PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Soil bacterial and fungal communities of six bahiagrass cultivars
items: Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle
items: The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species
items: Genetic assessment of three Fagaceae species in forest restoration trials
items: Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico
items: Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images
items: Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
items: Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population
items: Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis
items: Returning a lost process by reintroducing a locally extinct digging marsupial

Soil bacterial and fungal communities of six bahiagrass cultivars
type: item
type: AcademicArticle
description: Background Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. Objectives This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. Methods Six bahiagrass cultivars (‘Argentine’, ‘Pensacola’, ‘Sand Mountain’, ‘Tifton 9’, ‘TifQuik’, and ‘UF-Riata’) were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. Results The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under ‘Sand Mountain’ than ‘UF-Riata’. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. Conclusions Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynam…
format: application/pdf
format: text/html
creator: Lukas Beule
creator: Ko-Hsuan Chen
creator: Chih-Ming Hsu
creator: Cheryl Mackowiak
creator: Jose C.B. Dubeux Jr.
creator: Ann Blount
creator: Hui-Ling Liao
subject: Agricultural Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.7014
publisher: PeerJ Inc.
rights: © 2019 Beule et al.
abstract: Background Cultivars of bahiagrass (Paspalum notatum Flüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance. Objectives This study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities. Methods Six bahiagrass cultivars (‘Argentine’, ‘Pensacola’, ‘Sand Mountain’, ‘Tifton 9’, ‘TifQuik’, and ‘UF-Riata’) were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano. Results The soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizing Nitrospira was greater under ‘Sand Mountain’ than ‘UF-Riata’. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists. Conclusions Our results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance of Nitrospira members in response to cultivar choice may have implications for soil N dynam…
bibliographic citation: Beule et al. (2019) Soil bacterial and fungal communities of six bahiagrass cultivars. PeerJ 7:e7014 https://doi.org/10.7717/peerj.7014
date submitted: 2019-02-25
date accepted: 2019-04-19
issued: 2019-05-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beule
  given name: Lukas
author list: Agent
  family name: Chen
  given name: Ko-Hsuan
author list: Agent
  family name: Hsu
  given name: Chih-Ming
author list: Agent
  family name: Mackowiak
  given name: Cheryl
author list: Agent
  family name: Dubeux Jr.
  given name: Jose C.B.
author list: Agent
  family name: Blount
  given name: Ann
author list: Agent
  family name: Liao
  given name: Hui-Ling
doi: 10.7717/peerj.7014
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-29
copyright: ©2019 Beule et al.
attribution name: Beule et al.

Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle
type: item
type: AcademicArticle
description: Background Self-administered foam rolling (SAFR) is an effective massage technique often used in sport and rehabilitation settings to improve range of motion (ROM) without impairing the strength performance. However, the effects of unilateral SAFR on contralateral non-intervened muscle’s rate of force development (RFD) are unknown. Therefore, the purpose of this investigation was to examine the acute effects of unilateral hamstrings SAFR on the contralateral limb flexibility, the isometric strength, and the RFD parameters. Methods Thirty-four subjects (21 women) completed two separate randomly sequenced experimental visits, during which the control (rested for 10 min) or ten, 30-second SAFR were performed with the dominant hamstring muscle group. Before (Pre) and after (Post) the interventions, the contralateral hip flexion passive ROM, the maximal explosive isometric strength of the contralateral knee flexors with the corresponding prime mover muscles’ surface electromyographic (EMG) amplitude were measured. Separate two-way (time ×intervention) repeated measures analyses of variance (ANOVAs) were used to examine the potential changes of the dependent variables. Results The SAFR significantly improved the contralateral limb ROM (Pre vs. Post: 68.3 ± 21.0 vs. 73.2 ± 23.2 degrees, p < 0.001; d = 0.22). No change was found for the contralateral isometric strength or the maximal EMG amplitude. For the RFD parameters, the percent changes of the RFDs for the first 50, 100, and 200 ms of the maximal explosive isometric contraction were −31.2%, −16.8%, and −10.1%, respectively, following the unilateral SAFR, relative to the control condition. In addition, the decrement of the first 50-ms RFD reached statistical significance (p = 0.007; Cohen’s d = 0.44). Conclusion Ten sets of 30-second unilateral hamstring SAFR improved the ROM of the non-intervened contralateral limb, but decreased its ability to generate force, especially during the early phase (e.g., 50 ms) of the maxi…
format: application/pdf
format: text/html
creator: Xin Ye
creator: Benjamin S. Killen
creator: Krista L. Zelizney
creator: William M. Miller
creator: Sunggun Jeon
subject: Neuroscience
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.7028
publisher: PeerJ Inc.
rights: © 2019 Ye et al.
abstract: Background Self-administered foam rolling (SAFR) is an effective massage technique often used in sport and rehabilitation settings to improve range of motion (ROM) without impairing the strength performance. However, the effects of unilateral SAFR on contralateral non-intervened muscle’s rate of force development (RFD) are unknown. Therefore, the purpose of this investigation was to examine the acute effects of unilateral hamstrings SAFR on the contralateral limb flexibility, the isometric strength, and the RFD parameters. Methods Thirty-four subjects (21 women) completed two separate randomly sequenced experimental visits, during which the control (rested for 10 min) or ten, 30-second SAFR were performed with the dominant hamstring muscle group. Before (Pre) and after (Post) the interventions, the contralateral hip flexion passive ROM, the maximal explosive isometric strength of the contralateral knee flexors with the corresponding prime mover muscles’ surface electromyographic (EMG) amplitude were measured. Separate two-way (time ×intervention) repeated measures analyses of variance (ANOVAs) were used to examine the potential changes of the dependent variables. Results The SAFR significantly improved the contralateral limb ROM (Pre vs. Post: 68.3 ± 21.0 vs. 73.2 ± 23.2 degrees, p < 0.001; d = 0.22). No change was found for the contralateral isometric strength or the maximal EMG amplitude. For the RFD parameters, the percent changes of the RFDs for the first 50, 100, and 200 ms of the maximal explosive isometric contraction were −31.2%, −16.8%, and −10.1%, respectively, following the unilateral SAFR, relative to the control condition. In addition, the decrement of the first 50-ms RFD reached statistical significance (p = 0.007; Cohen’s d = 0.44). Conclusion Ten sets of 30-second unilateral hamstring SAFR improved the ROM of the non-intervened contralateral limb, but decreased its ability to generate force, especially during the early phase (e.g., 50 ms) of the maxi…
bibliographic citation: Ye et al. (2019) Unilateral hamstring foam rolling does not impair strength but the rate of force development of the contralateral muscle. PeerJ 7:e7028 https://doi.org/10.7717/peerj.7028
date submitted: 2018-12-10
date accepted: 2019-04-26
issued: 2019-05-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Xin
author list: Agent
  family name: Killen
  given name: Benjamin S.
author list: Agent
  family name: Zelizney
  given name: Krista L.
author list: Agent
  family name: Miller
  given name: William M.
author list: Agent
  family name: Jeon
  given name: Sunggun
doi: 10.7717/peerj.7028
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-29
copyright: ©2019 Ye et al.
attribution name: Ye et al.

The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species
type: item
type: AcademicArticle
description: Background The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy. Methods We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato. Results The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confide…
format: application/pdf
format: text/html
creator: Daniel Jablonski
creator: Oleg V. Kukushkin
creator: Aziz Avcı
creator: Sabina Bunyatova
creator: Yusuf Kumlutaş
creator: Çetin Ilgaz
creator: Ekaterina Polyakova
creator: Konstantin Shiryaev
creator: Boris Tuniyev
creator: David Jandzik
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6944
publisher: PeerJ Inc.
rights: © 2019 Jablonski et al.
abstract: Background The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy. Methods We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato. Results The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confide…
bibliographic citation: Jablonski et al. (2019) The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species. PeerJ 7:e6944 https://doi.org/10.7717/peerj.6944
date submitted: 2019-02-01
date accepted: 2019-04-12
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jablonski
  given name: Daniel
author list: Agent
  family name: Kukushkin
  given name: Oleg V.
author list: Agent
  family name: Avcı
  given name: Aziz
author list: Agent
  family name: Bunyatova
  given name: Sabina
author list: Agent
  family name: Kumlutaş
  given name: Yusuf
author list: Agent
  family name: Ilgaz
  given name: Çetin
author list: Agent
  family name: Polyakova
  given name: Ekaterina
author list: Agent
  family name: Shiryaev
  given name: Konstantin
author list: Agent
  family name: Tuniyev
  given name: Boris
author list: Agent
  family name: Jandzik
  given name: David
doi: 10.7717/peerj.6944
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: © 2019 Jablonski et al.
attribution name: Jablonski et al.

Genetic assessment of three Fagaceae species in forest restoration trials
type: item
type: AcademicArticle
description: Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
format: application/pdf
format: text/html
creator: Patcharawadee Thongkumkoon
creator: Siriwadee Chomdej
creator: Jatupol Kampuansai
creator: Waranee Pradit
creator: Pimubon Waikham
creator: Stephen Elliott
creator: Sutthathorn Chairuangsri
creator: Dia Panitnard Shannon
creator: Prasit Wangpakapattanawong
creator: Aizhong Liu
subject: Molecular Biology
subject: Forestry
subject: Population Biology
description: doi:10.7717/peerj.6958
publisher: PeerJ Inc.
rights: © 2019 Thongkumkoon et al.
abstract: Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
bibliographic citation: Thongkumkoon et al. (2019) Genetic assessment of three Fagaceae species in forest restoration trials. PeerJ 7:e6958 https://doi.org/10.7717/peerj.6958
date submitted: 2019-01-25
date accepted: 2019-04-14
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thongkumkoon
  given name: Patcharawadee
author list: Agent
  family name: Chomdej
  given name: Siriwadee
author list: Agent
  family name: Kampuansai
  given name: Jatupol
author list: Agent
  family name: Pradit
  given name: Waranee
author list: Agent
  family name: Waikham
  given name: Pimubon
author list: Agent
  family name: Elliott
  given name: Stephen
author list: Agent
  family name: Chairuangsri
  given name: Sutthathorn
author list: Agent
  family name: Shannon
  given name: Dia Panitnard
author list: Agent
  family name: Wangpakapattanawong
  given name: Prasit
author list: Agent
  family name: Liu
  given name: Aizhong
doi: 10.7717/peerj.6958
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: ©2019 Thongkumkoon et al.
attribution name: Thongkumkoon et al.

Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico
type: item
type: AcademicArticle
description: The role of invasive species in ecosystem functioning represents one of the main challenges in ecology. Pteridium aquilinum is a successful cosmopolitan invasive species with negative effects on the ecological mechanisms that allow secondary succession. In this study, we evaluated the influence of P. aquilinumon secondary succession under different disturbances in a seasonal dry forest of the Yucatán Peninsula. We determined species richness, composition and the relative importance value in four sampling units. Fabaceae followed by Asteraceae, Meliaceae, Rubiaceae, Sapindaceae and Verbenaceae were the most species rich families. A dissimilarity analysis determined significant differences in beta diversity between sampling units. With a generalized linear model we found that species richness was best explained by site conditions, followed by calcium and soil organic matter. Also, the generalized linear model showed that abundance resulted in a strong correlation with site conditions and soil characteristics. Specific soil conditions related to phosphoro and calcium were also detected as beneficiary to the successional processes. Our results suggest that applying fire restriction and periodic cutting of the bracken fern, this can increase a higher diversity of species.
format: application/pdf
format: text/html
creator: Alberto Jean Baptiste
creator: Pedro A. Macario
creator: Gerald A. Islebe
creator: Benedicto Vargas-Larreta
creator: Luciano Pool
creator: Mirna Valdez-Hernández
creator: Jorge O. López-Martínez
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.6974
publisher: PeerJ Inc.
rights: © 2019 Jean Baptiste et al.
abstract: The role of invasive species in ecosystem functioning represents one of the main challenges in ecology. Pteridium aquilinum is a successful cosmopolitan invasive species with negative effects on the ecological mechanisms that allow secondary succession. In this study, we evaluated the influence of P. aquilinumon secondary succession under different disturbances in a seasonal dry forest of the Yucatán Peninsula. We determined species richness, composition and the relative importance value in four sampling units. Fabaceae followed by Asteraceae, Meliaceae, Rubiaceae, Sapindaceae and Verbenaceae were the most species rich families. A dissimilarity analysis determined significant differences in beta diversity between sampling units. With a generalized linear model we found that species richness was best explained by site conditions, followed by calcium and soil organic matter. Also, the generalized linear model showed that abundance resulted in a strong correlation with site conditions and soil characteristics. Specific soil conditions related to phosphoro and calcium were also detected as beneficiary to the successional processes. Our results suggest that applying fire restriction and periodic cutting of the bracken fern, this can increase a higher diversity of species.
bibliographic citation: Jean Baptiste et al. (2019) Secondary Succession under invasive species (Pteridium aquilinum) conditions in a seasonal dry tropical forest in southeastern Mexico. PeerJ 7:e6974 https://doi.org/10.7717/peerj.6974
date submitted: 2019-03-02
date accepted: 2019-04-15
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jean Baptiste
  given name: Alberto
author list: Agent
  family name: Macario
  given name: Pedro A.
author list: Agent
  family name: Islebe
  given name: Gerald A.
author list: Agent
  family name: Vargas-Larreta
  given name: Benedicto
author list: Agent
  family name: Pool
  given name: Luciano
author list: Agent
  family name: Valdez-Hernández
  given name: Mirna
author list: Agent
  family name: López-Martínez
  given name: Jorge O.
doi: 10.7717/peerj.6974
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: ©2019 Jean Baptiste et al.
attribution name: Jean Baptiste et al.

Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images
type: item
type: AcademicArticle
description: Background Malaria is a life-threatening disease caused by Plasmodium parasites that infect the red blood cells (RBCs). Manual identification and counting of parasitized cells in microscopic thick/thin-film blood examination remains the common, but burdensome method for disease diagnosis. Its diagnostic accuracy is adversely impacted by inter/intra-observer variability, particularly in large-scale screening under resource-constrained settings. Introduction State-of-the-art computer-aided diagnostic tools based on data-driven deep learning algorithms like convolutional neural network (CNN) has become the architecture of choice for image recognition tasks. However, CNNs suffer from high variance and may overfit due to their sensitivity to training data fluctuations. Objective The primary aim of this study is to reduce model variance, improve robustness and generalization through constructing model ensembles toward detecting parasitized cells in thin-blood smear images. Methods We evaluate the performance of custom and pretrained CNNs and construct an optimal model ensemble toward the challenge of classifying parasitized and normal cells in thin-blood smear images. Cross-validation studies are performed at the patient level to ensure preventing data leakage into the validation and reduce generalization errors. The models are evaluated in terms of the following performance metrics: (a) Accuracy; (b) Area under the receiver operating characteristic (ROC) curve (AUC); (c) Mean squared error (MSE); (d) Precision; (e) F-score; and (f) Matthews Correlation Coefficient (MCC). Results It is observed that the ensemble model constructed with VGG-19 and SqueezeNet outperformed the state-of-the-art in several performance metrics toward classifying the parasitized and uninfected cells to aid in improved disease screening. Conclusions Ensemble learning reduces the model variance by optimally combining the predictions of multiple models and decreases the sensitivity to the specifics …
format: application/pdf
format: text/html
creator: Sivaramakrishnan Rajaraman
creator: Stefan Jaeger
creator: Sameer K. Antani
subject: Hematology
subject: Infectious Diseases
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.6977
publisher: PeerJ Inc.
rights: © 2019
abstract: Background Malaria is a life-threatening disease caused by Plasmodium parasites that infect the red blood cells (RBCs). Manual identification and counting of parasitized cells in microscopic thick/thin-film blood examination remains the common, but burdensome method for disease diagnosis. Its diagnostic accuracy is adversely impacted by inter/intra-observer variability, particularly in large-scale screening under resource-constrained settings. Introduction State-of-the-art computer-aided diagnostic tools based on data-driven deep learning algorithms like convolutional neural network (CNN) has become the architecture of choice for image recognition tasks. However, CNNs suffer from high variance and may overfit due to their sensitivity to training data fluctuations. Objective The primary aim of this study is to reduce model variance, improve robustness and generalization through constructing model ensembles toward detecting parasitized cells in thin-blood smear images. Methods We evaluate the performance of custom and pretrained CNNs and construct an optimal model ensemble toward the challenge of classifying parasitized and normal cells in thin-blood smear images. Cross-validation studies are performed at the patient level to ensure preventing data leakage into the validation and reduce generalization errors. The models are evaluated in terms of the following performance metrics: (a) Accuracy; (b) Area under the receiver operating characteristic (ROC) curve (AUC); (c) Mean squared error (MSE); (d) Precision; (e) F-score; and (f) Matthews Correlation Coefficient (MCC). Results It is observed that the ensemble model constructed with VGG-19 and SqueezeNet outperformed the state-of-the-art in several performance metrics toward classifying the parasitized and uninfected cells to aid in improved disease screening. Conclusions Ensemble learning reduces the model variance by optimally combining the predictions of multiple models and decreases the sensitivity to the specifics …
bibliographic citation: Rajaraman et al. (2019) Performance evaluation of deep neural ensembles toward malaria parasite detection in thin-blood smear images. PeerJ 7:e6977 https://doi.org/10.7717/peerj.6977
date submitted: 2019-02-05
date accepted: 2019-04-14
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Rajaraman
  given name: Sivaramakrishnan
author list: Agent
  family name: Jaeger
  given name: Stefan
author list: Agent
  family name: Antani
  given name: Sameer K.
doi: 10.7717/peerj.6977
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28

Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma
type: item
type: AcademicArticle
description: Backround Tongue squamous cell carcinoma (TSCC) is the most common malignant tumor in the oral cavity. An increasing number of studies have suggested that long noncoding RNA (lncRNA) plays an important role in the biological process of disease and is closely related to the occurrence and development of disease, including TSCC. Although many lncRNAs have been discovered, there remains a lack of research on the function and mechanism of lncRNAs. To better understand the clinical role and biological function of lncRNAs in TSCC, we conducted this study. Methods In this study, 162 tongue samples, including 147 TSCC samples and 15 normal control samples, were investigated and downloaded from The Cancer Genome Atlas (TCGA). We constructed a competitive endogenous RNA (ceRNA) regulatory network. Then, we investigated two lncRNAs as key lncRNAs using Kaplan–Meier curve analysis and constructed a key lncRNA-miRNA-mRNA subnetwork. Furthermore, gene set enrichment analysis (GSEA) was carried out on mRNAs in the subnetwork after multivariate survival analysis of the Cox proportional hazards regression model. Results The ceRNA regulatory network consists of six differentially expressed miRNAs (DEmiRNAs), 29 differentially expressed lncRNAs (DElncRNAs) and six differentially expressed mRNAs (DEmRNAs). Kaplan-Meier curve analysis of lncRNAs in the TSCC ceRNA regulatory network showed that only two lncRNAs, including LINC00261 and PART1, are correlated with the total survival time of TSCC patients. After we constructed the key lncRNA-miRNA -RNA sub network, the GSEA results showed that key lncRNA are mainly related to cytokines and the immune system. High expression levels of LINC00261 indicate a poor prognosis, while a high expression level of PART1 indicates a better prognosis.
format: application/pdf
format: text/html
creator: Yidan Song
creator: Yihua Pan
creator: Jun Liu
subject: Bioinformatics
subject: Dermatology
subject: Oncology
description: doi:10.7717/peerj.6991
publisher: PeerJ Inc.
rights: © 2019 Song et al.
abstract: Backround Tongue squamous cell carcinoma (TSCC) is the most common malignant tumor in the oral cavity. An increasing number of studies have suggested that long noncoding RNA (lncRNA) plays an important role in the biological process of disease and is closely related to the occurrence and development of disease, including TSCC. Although many lncRNAs have been discovered, there remains a lack of research on the function and mechanism of lncRNAs. To better understand the clinical role and biological function of lncRNAs in TSCC, we conducted this study. Methods In this study, 162 tongue samples, including 147 TSCC samples and 15 normal control samples, were investigated and downloaded from The Cancer Genome Atlas (TCGA). We constructed a competitive endogenous RNA (ceRNA) regulatory network. Then, we investigated two lncRNAs as key lncRNAs using Kaplan–Meier curve analysis and constructed a key lncRNA-miRNA-mRNA subnetwork. Furthermore, gene set enrichment analysis (GSEA) was carried out on mRNAs in the subnetwork after multivariate survival analysis of the Cox proportional hazards regression model. Results The ceRNA regulatory network consists of six differentially expressed miRNAs (DEmiRNAs), 29 differentially expressed lncRNAs (DElncRNAs) and six differentially expressed mRNAs (DEmRNAs). Kaplan-Meier curve analysis of lncRNAs in the TSCC ceRNA regulatory network showed that only two lncRNAs, including LINC00261 and PART1, are correlated with the total survival time of TSCC patients. After we constructed the key lncRNA-miRNA -RNA sub network, the GSEA results showed that key lncRNA are mainly related to cytokines and the immune system. High expression levels of LINC00261 indicate a poor prognosis, while a high expression level of PART1 indicates a better prognosis.
bibliographic citation: Song et al. (2019) Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma. PeerJ 7:e6991 https://doi.org/10.7717/peerj.6991
date submitted: 2019-01-24
date accepted: 2019-04-21
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Yidan
author list: Agent
  family name: Pan
  given name: Yihua
author list: Agent
  family name: Liu
  given name: Jun
doi: 10.7717/peerj.6991
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: ©2019 Song et al.
attribution name: Song et al.

Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population
type: item
type: AcademicArticle
description: Objective Gastrointestinal cancer is the leading cause of cancer-related death worldwide. The aim of this study was to verify whether the genotype of six short tandem repeat (STR) loci including AR, Bat-25, D5S346, ER1, ER2, and FGA is associated with the risk of gastric cancer (GC) and colorectal cancer (CRC) and to develop a model that allows early diagnosis and prediction of inherited genomic susceptibility to GC and CRC. Methods Alleles of six STR loci were determined using the peripheral blood of six colon cancer patients, five rectal cancer patients, eight GC patients, and 30 healthy controls. Fisher linear discriminant analysis (FDA) was used to establish the discriminant formula to distinguish GC and CRC patients from healthy controls. Leave-one-out cross validation and receiver operating characteristic (ROC) curves were used to validate the accuracy of the formula. The relationship between the STR status and immunohistochemical (IHC) and tumor markers was analyzed using multiple correspondence analysis. Results D5S346 was confirmed as a GC- and CRC-related STR locus. For the first time, we established a discriminant formula on the basis of the six STR loci, which was used to estimate the risk coefficient of suffering from GC and CRC. The model was statistically significant (Wilks’ lambda = 0.471, χ2 = 30.488, df = 13, and p = 0.004). The results of leave-one-out cross validation showed that the sensitivity of the formula was 73.7% and the specificity was 76.7%. The area under the ROC curve (AUC) was 0.926, with a sensitivity of 73.7% and a specificity of 93.3%. The STR status was shown to have a certain relationship with the expression of some IHC markers and the level of some tumor markers. Conclusions The results of this study complement clinical diagnostic criteria and present markers for early prediction of GC and CRC. This approach will aid in improving risk awareness of susceptible individuals and contribute to reducing the incidence of GC and CRC by …
format: application/pdf
format: text/html
creator: Shuhong Hao
creator: Ming Ren
creator: Dong Li
creator: Yujie Sui
creator: Qingyu Wang
creator: Gaoyang Chen
creator: Zhaoyan Li
creator: Qiwei Yang
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.7004
publisher: PeerJ Inc.
rights: © 2019 Hao et al.
abstract: Objective Gastrointestinal cancer is the leading cause of cancer-related death worldwide. The aim of this study was to verify whether the genotype of six short tandem repeat (STR) loci including AR, Bat-25, D5S346, ER1, ER2, and FGA is associated with the risk of gastric cancer (GC) and colorectal cancer (CRC) and to develop a model that allows early diagnosis and prediction of inherited genomic susceptibility to GC and CRC. Methods Alleles of six STR loci were determined using the peripheral blood of six colon cancer patients, five rectal cancer patients, eight GC patients, and 30 healthy controls. Fisher linear discriminant analysis (FDA) was used to establish the discriminant formula to distinguish GC and CRC patients from healthy controls. Leave-one-out cross validation and receiver operating characteristic (ROC) curves were used to validate the accuracy of the formula. The relationship between the STR status and immunohistochemical (IHC) and tumor markers was analyzed using multiple correspondence analysis. Results D5S346 was confirmed as a GC- and CRC-related STR locus. For the first time, we established a discriminant formula on the basis of the six STR loci, which was used to estimate the risk coefficient of suffering from GC and CRC. The model was statistically significant (Wilks’ lambda = 0.471, χ2 = 30.488, df = 13, and p = 0.004). The results of leave-one-out cross validation showed that the sensitivity of the formula was 73.7% and the specificity was 76.7%. The area under the ROC curve (AUC) was 0.926, with a sensitivity of 73.7% and a specificity of 93.3%. The STR status was shown to have a certain relationship with the expression of some IHC markers and the level of some tumor markers. Conclusions The results of this study complement clinical diagnostic criteria and present markers for early prediction of GC and CRC. This approach will aid in improving risk awareness of susceptible individuals and contribute to reducing the incidence of GC and CRC by …
bibliographic citation: Hao et al. (2019) Fisher linear discriminant analysis for classification and prediction of genomic susceptibility to stomach and colorectal cancers based on six STR loci in a northern Chinese Han population. PeerJ 7:e7004 https://doi.org/10.7717/peerj.7004
date submitted: 2019-01-15
date accepted: 2019-04-23
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Shuhong
author list: Agent
  family name: Ren
  given name: Ming
author list: Agent
  family name: Li
  given name: Dong
author list: Agent
  family name: Sui
  given name: Yujie
author list: Agent
  family name: Wang
  given name: Qingyu
author list: Agent
  family name: Chen
  given name: Gaoyang
author list: Agent
  family name: Li
  given name: Zhaoyan
author list: Agent
  family name: Yang
  given name: Qiwei
doi: 10.7717/peerj.7004
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: ©2019 Hao et al.
attribution name: Hao et al.

Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis
type: item
type: AcademicArticle
description: Background Osteoarthritis (OA) is one of the most important age-related degenerative diseases, and the leading cause of disability and chronic pain in the aging population. Recent studies have identified several lncRNA-associated functions involved in the development of OA. Because age is a key risk factor for OA, we investigated the differential expression of age-related lncRNAs in each stage of OA. Methods Two gene expression profiles were downloaded from the GEO database and differentially expressed genes (DEGs) were identified across each of the different developmental stages of OA. Next, gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the function of the DEGs. Finally, a lncRNA-targeted DEG network was used to identify hub-lncRNAs. Results A total of 174 age-related DEGs were identified. GO analyses confirmed that age-related degradation was strongly associated with cell adhesion, endodermal cell differentiation and collagen fibril organization. Significantly enriched KEGG pathways associated with these DEGs included the PI3K–Akt signaling pathway, focal adhesion, and ECM–receptor interaction. Further analyses via a protein–protein interaction (PPI) network identified two hub lncRNAs, CRNDE and LINC00152, involved in the process of age-related degeneration of articular cartilage. Our findings suggest that lncRNAs may play active roles in the development of OA. Investigation of the gene expression profiles in different development stages may supply a new target for OA treatment.
format: application/pdf
format: text/html
creator: Pengfei Hu
creator: Fangfang Sun
creator: Jisheng Ran
creator: Lidong Wu
subject: Bioinformatics
subject: Geriatrics
subject: Orthopedics
description: doi:10.7717/peerj.7024
publisher: PeerJ Inc.
rights: © 2019 Hu et al.
abstract: Background Osteoarthritis (OA) is one of the most important age-related degenerative diseases, and the leading cause of disability and chronic pain in the aging population. Recent studies have identified several lncRNA-associated functions involved in the development of OA. Because age is a key risk factor for OA, we investigated the differential expression of age-related lncRNAs in each stage of OA. Methods Two gene expression profiles were downloaded from the GEO database and differentially expressed genes (DEGs) were identified across each of the different developmental stages of OA. Next, gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to annotate the function of the DEGs. Finally, a lncRNA-targeted DEG network was used to identify hub-lncRNAs. Results A total of 174 age-related DEGs were identified. GO analyses confirmed that age-related degradation was strongly associated with cell adhesion, endodermal cell differentiation and collagen fibril organization. Significantly enriched KEGG pathways associated with these DEGs included the PI3K–Akt signaling pathway, focal adhesion, and ECM–receptor interaction. Further analyses via a protein–protein interaction (PPI) network identified two hub lncRNAs, CRNDE and LINC00152, involved in the process of age-related degeneration of articular cartilage. Our findings suggest that lncRNAs may play active roles in the development of OA. Investigation of the gene expression profiles in different development stages may supply a new target for OA treatment.
bibliographic citation: Hu et al. (2019) Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis. PeerJ 7:e7024 https://doi.org/10.7717/peerj.7024
date submitted: 2019-01-29
date accepted: 2019-04-24
issued: 2019-05-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Pengfei
author list: Agent
  family name: Sun
  given name: Fangfang
author list: Agent
  family name: Ran
  given name: Jisheng
author list: Agent
  family name: Wu
  given name: Lidong
doi: 10.7717/peerj.7024
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-28
copyright: ©2019 Hu et al.
attribution name: Hu et al.

Returning a lost process by reintroducing a locally extinct digging marsupial
type: item
type: AcademicArticle
description: The eastern bettong (Bettongia gaimardi), a medium-sized digging marsupial, was reintroduced to a predator-free reserve after 100 years of absence from the Australian mainland. The bettong may have the potential to restore temperate woodlands degraded by a history of livestock grazing, by creating numerous small disturbances by digging. We investigated the digging capacity of the bettong and compared this to extant fauna, to answer the first key question of whether this species could be considered an ecosystem engineer, and ultimately if it has the capacity to restore lost ecological processes. We found that eastern bettongs were frequent diggers and, at a density of 0.3–0.4 animals ha−1, accounted for over half the total foraging pits observed (55%), with echidnas (Tachyglossus aculeatus), birds and feral rabbits (Oryctolagus cuniculus) accounting for the rest. We estimated that the population of bettongs present dug 985 kg of soil per ha per year in our study area. Bettongs dug more where available phosphorus was higher, where there was greater basal area of Acacia spp. and where kangaroo grazing was less. There was no effect on digging of eucalypt stem density or volume of logs on the ground. While bettong digging activity was more frequent under trees, digging also occurred in open grassland, and bettongs were the only species observed to dig in scalds (areas where topsoil has eroded to the B Horizon). These results highlight the potential for bettongs to enhance soil processes in a way not demonstrated by the existing fauna (native birds and echidna), and introduced rabbit.
format: application/pdf
format: text/html
creator: Nicola T. Munro
creator: Sue McIntyre
creator: Ben Macdonald
creator: Saul A. Cunningham
creator: Iain J. Gordon
creator: Ross B. Cunningham
creator: Adrian D. Manning
subject: Bioengineering
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6622
publisher: PeerJ Inc.
rights: © 2019 Munro et al.
abstract: The eastern bettong (Bettongia gaimardi), a medium-sized digging marsupial, was reintroduced to a predator-free reserve after 100 years of absence from the Australian mainland. The bettong may have the potential to restore temperate woodlands degraded by a history of livestock grazing, by creating numerous small disturbances by digging. We investigated the digging capacity of the bettong and compared this to extant fauna, to answer the first key question of whether this species could be considered an ecosystem engineer, and ultimately if it has the capacity to restore lost ecological processes. We found that eastern bettongs were frequent diggers and, at a density of 0.3–0.4 animals ha−1, accounted for over half the total foraging pits observed (55%), with echidnas (Tachyglossus aculeatus), birds and feral rabbits (Oryctolagus cuniculus) accounting for the rest. We estimated that the population of bettongs present dug 985 kg of soil per ha per year in our study area. Bettongs dug more where available phosphorus was higher, where there was greater basal area of Acacia spp. and where kangaroo grazing was less. There was no effect on digging of eucalypt stem density or volume of logs on the ground. While bettong digging activity was more frequent under trees, digging also occurred in open grassland, and bettongs were the only species observed to dig in scalds (areas where topsoil has eroded to the B Horizon). These results highlight the potential for bettongs to enhance soil processes in a way not demonstrated by the existing fauna (native birds and echidna), and introduced rabbit.
bibliographic citation: Munro et al. (2019) Returning a lost process by reintroducing a locally extinct digging marsupial. PeerJ 7:e6622 https://doi.org/10.7717/peerj.6622
date submitted: 2018-11-02
date accepted: 2019-02-14
issued: 2019-05-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Munro
  given name: Nicola T.
author list: Agent
  family name: McIntyre
  given name: Sue
author list: Agent
  family name: Macdonald
  given name: Ben
author list: Agent
  family name: Cunningham
  given name: Saul A.
author list: Agent
  family name: Gordon
  given name: Iain J.
author list: Agent
  family name: Cunningham
  given name: Ross B.
author list: Agent
  family name: Manning
  given name: Adrian D.
doi: 10.7717/peerj.6622
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-27
copyright: © 2019 Munro et al.
attribution name: Munro et al.

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