PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach
items: CASPredict: a web service for identifying Cas proteins
items: Morphological variation of the relictual alveolar structures in the mandibles of baleen whales
items: Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data
items: Transcriptional landscape in rat intestines under hypobaric hypoxia
items: Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation
items: Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period
items: Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer
items: Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand
items: Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil

Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach
type: item
type: AcademicArticle
description: Background Reliable assessment and understanding of student-athletes’ motivation for dual careers are crucial to support their career development and transitions. The purpose of this research was to examine the validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire (SAMSAQ-PT) in the Brazilian higher education context. Four studies were performed. Methods In study one, conceptually and semantic translation of the questionnaire and Bayesian exploratory factor analysis were conducted. In study two, a Bayesian confirmatory factor analysis with an independent sample was performed. In study three, Bayesian multilevel modeling was applied to examine the construct validity of the questionnaire in a cross-sectional sample. In study four, the SAMSAQ-PT sensitiveness was examined in a longitudinal sample, and the results were interpreted based on multilevel regression and poststratification. Results Altogether the results provided evidence validity and usefulness of the SAMSAQ-PT in Brazilian student-athletes. The Brazilian student-athletes’ motivation scores were sensitive to the influence of sex, sport level, and type of university on career and sport motivation. SAMSAQ-PT estimate scores across an academic year showed a trend of stability in the scores, adjusting for sex, sport level, type of university, and student-athlete status. Conclusion The SAMSAQ-PT proved to be a robust and valuable questionnaire, which could be used in Portuguese-speaking countries. The findings of the cross-sectional and longitudinal surveys urge to consider individual and contextual characteristics when investigating motivation of dual-career of athletes, also concerning the sex-related opportunities in university sports. Furthermore, there is a need for a call for action to promote and nurture the student-athletes motivation to remain engaged in both sports and educational commitments.
format: application/pdf
format: text/html
creator: Ricardo T. Quinaud
creator: Carlos E. Gonçalves
creator: Kauana Possamai
creator: Cristiano Zarbato Morais
creator: Laura Capranica
creator: Humberto M. Carvalho
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11863
publisher: PeerJ Inc.
rights: © 2021 Quinaud et al.
abstract: Background Reliable assessment and understanding of student-athletes’ motivation for dual careers are crucial to support their career development and transitions. The purpose of this research was to examine the validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire (SAMSAQ-PT) in the Brazilian higher education context. Four studies were performed. Methods In study one, conceptually and semantic translation of the questionnaire and Bayesian exploratory factor analysis were conducted. In study two, a Bayesian confirmatory factor analysis with an independent sample was performed. In study three, Bayesian multilevel modeling was applied to examine the construct validity of the questionnaire in a cross-sectional sample. In study four, the SAMSAQ-PT sensitiveness was examined in a longitudinal sample, and the results were interpreted based on multilevel regression and poststratification. Results Altogether the results provided evidence validity and usefulness of the SAMSAQ-PT in Brazilian student-athletes. The Brazilian student-athletes’ motivation scores were sensitive to the influence of sex, sport level, and type of university on career and sport motivation. SAMSAQ-PT estimate scores across an academic year showed a trend of stability in the scores, adjusting for sex, sport level, type of university, and student-athlete status. Conclusion The SAMSAQ-PT proved to be a robust and valuable questionnaire, which could be used in Portuguese-speaking countries. The findings of the cross-sectional and longitudinal surveys urge to consider individual and contextual characteristics when investigating motivation of dual-career of athletes, also concerning the sex-related opportunities in university sports. Furthermore, there is a need for a call for action to promote and nurture the student-athletes motivation to remain engaged in both sports and educational commitments.
bibliographic citation: Quinaud et al. (2021) Validity and usefulness of the student-athletes’ motivation toward sport and academics questionnaire: a Bayesian multilevel approach. PeerJ 9:e11863 https://doi.org/10.7717/peerj.11863
date submitted: 2021-03-25
date accepted: 2021-07-05
issued: 2021-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quinaud
  given name: Ricardo T.
author list: Agent
  family name: Gonçalves
  given name: Carlos E.
author list: Agent
  family name: Possamai
  given name: Kauana
author list: Agent
  family name: Morais
  given name: Cristiano Zarbato
author list: Agent
  family name: Capranica
  given name: Laura
author list: Agent
  family name: Carvalho
  given name: Humberto M.
doi: 10.7717/peerj.11863
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-30
copyright: ©2021 Quinaud et al.
attribution name: Quinaud et al.

CASPredict: a web service for identifying Cas proteins
type: item
type: AcademicArticle
description: Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area.
format: application/pdf
format: text/html
creator: Shanshan Yang
creator: Jian Huang
creator: Bifang He
subject: Bioinformatics
subject: Molecular Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.11887
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area.
bibliographic citation: Yang et al. (2021) CASPredict: a web service for identifying Cas proteins. PeerJ 9:e11887 https://doi.org/10.7717/peerj.11887
date submitted: 2020-11-26
date accepted: 2021-07-09
issued: 2021-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Shanshan
author list: Agent
  family name: Huang
  given name: Jian
author list: Agent
  family name: He
  given name: Bifang
doi: 10.7717/peerj.11887
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-30
copyright: © 2021 Yang et al.
attribution name: Yang et al.

Morphological variation of the relictual alveolar structures in the mandibles of baleen whales
type: item
type: AcademicArticle
description: Living baleen whales (mysticetes) are bulk filter feeders that use keratinous baleen plates to filter food from prey laden water. Extant mysticetes are born entirely edentulous, though they possess tooth buds early in ontogeny, a trait inherited from toothed ancestors. The mandibles of extant baleen whales have neither teeth nor baleen; teeth are resorbed in utero and baleen grows only on the palate. The mandibles of extant baleen whales also preserve a series of foramina and associated sulci that collectively form an elongated trough, called the alveolar groove. Despite this name, it remains unclear if the alveolar groove of edentulous mysticetes and the dental structures of toothed mammals are homologous. Here, we describe and quantify the anatomical diversity of these structures across extant mysticetes and compare their variable morphologies across living taxonomic groups (i.e., Balaenidae, Neobalaenidae, Eschrichtiidae, and Balaenopteridae). Although we found broad variability across taxonomic groups for the alveolar groove length, occupying approximately 60–80 percent of the mandible’s total curvilinear length (CLL) across all taxa, the relictual alveolar foramen showed distinct patterns, ranging between 15–25% CLL in balaenids, while ranging between 3–12% CLL in balaenopterids. This variability and the morphological patterning along the body of the mandible is consistent with the hypothesis that the foramina underlying the alveolar groove reflect relictual alveoli. These findings also lay the groundwork for future histological studies to examine the contents of these foramina and clarify their potential role in the feeding process.
format: application/pdf
format: text/html
creator: Carlos Mauricio Peredo
creator: Nicholas D. Pyenson
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11890
publisher: PeerJ Inc.
rights: © 2021 Peredo and Pyenson
abstract: Living baleen whales (mysticetes) are bulk filter feeders that use keratinous baleen plates to filter food from prey laden water. Extant mysticetes are born entirely edentulous, though they possess tooth buds early in ontogeny, a trait inherited from toothed ancestors. The mandibles of extant baleen whales have neither teeth nor baleen; teeth are resorbed in utero and baleen grows only on the palate. The mandibles of extant baleen whales also preserve a series of foramina and associated sulci that collectively form an elongated trough, called the alveolar groove. Despite this name, it remains unclear if the alveolar groove of edentulous mysticetes and the dental structures of toothed mammals are homologous. Here, we describe and quantify the anatomical diversity of these structures across extant mysticetes and compare their variable morphologies across living taxonomic groups (i.e., Balaenidae, Neobalaenidae, Eschrichtiidae, and Balaenopteridae). Although we found broad variability across taxonomic groups for the alveolar groove length, occupying approximately 60–80 percent of the mandible’s total curvilinear length (CLL) across all taxa, the relictual alveolar foramen showed distinct patterns, ranging between 15–25% CLL in balaenids, while ranging between 3–12% CLL in balaenopterids. This variability and the morphological patterning along the body of the mandible is consistent with the hypothesis that the foramina underlying the alveolar groove reflect relictual alveoli. These findings also lay the groundwork for future histological studies to examine the contents of these foramina and clarify their potential role in the feeding process.
bibliographic citation: Peredo et al. (2021) Morphological variation of the relictual alveolar structures in the mandibles of baleen whales. PeerJ 9:e11890 https://doi.org/10.7717/peerj.11890
date submitted: 2021-05-24
date accepted: 2021-07-10
issued: 2021-07-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peredo
  given name: Carlos Mauricio
author list: Agent
  family name: Pyenson
  given name: Nicholas D.
doi: 10.7717/peerj.11890
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-30
copyright: ©2021 Peredo and Pyenson
attribution name: Peredo and Pyenson

Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data
type: item
type: AcademicArticle
description: Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were captured by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will …
format: application/pdf
format: text/html
creator: Victoria M. Scholl
creator: Joseph McGlinchy
creator: Teo Price-Broncucia
creator: Jennifer K. Balch
creator: Maxwell B. Joseph
subject: Ecology
subject: Plant Science
subject: Data Mining and Machine Learning
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11790
publisher: PeerJ Inc.
rights: © 2021 Scholl et al.
abstract: Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were captured by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will …
bibliographic citation: Scholl et al. (2021) Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data. PeerJ 9:e11790 https://doi.org/10.7717/peerj.11790
date submitted: 2021-01-27
date accepted: 2021-06-25
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scholl
  given name: Victoria M.
author list: Agent
  family name: McGlinchy
  given name: Joseph
author list: Agent
  family name: Price-Broncucia
  given name: Teo
author list: Agent
  family name: Balch
  given name: Jennifer K.
author list: Agent
  family name: Joseph
  given name: Maxwell B.
doi: 10.7717/peerj.11790
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: © 2021 Scholl et al.
attribution name: Scholl et al.

Transcriptional landscape in rat intestines under hypobaric hypoxia
type: item
type: AcademicArticle
description: Oxygen metabolism is closely related to the intestinal homeostasis environment, and the occurrence of many intestinal diseases is as a result of the destruction of oxygen gradients. The hypobaric hypoxic environment of the plateau can cause dysfunction of the intestine for humans, such as inflammation. The compensatory response of the small intestine cells to the harsh environment definitely changes their gene expression. How the small intestine cells response the hypobaric hypoxic environment is still unclear. We studied the rat small intestine under hypobaric hypoxic conditions to explore the transcriptional changes in rats under acute/chronic hypobaric hypoxic conditions. We randomly divided rats into three groups: normal control group (S), acute hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 2 weeks (W2S) and chronic hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 4 weeks (W4S). The RNA sequencing was performed on the small intestine tissues of the three groups of rats. The results of principal component analysis showed that the W4S and W2S groups were quite different from the control group. We identified a total of 636 differentially expressed genes, such as ATP binding cassette, Ace2 and Fabp. KEGG pathway analysis identified several metabolic and digestive pathways, such as PPAR signaling pathway, glycerolipid metabolism, fat metabolism, mineral absorption and vitamin metabolism. Cogena analysis found that up-regulation of digestive and metabolic functions began from the second week of high altitude exposure. Our study highlights the critical role of metabolic and digestive pathways of the intestine in response to the hypobaric hypoxic environment, provides new aspects for the molecular effects of hypobaric hypoxic environment on intestine, and raises further questions about between the lipid metabolism disorders and inflammation.
format: application/pdf
format: text/html
creator: Liuyang Tian
creator: Zhilong Jia
creator: Zhenguo Xu
creator: Jinlong Shi
creator: XiaoJing Zhao
creator: Kunlun He
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.11823
publisher: PeerJ Inc.
rights: © 2021 Tian et al.
abstract: Oxygen metabolism is closely related to the intestinal homeostasis environment, and the occurrence of many intestinal diseases is as a result of the destruction of oxygen gradients. The hypobaric hypoxic environment of the plateau can cause dysfunction of the intestine for humans, such as inflammation. The compensatory response of the small intestine cells to the harsh environment definitely changes their gene expression. How the small intestine cells response the hypobaric hypoxic environment is still unclear. We studied the rat small intestine under hypobaric hypoxic conditions to explore the transcriptional changes in rats under acute/chronic hypobaric hypoxic conditions. We randomly divided rats into three groups: normal control group (S), acute hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 2 weeks (W2S) and chronic hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 4 weeks (W4S). The RNA sequencing was performed on the small intestine tissues of the three groups of rats. The results of principal component analysis showed that the W4S and W2S groups were quite different from the control group. We identified a total of 636 differentially expressed genes, such as ATP binding cassette, Ace2 and Fabp. KEGG pathway analysis identified several metabolic and digestive pathways, such as PPAR signaling pathway, glycerolipid metabolism, fat metabolism, mineral absorption and vitamin metabolism. Cogena analysis found that up-regulation of digestive and metabolic functions began from the second week of high altitude exposure. Our study highlights the critical role of metabolic and digestive pathways of the intestine in response to the hypobaric hypoxic environment, provides new aspects for the molecular effects of hypobaric hypoxic environment on intestine, and raises further questions about between the lipid metabolism disorders and inflammation.
bibliographic citation: Tian et al. (2021) Transcriptional landscape in rat intestines under hypobaric hypoxia. PeerJ 9:e11823 https://doi.org/10.7717/peerj.11823
date submitted: 2020-12-31
date accepted: 2021-06-29
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Liuyang
author list: Agent
  family name: Jia
  given name: Zhilong
author list: Agent
  family name: Xu
  given name: Zhenguo
author list: Agent
  family name: Shi
  given name: Jinlong
author list: Agent
  family name: Zhao
  given name: XiaoJing
author list: Agent
  family name: He
  given name: Kunlun
doi: 10.7717/peerj.11823
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Tian et al.
attribution name: Tian et al.

Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation
type: item
type: AcademicArticle
description: Background Soil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation. Methods A 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha). Results Our results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of cr…
format: application/pdf
format: text/html
creator: Qian Lyu
creator: Yi Shen
creator: Xianwei Li
creator: Gang Chen
creator: Dehui Li
creator: Chuan Fan
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.11852
publisher: PeerJ Inc.
rights: © 2021 Lyu et al.
abstract: Background Soil and understory vegetation are vital components of forest ecosystems. Identifying the interaction of plantation management to vegetation and soil is crucial for developing sustainable plantation ecosystem management strategies. As one of the main measures of close-to-nature management of forest plantation, few studies have paid attention to the effect of crop tree management on the soil properties and understory vegetation. Methods A 36-year-old Pinus massoniana plantation in Huaying city, Sichuan Province was taken as the research object to analyse the changes in undergrowth plant diversity and soil physicochemical properties under three different crop tree densities (100, 150, and 200 N/ha). Results Our results showed that the contents of available phosphorus, organic matter and hydrolysable nitrogen in the topsoil increased significantly after crop tree management, while content of available potassium decreased. The composition of shrub and herb layer was richer, and the dominant species were obviously replaced after crop tree management. The Shannon–Wiener index and Richness index of shrub layer, and the diversity of herb layer increased significantly after crop tree management. Herb layer diversity indexes and Richness index of shrub layer were closely related to soil organic matter, available phosphorus, hydrolysable nitrogen, available potassium, soil moisture and bulk density. As the main limiting factors for plant growth, nitrogen, phosphorus and potassium were closely related to plant diversity and to the distribution of the dominant species. At the initial stage of crop tree management, each treatment significantly improved the soil physicochemical properties and plant diversity of Pinus massoniana plantation, and the comprehensive evaluation was 200 N/ha >100 N/ha >150 N/ha >CK. Compared with other treatments, 200 N/ha had the best effect on improving the undergrowth environment of the Pinus massoniana plantation in the initial stage of cr…
bibliographic citation: Lyu et al. (2021) Early effects of crop tree management on undergrowth plant diversity and soil physicochemical properties in a Pinus massoniana plantation. PeerJ 9:e11852 https://doi.org/10.7717/peerj.11852
date submitted: 2021-03-12
date accepted: 2021-07-04
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lyu
  given name: Qian
author list: Agent
  family name: Shen
  given name: Yi
author list: Agent
  family name: Li
  given name: Xianwei
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Li
  given name: Dehui
author list: Agent
  family name: Fan
  given name: Chuan
doi: 10.7717/peerj.11852
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Lyu et al.
attribution name: Lyu et al.

Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period
type: item
type: AcademicArticle
description: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary …
format: application/pdf
format: text/html
creator: Ruochen Yang
creator: Chunhui Duan
creator: Yunxia Guo
creator: Yujing Ma
creator: Nazi Niu
creator: Yingjie Zhang
creator: Yueqin Liu
subject: Agricultural Science
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.11868
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Few studies on mRNA expression of the prolactin receptor (PRLR) isoforms in different tissues of sheep were reported. The objective of this study was to analyze the gene sequence and mRNA expression of PRLR isoforms in the uterus, mammary gland, ovary, spleen and lymph tissue of ewes during the lactation and post-weaning periods. Ten lactating crossbred ewes (Dorper×Hu sheep) with twin lambs were used in this study. Five ewes were chosen randomly and slaughtered at mid-lactation (35 days after lambing). The remaining five ewes were slaughtered on the 5th day after weaning. Samples of uterus, mammary gland, ovary, spleen and lymph tissue were collected from each ewe to determine the mRNA expression of long PRLR (L-PRLR) and short PRLR (S-PRLR) by RT-qPCR. The physical and chemical properties, the similarity of the nucleotides L-PRLR and S-PRLR genes and the secondary and tertiary structure of the L-PRLR and S-PRLR proteins of sheep were analyzed. The results indicated that the predicted protein molecular weights of L-PRLR and S-PRLR are 65235.36 KD and 33847.48 KD, respectively, with isoelectric points of 5.12 and 8.34, respectively. The secondary protein structures of L-PRLR and S-PRLR are different. For L-PRLR these include alpha helix, extended strand and random coils and β-turns for which the content was 16.01%, 21%, 59.55% and 3.44%, respectively, whereas the secondary protein structures of S-PRLR contain only alpha helices, extended strand and random coils, comprising 18.24%, 30.07% and 48.99%, respectively. The L-PRLR and S-PRLR genes of the sheep (Ovis aries) had nucleotide sequences showing much similarity among ruminants. In these sheep, mRNA expression of L-PRLR and S-PRLR was highest in the uterus and differed between the uterus, ovary, mammary gland, spleen and lymph tissue. The mRNA expression of L-PRLR in lymph tissue was higher during lactation than in the post-weaning period (P < 0.01), whereas mRNA expression of S-PRLR in the uterus and the mammary …
bibliographic citation: Yang et al. (2021) Sequence analysis and mRNA expression of prolactin receptor gene isoforms in different tissues of sheep during lactation and the post-weaning period. PeerJ 9:e11868 https://doi.org/10.7717/peerj.11868
date submitted: 2021-03-05
date accepted: 2021-07-05
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Ruochen
author list: Agent
  family name: Duan
  given name: Chunhui
author list: Agent
  family name: Guo
  given name: Yunxia
author list: Agent
  family name: Ma
  given name: Yujing
author list: Agent
  family name: Niu
  given name: Nazi
author list: Agent
  family name: Zhang
  given name: Yingjie
author list: Agent
  family name: Liu
  given name: Yueqin
doi: 10.7717/peerj.11868
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Yang et al.
attribution name: Yang et al.

Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer
type: item
type: AcademicArticle
description: Background We investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis. Methods We obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network. Results We found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1. Conclusion Our study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis.
format: application/pdf
format: text/html
creator: Lili Li
creator: Rongrong Xie
creator: Qichun Wei
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.11893
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background We investigated the miRNA-m6A related gene network and identified a miRNA-based prognostic signature in patients with esophageal cancer using integrated genomic analysis. Methods We obtained expression data for m6A-related genes and miRNAs from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Survival analysis was conducted to identify potential prognostic biomarkers. LASSO Cox regression was performed to construct the overall survival (OS) associated prediction signature. We used the Kaplan–Meier (K–M) curve and receiver operating characteristic (ROC) curves to explore the signature’s efficiency and accuracy. Interactions between the m6A-related genes and miRNAs were identified in starBase3.0 and used to construct the miRNA-m6A related gene network. Results We found that HNRNPC, YTHDF, ZC3H13, YTHDC2, and METTL14 were dysregulated in esophageal cancer tissues. Multivariate Cox regression analysis revealed that HNRNPC may be an independent risk factor for OS. Five hundred twenty-two potential upstream miRNAs were obtained from starBase3.0. Four miRNAs (miR-186, miR-320c, miR-320d, and miR-320b) were used to construct a prognostic signature, which could serve as a prognostic predictor independent from routine clinicopathological features. Finally, we constructed a key miRNA-m6A related gene network and used one m6A-related gene and four miRNAs associated with the prognosis. The results of our bioinformatics analysis were successfully validated in the human esophageal carcinoma cell lines KYSE30 and TE-1. Conclusion Our study identified a 4-miRNA prognostic signature and established a key miRNA-m6A related gene network. These tools may reliably assist with esophageal cancer patient prognosis.
bibliographic citation: Li et al. (2021) Network analysis of miRNA targeting m6A-related genes in patients with esophageal cancer. PeerJ 9:e11893 https://doi.org/10.7717/peerj.11893
date submitted: 2021-01-28
date accepted: 2021-07-29
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Lili
author list: Agent
  family name: Xie
  given name: Rongrong
author list: Agent
  family name: Wei
  given name: Qichun
doi: 10.7717/peerj.11893
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: © 2021 Li et al.
attribution name: Li et al.

Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand
type: item
type: AcademicArticle
description: Background The populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts. Methods We monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors. Results One hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope. Conclusions According to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants.
format: application/pdf
format: text/html
creator: Nyi Nyi Phyo Htet
creator: Rattanawat Chaiyarat
creator: Nikorn Thongthip
creator: Panat Anuracpreeda
creator: Namphung Youngpoy
creator: Phonlugsamee Chompoopong
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.11896
publisher: PeerJ Inc.
rights: © 2021 Htet et al.
abstract: Background The populations of wild Asian elephants (Elephas maximus) have increased recently after a period of worldwide decline in protected areas. It is important to understand the dynamics and distribution of the remaining populations to ensure their conservation and prevent human-elephant conflicts. Methods We monitored the population distribution of elephants between 2016 and 2019 in the Phu Khieo Wildlife Sanctuary, Thailand. We set one hundred forty-nine camera trap locations; cameras recorded 38,834 photos over 6,896 trap nights. Elephants were captured in 4,319 photographs. The maximum entropy modeling software MaxEntwas used to identify elephants’ habitat preferences within 49 of the 149 total camera trap locations according to five environmental factors. Results One hundred fourteen elephants were identified. We identified 30 adult males, 43 adult females, 14 sub-adult males, nine sub-adult females, 11 juveniles, and seven calves. The age structure ratio based on adult femaleswas 0.7:1:0.3:0.2:0.3:0.2, and the ratio of reproductive ability between adult females, juveniles, and calves was 1:0.2:0.1. A suitable elephant habitat was determined to be 1,288.9 km2 using Area Under the Curve (AUC). An AUC = 0.061 indicated good performance. Our model classified habitat preferences associated with elevation, forests, salt licks, human activity, and slope. Conclusions According to our probability map this sanctuary can provide a suitable habitat for elephants. Our results indicate that effective management practices can protect wild Asian elephants in the region and reduce conflict between humans and elephants.
bibliographic citation: Htet et al. (2021) Population and distribution of wild Asian elephants (Elephas maximus) in Phu Khieo Wildlife Sanctuary, Thailand. PeerJ 9:e11896 https://doi.org/10.7717/peerj.11896
date submitted: 2021-01-26
date accepted: 2021-07-12
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Htet
  given name: Nyi Nyi Phyo
author list: Agent
  family name: Chaiyarat
  given name: Rattanawat
author list: Agent
  family name: Thongthip
  given name: Nikorn
author list: Agent
  family name: Anuracpreeda
  given name: Panat
author list: Agent
  family name: Youngpoy
  given name: Namphung
author list: Agent
  family name: Chompoopong
  given name: Phonlugsamee
doi: 10.7717/peerj.11896
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: ©2021 Htet et al.
attribution name: Htet et al.

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
type: item
type: AcademicArticle
description: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic dist…
format: application/pdf
format: text/html
creator: Patricia Sarcinelli Stelzer
creator: Ana Carolina A. Mazzuco
creator: Luiz Eduardo Gomes
creator: João Martins
creator: Sergio Netto
creator: Angelo F. Bernardino
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.11903
publisher: PeerJ Inc.
rights: © 2021 Stelzer et al.
abstract: Rhodoliths are free-living and morphologically diverse marine calcareous algae commonly distributed over the continental shelf seafloor. They increase the seabed structural complexity and are of potential value as feeding and reproductive grounds for a myriad of marine fauna. The higher structural seabed complexity within rhodolith beds may also increase benthic diversity by creating microhabitats, but this relationship has been rarely explored within rhodolith beds worldwide. Here we compared benthic macrofaunal (>500 µm) structure on rhodolith beds (nodule epifauna) and within unconsolidated sediments (sediment infauna) under high and low-density beds to test whether rhodolith bed density and nodule morphology influenced macrofaunal assemblages. We observed that macrofaunal density on nodules (2538 ± 288.7 ind·m−2) was 15-fold higher when compared to sediments under those beds (166 ± 38.8 ind·m−2). Rhodolith bed density was positively related to macrofaunal density, composition, and functional diversity on the rhodoliths. Low-density beds (61 ± 27.1 nodules·m−2) with discoid-shape nodules were dominated by peracarid crustaceans whereas high-density beds (204 ± 18.7 nodules·m−2) with spheroidal nodules were dominated by Annelid polychaetes. The sediment macrofauna was also positively influenced by the density of rhodolith nodules, which increased sediment carbonate and organic quality (protein and lipids) under high-density beds. Macrofaunal functional diversity was generally higher on rhodoliths, with low similarity (low nestedness) and high taxa turnover between macrofaunal assemblages of rhodoliths and sediments. These findings indicate that rhodolith beds provide an unique habitat for benthic macrofaunal communities, with exclusive functional and taxonomic richness that are likely not typical in the unconsolidated sediment below these beds in SE Brazil. This study highlights the importance of protecting rhodolith beds from multiple sources of anthropogenic dist…
bibliographic citation: Stelzer et al. (2021) Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil. PeerJ 9:e11903 https://doi.org/10.7717/peerj.11903
date submitted: 2021-03-26
date accepted: 2021-07-13
issued: 2021-07-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stelzer
  given name: Patricia Sarcinelli
author list: Agent
  family name: Mazzuco
  given name: Ana Carolina A.
author list: Agent
  family name: Gomes
  given name: Luiz Eduardo
author list: Agent
  family name: Martins
  given name: João
author list: Agent
  family name: Netto
  given name: Sergio
author list: Agent
  family name: Bernardino
  given name: Angelo F.
doi: 10.7717/peerj.11903
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-29
copyright: © 2021 Stelzer et al.
attribution name: Stelzer et al.

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