in HCC and its correlation with prognosis and immune infiltration. Immunohistochemical staining images of FBXO43 in HCC were acquired from the HPA website. HCC cells (BEL-7404 and SMMC-7721) were transfected with the lentivirus targeting FBXO43 to decrease FBXO43 expression in HCC cells. Western blotting assay was conducted to evaluate the expression level of FBXO43 protein. MTT assay was used to detect the proliferation of HCC cells. The migration and invasion of HCC cells were investigated by performing scratch wound-healing and Transwell invasion assays, respectively. Results In comparison to normal tissues, FBXO43 is overexpressed in HCC tissue, and high FBXO43 expression is linked to late T stage, TNM stage and tumor grade. Elevated FBXO43 expression is a risk factor for HCC. In patients with high FBXO43 expression, the overall survival, disease-specific survival, progression-free survival and disease-free survival are poorer. The proliferation, migration and invasion of HCC cells are significantly attenuated in FBXO43 knockdown cells. Also, TCGA data analysis reveals that FBXO43 exhibits a positive correlation with immunosuppression of HCC. Conclusion FBXO43 is overexpressed in HCC, and is linked to late tumor stage, worse prognosis and tumor immunosuppression. FBXO43 knockdown restrains the proliferation, migration and invasion of HCC.
bibliographic citation: Ma et al. (2023) Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion. PeerJ 11:e15373 https://doi.org/10.7717/peerj.15373
date submitted: 2023-02-17
date accepted: 2023-04-18
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Rulan
author list: Agent
  family name: Liu
  given name: Wenbo
author list: Agent
  family name: Sun
  given name: Tuanhe
author list: Agent
  family name: Dang
  given name: Chengxue
author list: Agent
  family name: Li
  given name: Kang
doi: 10.7717/peerj.15373
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 Ma et al.
attribution name: Ma et al.

Optimising sampling of fish assemblages on intertidal reefs using remote underwater video
type: item
type: AcademicArticle
description: Background Assessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks. Methods Here, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematic vs random) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNT and MeanCountT, which have not been evaluated previously for complex intertidal habitats. Results Results suggest that MaxNT and species richness should be recorded in real time, whereas optimal sampling for MeanCountT is every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.
format: application/pdf
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creator: Katherine R. Erickson
creator: Ana B. Bugnot
creator: Will F. Figueira
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.15426
publisher: PeerJ Inc.
rights: © 2023 Erickson et al.
abstract: Background Assessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks. Methods Here, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematic vs random) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNT and MeanCountT, which have not been evaluated previously for complex intertidal habitats. Results Results suggest that MaxNT and species richness should be recorded in real time, whereas optimal sampling for MeanCountT is every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.
bibliographic citation: Erickson et al. (2023) Optimising sampling of fish assemblages on intertidal reefs using remote underwater video. PeerJ 11:e15426 https://doi.org/10.7717/peerj.15426
date submitted: 2022-11-21
date accepted: 2023-04-25
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erickson
  given name: Katherine R.
author list: Agent
  family name: Bugnot
  given name: Ana B.
author list: Agent
  family name: Figueira
  given name: Will F.
doi: 10.7717/peerj.15426
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Erickson et al.
attribution name: Erickson et al.

Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico
type: item
type: AcademicArticle
description: Background Vegetation structure is defined as the temporal and spatial distribution of plant species in a particular site. Vegetation structure includes vertical and horizontal distribution and has been widely used as an indicator of successional changes. Ecological succession plays an essential role in the determination of the mechanisms that structure plant communities under anthropogenic disturbances. After an anthropogenic disturbance, such as grazing, forests follow changes in the original composition and vegetation structure, which eventually could restore some of their attributes to become mature forests again. To know how the time of abandonment affects woody plant communities, we ask the following questions: (1) How does the species richness, diversity, and vertical structure (A index) change concerning the time of abandonment? (2) Are species similarities among woody vegetation communities determined by land abandonment? (3) Which woody species have the highest ecological importance in each successional stage? Methods We explored how successional stages after land abandonment mediated the species richness, species diversity (alpha and beta), and ecological importance value index on four areas of Tamaulipan thornscrub. We selected four areas that differed in time of abandonment: 10, 20, 30, and >30 years. The first three areas were used for cattle grazing, whereas the >30-year area was selected as a control since it does not have a record of disturbance by cattle grazing or agriculture. During the summer of 2012, we randomly established four square plots (40 m × 40 m) in each area, separated at least 200 m from each other. In each plot, we recorded all woody individuals per species with a basal diameter ≥1 cm at 10 cm above ground level. We estimated species richness indices, species diversity (alpha and beta), and ecological importance value index. Results We recorded 27 woody species belonging to 23 genera and 15 families. Fabaceae accounted for 40% of th…
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creator: Eduardo Alanís-Rodríguez
creator: Cristian A. Martínez-Adriano
creator: Laura Sanchez-Castillo
creator: Ernesto Alonso Rubio-Camacho
creator: Alejandro Valdecantos
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Environmental Impacts
description: doi:10.7717/peerj.15438
publisher: PeerJ Inc.
rights: © 2023 Alanís-Rodríguez et al.
abstract: Background Vegetation structure is defined as the temporal and spatial distribution of plant species in a particular site. Vegetation structure includes vertical and horizontal distribution and has been widely used as an indicator of successional changes. Ecological succession plays an essential role in the determination of the mechanisms that structure plant communities under anthropogenic disturbances. After an anthropogenic disturbance, such as grazing, forests follow changes in the original composition and vegetation structure, which eventually could restore some of their attributes to become mature forests again. To know how the time of abandonment affects woody plant communities, we ask the following questions: (1) How does the species richness, diversity, and vertical structure (A index) change concerning the time of abandonment? (2) Are species similarities among woody vegetation communities determined by land abandonment? (3) Which woody species have the highest ecological importance in each successional stage? Methods We explored how successional stages after land abandonment mediated the species richness, species diversity (alpha and beta), and ecological importance value index on four areas of Tamaulipan thornscrub. We selected four areas that differed in time of abandonment: 10, 20, 30, and >30 years. The first three areas were used for cattle grazing, whereas the >30-year area was selected as a control since it does not have a record of disturbance by cattle grazing or agriculture. During the summer of 2012, we randomly established four square plots (40 m × 40 m) in each area, separated at least 200 m from each other. In each plot, we recorded all woody individuals per species with a basal diameter ≥1 cm at 10 cm above ground level. We estimated species richness indices, species diversity (alpha and beta), and ecological importance value index. Results We recorded 27 woody species belonging to 23 genera and 15 families. Fabaceae accounted for 40% of th…
bibliographic citation: Alanís-Rodríguez et al. (2023) Land abandonment as driver of woody vegetation dynamics in Tamaulipan thornscrub at Northeastern Mexico. PeerJ 11:e15438 https://doi.org/10.7717/peerj.15438
date submitted: 2022-07-12
date accepted: 2023-04-28
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alanís-Rodríguez
  given name: Eduardo
author list: Agent
  family name: Martínez-Adriano
  given name: Cristian A.
author list: Agent
  family name: Sanchez-Castillo
  given name: Laura
author list: Agent
  family name: Rubio-Camacho
  given name: Ernesto Alonso
author list: Agent
  family name: Valdecantos
  given name: Alejandro
doi: 10.7717/peerj.15438
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Alanis et al.
attribution name: Alanís-Rodríguez et al.

Valence moderates the effect of stimulus-hand proximity on conflict processing and gaze-cueing
type: item
type: AcademicArticle
description: An effective interaction with the environment requires adaptation of one’s own behaviour to environmental demands. We do so by using cues from our environment and relating these cues to our body to predict the outcomes of events. The recent literature on embodied cognition suggests that task-relevant stimuli, presented near the hands, receive more attentional capacity and are processed differently than stimuli, presented spatially more distant to our body. It has also been proposed that near-hand processing is beneficial to conflict resolution. In the current study, we tested the assumption of an attentional bias towards the near hand space in the context of our previous work by combining a cueing paradigm (allocation of visual attention) with a conflict processing paradigm (Simon task) in the near vs far hand space. In addition, the relevance of processing was manipulated by using affective (angry vs neutral smileys) gaze cues (i.e., varying the valence of the cues). Our results indicate that (a) the interaction of valence × cue congruency × hand proximity was significant, indicating that the cueing effect was larger for negative valence in the proximal condition. (b) The interaction of valence × Simon compatibility × stimulus-hand proximity interaction was significant, indicating that for negative valence processing, the Simon effect was smaller in the proximal than in the distal stimulus-hand condition. This effect was at least numerically but not significantly reversed in the neutral valence condition. (c) Overall, cue congruency, indicating the correct vs incorrect attention allocation to the target stimulus onset, did not reveal any effect on Simon compatibility × stimulus-hand proximity. Our results suggest that valence, the allocation of attention, and conflict, seem to be decisive factors determining the direction and strength of hand proximity effects.
format: application/pdf
format: text/html
creator: Sven Hoffmann
creator: Rico Fischer
creator: Roman Liepelt
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.15286
publisher: PeerJ Inc.
rights: © 2023 Hoffmann et al.
abstract: An effective interaction with the environment requires adaptation of one’s own behaviour to environmental demands. We do so by using cues from our environment and relating these cues to our body to predict the outcomes of events. The recent literature on embodied cognition suggests that task-relevant stimuli, presented near the hands, receive more attentional capacity and are processed differently than stimuli, presented spatially more distant to our body. It has also been proposed that near-hand processing is beneficial to conflict resolution. In the current study, we tested the assumption of an attentional bias towards the near hand space in the context of our previous work by combining a cueing paradigm (allocation of visual attention) with a conflict processing paradigm (Simon task) in the near vs far hand space. In addition, the relevance of processing was manipulated by using affective (angry vs neutral smileys) gaze cues (i.e., varying the valence of the cues). Our results indicate that (a) the interaction of valence × cue congruency × hand proximity was significant, indicating that the cueing effect was larger for negative valence in the proximal condition. (b) The interaction of valence × Simon compatibility × stimulus-hand proximity interaction was significant, indicating that for negative valence processing, the Simon effect was smaller in the proximal than in the distal stimulus-hand condition. This effect was at least numerically but not significantly reversed in the neutral valence condition. (c) Overall, cue congruency, indicating the correct vs incorrect attention allocation to the target stimulus onset, did not reveal any effect on Simon compatibility × stimulus-hand proximity. Our results suggest that valence, the allocation of attention, and conflict, seem to be decisive factors determining the direction and strength of hand proximity effects.
bibliographic citation: Hoffmann et al. (2023) Valence moderates the effect of stimulus-hand proximity on conflict processing and gaze-cueing. PeerJ 11:e15286 https://doi.org/10.7717/peerj.15286
date submitted: 2022-10-20
date accepted: 2023-04-03
issued: 2023-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoffmann
  given name: Sven
author list: Agent
  family name: Fischer
  given name: Rico
author list: Agent
  family name: Liepelt
  given name: Roman
doi: 10.7717/peerj.15286
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-19
copyright: © 2023 Hoffmann et al.
attribution name: Hoffmann et al.

A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis
type: item
type: AcademicArticle
description: Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.
format: application/pdf
format: text/html
creator: Fang Liu
creator: Peng Zhao
creator: Guangxia Chen
creator: Yongqiang Wang
creator: Yuanjun Yang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15349
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.
bibliographic citation: Liu et al. (2023) A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis. PeerJ 11:e15349 https://doi.org/10.7717/peerj.15349
date submitted: 2022-04-15
date accepted: 2023-04-13
issued: 2023-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Fang
author list: Agent
  family name: Zhao
  given name: Peng
author list: Agent
  family name: Chen
  given name: Guangxia
author list: Agent
  family name: Wang
  given name: Yongqiang
author list: Agent
  family name: Yang
  given name: Yuanjun
doi: 10.7717/peerj.15349
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-19
copyright: ©2023 Liu et al.
attribution name: Liu et al.

https://peerj.com/articles/15357
type: item
type: AcademicArticle
title: Single fraction stereotactic radiosurgery and fractionated stereotactic radiotherapy provide equal prognosis with overall survival in patients with brain metastases at diagnosis without surgery at primary site
description: Background and purpose Stereotactic radiosurgery (SRS) and fractionated stereotactic radiation therapy (SRT) are both treatments shown to be effective in treating brain metastases (BMs). However, it is unknown how these treatments compare in effectiveness and safety in cancer patients with BMs regardless of the primary cancer. The main objective of this study is to investigate the SRS and SRT treatments’ associations with the overall survival (OS) of patients diagnosed with BMs using the National Cancer Database (NCDB). Materials and methods Patients in the NCDB with breast cancer, non-small cell lung cancer, small cell lung cancer, other lung cancers, melanoma, colorectal cancer, or kidney cancer who had BMs at the time of their primary cancer diagnosis and received either SRS or SRT as treatment for their BMs were included in the study. We analyzed OS with a Cox proportional hazard analysis that adjusted variables associated with improved OS during univariable analysis. Results Of the total 6,961 patients that fit the criteria for the study, 5,423 (77.9%) received SRS and 1,538 (22.1%) received SRT. Patients who received SRS treatment had a median survival time of 10.9 (95% CI [10.5–11.3]), and those who received SRT treatment had a median survival time of 11.3 (95% CI [10.4–12.3]) months. This difference was not found to be significant (Log-rank P = 0.31). Multivariable Cox proportional hazard analysis did not yield a significant difference between the treatments’ associations with OS (Hazard Ratio: 0.942, CI 95% [0.882–1.006]; P = .08) or SRS vs. SRT. Conclusions In this analysis, SRS and SRT did not show a significant difference in their associations with OS. Future studies investigating the neurotoxicity risks of SRS as compared to SRT are warranted.
format: application/pdf
format: text/html
creator: Garett Paul Ostdiek-Wille
creator: Saber Amin
creator: Shuo Wang
creator: Chi Zhang
creator: Chi Lin
subject: Neurology
subject: Oncology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
subject: Translational Medicine
description: doi:10.7717/peerj.15357
publisher: PeerJ Inc.
rights: © 2023 Ostdiek-Wille et al.
abstract: Background and purpose Stereotactic radiosurgery (SRS) and fractionated stereotactic radiation therapy (SRT) are both treatments shown to be effective in treating brain metastases (BMs). However, it is unknown how these treatments compare in effectiveness and safety in cancer patients with BMs regardless of the primary cancer. The main objective of this study is to investigate the SRS and SRT treatments’ associations with the overall survival (OS) of patients diagnosed with BMs using the National Cancer Database (NCDB). Materials and methods Patients in the NCDB with breast cancer, non-small cell lung cancer, small cell lung cancer, other lung cancers, melanoma, colorectal cancer, or kidney cancer who had BMs at the time of their primary cancer diagnosis and received either SRS or SRT as treatment for their BMs were included in the study. We analyzed OS with a Cox proportional hazard analysis that adjusted variables associated with improved OS during univariable analysis. Results Of the total 6,961 patients that fit the criteria for the study, 5,423 (77.9%) received SRS and 1,538 (22.1%) received SRT. Patients who received SRS treatment had a median survival time of 10.9 (95% CI [10.5–11.3]), and those who received SRT treatment had a median survival time of 11.3 (95% CI [10.4–12.3]) months. This difference was not found to be significant (Log-rank P = 0.31). Multivariable Cox proportional hazard analysis did not yield a significant difference between the treatments’ associations with OS (Hazard Ratio: 0.942, CI 95% [0.882–1.006]; P = .08) or SRS vs. SRT. Conclusions In this analysis, SRS and SRT did not show a significant difference in their associations with OS. Future studies investigating the neurotoxicity risks of SRS as compared to SRT are warranted.
bibliographic citation: Ostdiek-Wille et al. (2023) Single fraction stereotactic radiosurgery and fractionated stereotactic radiotherapy provide equal prognosis with overall survival in patients with brain metastases at diagnosis without surgery at primary site. PeerJ 11:e15357 https://doi.org/10.7717/peerj.15357
date submitted: 2022-12-08
date accepted: 2023-04-14
issued: 2023-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ostdiek-Wille
  given name: Garett Paul
author list: Agent
  family name: Amin
  given name: Saber
author list: Agent
  family name: Wang
  given name: Shuo
author list: Agent
  family name: Zhang
  given name: Chi
author list: Agent
  family name: Lin
  given name: Chi
doi: 10.7717/peerj.15357
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-19
copyright: ©2023 Ostdiek-Wille et al.
attribution name: Ostdiek-Wille et al.

Prediction study of prognostic nutrition index on the quality of life of patients with cervical cancer undergoing radiotherapy and chemotherapy
type: item
type: AcademicArticle
description: Objective To assess the prognostic nutritional index (PNI) and quality of life (QOL) of patients with cervical cancer (CC) who underwent radiotherapy and chemotherapy and to reveal the effect of PNI on QOL and its prognostic value. Methods A total of 138 CC patients who underwent radiotherapy and chemotherapy in the Second Affiliated Hospital of Fujian Medical University from January 2020 to October 2022 were selected as the study subjects via convenient sampling. According to the PNI cut-off value of 48.8, they were divided into a high-PNI group and a low-PNI group, and the quality of life of the two groups was compared. The Kaplan-Meier method was used to draw the survival curve, and the Log-Rank test was employed to compare the survival rates of the two groups. Results The scores of physical functioning and overall QOL in the high-PNI group were significantly higher than those in the low-PNI group (P < 0.05). The scores of fatigue, nausea and vomiting, pain and diarrhea were higher than those in the low-PNI group, and the difference was statistically significant (P < 0.05). The objective response rates were 96.77% and 81.25% in the high-PNI group and the low-PNI group, respectively, and the difference was statistically significant (P = 0.045). The 1-year survival rates of patients with high PNI and low PNI were 92.55% and 72.56% in the high-PNI group and the low-PNI group, respectively; the difference in survival rates was statistically significant (P = 0.006). Conclusion The overall quality of life of CC patients with low PNI receiving radiotherapy and chemotherapy is lower than that of patients with high PNI. Low PNI reduces the tolerance to radiotherapy and chemotherapy and the objective response rate, which can be used as a prognostic indicator for cervical cancer patients.
format: application/pdf
format: text/html
creator: Ying Chen
creator: Bifen Huang
creator: Jianqing Zheng
creator: Fangjie He
subject: Drugs and Devices
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.15442
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Objective To assess the prognostic nutritional index (PNI) and quality of life (QOL) of patients with cervical cancer (CC) who underwent radiotherapy and chemotherapy and to reveal the effect of PNI on QOL and its prognostic value. Methods A total of 138 CC patients who underwent radiotherapy and chemotherapy in the Second Affiliated Hospital of Fujian Medical University from January 2020 to October 2022 were selected as the study subjects via convenient sampling. According to the PNI cut-off value of 48.8, they were divided into a high-PNI group and a low-PNI group, and the quality of life of the two groups was compared. The Kaplan-Meier method was used to draw the survival curve, and the Log-Rank test was employed to compare the survival rates of the two groups. Results The scores of physical functioning and overall QOL in the high-PNI group were significantly higher than those in the low-PNI group (P < 0.05). The scores of fatigue, nausea and vomiting, pain and diarrhea were higher than those in the low-PNI group, and the difference was statistically significant (P < 0.05). The objective response rates were 96.77% and 81.25% in the high-PNI group and the low-PNI group, respectively, and the difference was statistically significant (P = 0.045). The 1-year survival rates of patients with high PNI and low PNI were 92.55% and 72.56% in the high-PNI group and the low-PNI group, respectively; the difference in survival rates was statistically significant (P = 0.006). Conclusion The overall quality of life of CC patients with low PNI receiving radiotherapy and chemotherapy is lower than that of patients with high PNI. Low PNI reduces the tolerance to radiotherapy and chemotherapy and the objective response rate, which can be used as a prognostic indicator for cervical cancer patients.
bibliographic citation: Chen et al. (2023) Prediction study of prognostic nutrition index on the quality of life of patients with cervical cancer undergoing radiotherapy and chemotherapy. PeerJ 11:e15442 https://doi.org/10.7717/peerj.15442
date submitted: 2023-02-24
date accepted: 2023-04-30
issued: 2023-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Huang
  given name: Bifen
author list: Agent
  family name: Zheng
  given name: Jianqing
author list: Agent
  family name: He
  given name: Fangjie
doi: 10.7717/peerj.15442
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-19
copyright: © 2023 Chen et al.
attribution name: Chen et al.

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