PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Levels of detail analysis of microwave scattering from human head models for brain stroke detection
items: Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach
items: Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
items: The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification
items: PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
items: Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation
items: The role of biomaterials in the treatment of meniscal tears
items: Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
items: NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1
items: A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma

Levels of detail analysis of microwave scattering from human head models for brain stroke detection
type: item
type: AcademicArticle
description: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model. After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to fi…
format: application/pdf
format: text/html
creator: Awais Munawar Qureshi
creator: Zartasha Mustansar
subject: Bioengineering
subject: Biophysics
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.4061
publisher: PeerJ Inc.
rights: © 2017 Qureshi and Mustansar
abstract: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model. After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to fi…
bibliographic citation: Qureshi et al. (2017) Levels of detail analysis of microwave scattering from human head models for brain stroke detection. PeerJ 5:e4061 https://doi.org/10.7717/peerj.4061
date submitted: 2017-06-08
date accepted: 2017-10-28
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qureshi
  given name: Awais Munawar
author list: Agent
  family name: Mustansar
  given name: Zartasha
doi: 10.7717/peerj.4061
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: © 2017 Qureshi and Mustansar
attribution name: Qureshi and Mustansar

Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach
type: item
type: AcademicArticle
description: Background Tartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear. Methods In this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases. Results A total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies. Conclusion For the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL.
format: application/pdf
format: text/html
creator: Chao-Long Lu
creator: Qi Zheng
creator: Qi Shen
creator: Chi Song
creator: Zhi-Ming Zhang
subject: Bioinformatics
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.4042
publisher: PeerJ Inc.
rights: © 2017 Lu et al.
abstract: Background Tartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear. Methods In this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases. Results A total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies. Conclusion For the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL.
bibliographic citation: Lu et al. (2017) Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PeerJ 5:e4042 https://doi.org/10.7717/peerj.4042
date submitted: 2017-07-21
date accepted: 2017-10-25
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Chao-Long
author list: Agent
  family name: Zheng
  given name: Qi
author list: Agent
  family name: Shen
  given name: Qi
author list: Agent
  family name: Song
  given name: Chi
author list: Agent
  family name: Zhang
  given name: Zhi-Ming
doi: 10.7717/peerj.4042
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Lu et al.
attribution name: Lu et al.

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta
type: item
type: AcademicArticle
description: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
format: application/pdf
format: text/html
creator: Kishor Dhaygude
creator: Kalevi Trontti
creator: Jenni Paviala
creator: Claire Morandin
creator: Christopher Wheat
creator: Liselotte Sundström
creator: Heikki Helanterä
subject: Bioinformatics
subject: Computational Biology
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.3998
publisher: PeerJ Inc.
rights: © 2017 Dhaygude et al.
abstract: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
bibliographic citation: Dhaygude et al. (2017) Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta. PeerJ 5:e3998 https://doi.org/10.7717/peerj.3998
date submitted: 2017-04-14
date accepted: 2017-10-17
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dhaygude
  given name: Kishor
author list: Agent
  family name: Trontti
  given name: Kalevi
author list: Agent
  family name: Paviala
  given name: Jenni
author list: Agent
  family name: Morandin
  given name: Claire
author list: Agent
  family name: Wheat
  given name: Christopher
author list: Agent
  family name: Sundström
  given name: Liselotte
author list: Agent
  family name: Helanterä
  given name: Heikki
doi: 10.7717/peerj.3998
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Dhaygude et al.
attribution name: Dhaygude et al.

The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification
type: item
type: AcademicArticle
description: Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
format: application/pdf
format: text/html
creator: Tao Pan
creator: Yanan Zhang
creator: Hui Wang
creator: Jun Wu
creator: Xing Kang
creator: Lifu Qian
creator: Jinyun Chen
creator: Dingqi Rao
creator: Jianping Jiang
creator: Baowei Zhang
subject: Biodiversity
subject: Biogeography
description: doi:10.7717/peerj.3995
publisher: PeerJ Inc.
rights: © 2017 Pan et al.
abstract: Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
bibliographic citation: Pan et al. (2017) The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification. PeerJ 5:e3995 https://doi.org/10.7717/peerj.3995
date submitted: 2017-08-15
date accepted: 2017-10-16
issued: 2017-11-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Tao
author list: Agent
  family name: Zhang
  given name: Yanan
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Wu
  given name: Jun
author list: Agent
  family name: Kang
  given name: Xing
author list: Agent
  family name: Qian
  given name: Lifu
author list: Agent
  family name: Chen
  given name: Jinyun
author list: Agent
  family name: Rao
  given name: Dingqi
author list: Agent
  family name: Jiang
  given name: Jianping
author list: Agent
  family name: Zhang
  given name: Baowei
doi: 10.7717/peerj.3995
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-21
copyright: ©2017 Pan et al.
attribution name: Pan et al.

PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
type: item
type: AcademicArticle
description: This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.
format: application/pdf
format: text/html
creator: Jonathan Barnoud
creator: Hubert Santuz
creator: Pierrick Craveur
creator: Agnel Praveen Joseph
creator: Vincent Jallu
creator: Alexandre G. de Brevern
creator: Pierre Poulain
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.4013
publisher: PeerJ Inc.
rights: © 2017 Barnoud et al.
abstract: This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.
bibliographic citation: Barnoud et al. (2017) PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks. PeerJ 5:e4013 https://doi.org/10.7717/peerj.4013
date submitted: 2017-08-28
date accepted: 2017-10-19
issued: 2017-11-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barnoud
  given name: Jonathan
author list: Agent
  family name: Santuz
  given name: Hubert
author list: Agent
  family name: Craveur
  given name: Pierrick
author list: Agent
  family name: Joseph
  given name: Agnel Praveen
author list: Agent
  family name: Jallu
  given name: Vincent
author list: Agent
  family name: de Brevern
  given name: Alexandre G.
author list: Agent
  family name: Poulain
  given name: Pierre
doi: 10.7717/peerj.4013
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-20
copyright: ©2017 Barnoud et al.
attribution name: Barnoud et al.

Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation
type: item
type: AcademicArticle
description: Morphological differentiation among closely related species provides opportunities to study mechanisms shaping natural phenotypic variation. Here, we address variation in the orientation of melanin-colored body stripes in three cichlid species of the tribe Haplochromini. Melanochromis auratus displays a common pattern of dark, straight horizontal body stripes, whereas in Aristochromis christyi and Buccochromis rhoadesii, oblique stripes extend from the anterior dorsal to the posterior mid-lateral trunk. We first validated a stably reference gene, and then, investigated the chromatophore distribution in the skin by assessing the expression levels of the iridophore and melanophore marker genes, ltk and slc24a5, respectively, as well as pmel, a melanophore pigmentation marker gene. We found anterior-posterior differences in the expression levels of the three genes in the oblique-striped species. The higher anterior expression of ltk, indicates increased iridophore density in the anterior region, i.e., uneven horizontal distribution of iridophores, which coincides with the anterior dorsalization of melanophore stripe in these species. The obliqueness of the horizontal body stripes might be a result of distinct migratory or patterning abilities of melanophores in anterior and posterior stripe regions which could be reflected by variation in the expression of genes involved in melanophore patterning. To address this, we investigated anterior-posterior expression levels of a primary set of candidate target genes with known functions in melanophore migration and stripe patterning in the adult zebrafish, and their related gene regulatory network. Among these genes, those with differences in anterior-posterior expression showed only species-specific differential expression, e.g., sdf1a, col14a1a, ifitm5, and agpat3, with the exception of fbxw4/hagoromo (differentially expressed in an oblique-and the straight-striped species). In summary, distinct anterior-posterior gradients …
format: application/pdf
format: text/html
creator: Ehsan Pashay Ahi
creator: Kristina M. Sefc
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.4080
publisher: PeerJ Inc.
rights: © 2017 Ahi and Sefc
abstract: Morphological differentiation among closely related species provides opportunities to study mechanisms shaping natural phenotypic variation. Here, we address variation in the orientation of melanin-colored body stripes in three cichlid species of the tribe Haplochromini. Melanochromis auratus displays a common pattern of dark, straight horizontal body stripes, whereas in Aristochromis christyi and Buccochromis rhoadesii, oblique stripes extend from the anterior dorsal to the posterior mid-lateral trunk. We first validated a stably reference gene, and then, investigated the chromatophore distribution in the skin by assessing the expression levels of the iridophore and melanophore marker genes, ltk and slc24a5, respectively, as well as pmel, a melanophore pigmentation marker gene. We found anterior-posterior differences in the expression levels of the three genes in the oblique-striped species. The higher anterior expression of ltk, indicates increased iridophore density in the anterior region, i.e., uneven horizontal distribution of iridophores, which coincides with the anterior dorsalization of melanophore stripe in these species. The obliqueness of the horizontal body stripes might be a result of distinct migratory or patterning abilities of melanophores in anterior and posterior stripe regions which could be reflected by variation in the expression of genes involved in melanophore patterning. To address this, we investigated anterior-posterior expression levels of a primary set of candidate target genes with known functions in melanophore migration and stripe patterning in the adult zebrafish, and their related gene regulatory network. Among these genes, those with differences in anterior-posterior expression showed only species-specific differential expression, e.g., sdf1a, col14a1a, ifitm5, and agpat3, with the exception of fbxw4/hagoromo (differentially expressed in an oblique-and the straight-striped species). In summary, distinct anterior-posterior gradients …
bibliographic citation: Ahi et al. (2017) Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation. PeerJ 5:e4080 https://doi.org/10.7717/peerj.4080
date submitted: 2017-07-17
date accepted: 2017-11-01
issued: 2017-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahi
  given name: Ehsan Pashay
author list: Agent
  family name: Sefc
  given name: Kristina M.
doi: 10.7717/peerj.4080
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-17
copyright: ©2017 Ahi and Sefc
attribution name: Ahi and Sefc

The role of biomaterials in the treatment of meniscal tears
type: item
type: AcademicArticle
description: Extensive investigations over the recent decades have established the anatomical, biomechanical and functional importance of the meniscus in the knee joint. As a functioning part of the joint, it serves to prevent the deterioration of articular cartilage and subsequent osteoarthritis. To this end, meniscus repair and regeneration is of particular interest from the biomaterial, bioengineering and orthopaedic research community. Even though meniscal research is previously of a considerable volume, the research community with evolving material science, biology and medical advances are all pushing toward emerging novel solutions and approaches to the successful treatment of meniscal difficulties. This review presents a tactical evaluation of the latest biomaterials, experiments to simulate meniscal tears and the state-of-the-art materials and strategies currently used to treat tears.
format: application/pdf
format: text/html
creator: Crystal O. Kean
creator: Robert J. Brown
creator: James Chapman
subject: Biotechnology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.4076
publisher: PeerJ Inc.
rights: © 2017 Kean et al.
abstract: Extensive investigations over the recent decades have established the anatomical, biomechanical and functional importance of the meniscus in the knee joint. As a functioning part of the joint, it serves to prevent the deterioration of articular cartilage and subsequent osteoarthritis. To this end, meniscus repair and regeneration is of particular interest from the biomaterial, bioengineering and orthopaedic research community. Even though meniscal research is previously of a considerable volume, the research community with evolving material science, biology and medical advances are all pushing toward emerging novel solutions and approaches to the successful treatment of meniscal difficulties. This review presents a tactical evaluation of the latest biomaterials, experiments to simulate meniscal tears and the state-of-the-art materials and strategies currently used to treat tears.
bibliographic citation: Kean et al. (2017) The role of biomaterials in the treatment of meniscal tears. PeerJ 5:e4076 https://doi.org/10.7717/peerj.4076
date submitted: 2017-06-05
date accepted: 2017-10-31
issued: 2017-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kean
  given name: Crystal O.
author list: Agent
  family name: Brown
  given name: Robert J.
author list: Agent
  family name: Chapman
  given name: James
doi: 10.7717/peerj.4076
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-17
copyright: ©2017 Kean et al.
attribution name: Kean et al.

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
type: item
type: AcademicArticle
description: Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).
format: application/pdf
format: text/html
creator: Simon M. Dittami
creator: Erwan Corre
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.4073
publisher: PeerJ Inc.
rights: © 2017 Dittami and Corre
abstract: Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).
bibliographic citation: Dittami et al. (2017) Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast. PeerJ 5:e4073 https://doi.org/10.7717/peerj.4073
date submitted: 2017-07-27
date accepted: 2017-10-30
issued: 2017-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dittami
  given name: Simon M.
author list: Agent
  family name: Corre
  given name: Erwan
doi: 10.7717/peerj.4073
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-17
copyright: © 2017 Dittami and Corre
attribution name: Dittami and Corre

NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1
type: item
type: AcademicArticle
description: Background Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data were mined to verify the change of NDUFA4L2 expression level in ccRCC tissues. The correlation between expression level of NDUFA4L2 and cell proliferation/apoptosis was explored by Gene Set Enrichment Analysis (GSEA). Protein-protein interaction (PPI) network of NDUFA4L2 was constructed. Biological process and involved pathways of NDUFA4L2 were analyzed by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The transcription factors (TFs) which can induce the expression of NDUFA4L2 were explored in clinical samples by correlation analysis and its regulation on the expression of NDUFA4L2 was verified by knockdown experiment. Results NDUFA4L2 was verified to be overexpressed in ccRCC tissues and its expression level was increased accordingly as the American Joint Committee on Cancer (AJCC) stage progressed. A high NDUFA4L2 level predicted the poor prognosis of ccRCC patients and correlated with enhanced cell proliferation and anti-apoptosis. NDUFA4L2 may interact with 14 tumor-related proteins, participate in growth and death processes and be involved in ccRCC-related pathways, such as insulin-like growth factor 1 (IGF-1), mammalian target of Rapamycin (mTOR) and phosphoinositide 3 kinase serine/threonine protein kinase (PI3K/AKT). ETS domain-containing protein ELK1 level positively correlated with the level of NDUFA4L2 in ccRCC tissues and ELK1 could regulate the expr…
format: application/pdf
format: text/html
creator: Lei Wang
creator: Zhiqiang Peng
creator: Kaizhen Wang
creator: Yijun Qi
creator: Ying Yang
creator: Yue Zhang
creator: Xinyuan An
creator: Shudong Luo
creator: Junfang Zheng
subject: Genomics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.4065
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Background Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data were mined to verify the change of NDUFA4L2 expression level in ccRCC tissues. The correlation between expression level of NDUFA4L2 and cell proliferation/apoptosis was explored by Gene Set Enrichment Analysis (GSEA). Protein-protein interaction (PPI) network of NDUFA4L2 was constructed. Biological process and involved pathways of NDUFA4L2 were analyzed by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The transcription factors (TFs) which can induce the expression of NDUFA4L2 were explored in clinical samples by correlation analysis and its regulation on the expression of NDUFA4L2 was verified by knockdown experiment. Results NDUFA4L2 was verified to be overexpressed in ccRCC tissues and its expression level was increased accordingly as the American Joint Committee on Cancer (AJCC) stage progressed. A high NDUFA4L2 level predicted the poor prognosis of ccRCC patients and correlated with enhanced cell proliferation and anti-apoptosis. NDUFA4L2 may interact with 14 tumor-related proteins, participate in growth and death processes and be involved in ccRCC-related pathways, such as insulin-like growth factor 1 (IGF-1), mammalian target of Rapamycin (mTOR) and phosphoinositide 3 kinase serine/threonine protein kinase (PI3K/AKT). ETS domain-containing protein ELK1 level positively correlated with the level of NDUFA4L2 in ccRCC tissues and ELK1 could regulate the expr…
bibliographic citation: Wang et al. (2017) NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1. PeerJ 5:e4065 https://doi.org/10.7717/peerj.4065
date submitted: 2017-03-29
date accepted: 2017-10-29
issued: 2017-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Peng
  given name: Zhiqiang
author list: Agent
  family name: Wang
  given name: Kaizhen
author list: Agent
  family name: Qi
  given name: Yijun
author list: Agent
  family name: Yang
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: An
  given name: Xinyuan
author list: Agent
  family name: Luo
  given name: Shudong
author list: Agent
  family name: Zheng
  given name: Junfang
doi: 10.7717/peerj.4065
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-17
copyright: ©2017 Wang et al.
attribution name: Wang et al.

A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature. A risk score was calculated as the summation of weighted expression levels with coefficients by Cox analysis. The signature was used to distinguish carcinoma, estimated by receiver operator characteristic curves and the area under the curve (AUC). All were validated in the GEO and TCGA data sets. Results Integrated analysis of GEO data sets revealed 300 DEGs. A 16-gene signature and a risk score were developed after survival analysis. The risk score was effective to stratify patients into high-risk and low-risk groups in the TCGA data set (P < 0.001). The 16-gene signature was valid to distinguish the carcinoma from normal samples (AUC 0.872, P < 0.001). Discussion We identified a useful 16-gene signature for prognosis of OTSCC patients, which could be applied to clinical practice. Further studies were needed to prove the findings.
format: application/pdf
format: text/html
creator: Zeting Qiu
creator: Wei Sun
creator: Shaowei Gao
creator: Huaqiang Zhou
creator: Wulin Tan
creator: Minghui Cao
creator: Wenqi Huang
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.4062
publisher: PeerJ Inc.
rights: © 2017 Qiu et al.
abstract: Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature. A risk score was calculated as the summation of weighted expression levels with coefficients by Cox analysis. The signature was used to distinguish carcinoma, estimated by receiver operator characteristic curves and the area under the curve (AUC). All were validated in the GEO and TCGA data sets. Results Integrated analysis of GEO data sets revealed 300 DEGs. A 16-gene signature and a risk score were developed after survival analysis. The risk score was effective to stratify patients into high-risk and low-risk groups in the TCGA data set (P < 0.001). The 16-gene signature was valid to distinguish the carcinoma from normal samples (AUC 0.872, P < 0.001). Discussion We identified a useful 16-gene signature for prognosis of OTSCC patients, which could be applied to clinical practice. Further studies were needed to prove the findings.
bibliographic citation: Qiu et al. (2017) A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma. PeerJ 5:e4062 https://doi.org/10.7717/peerj.4062
date submitted: 2017-09-15
date accepted: 2017-10-29
issued: 2017-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Zeting
author list: Agent
  family name: Sun
  given name: Wei
author list: Agent
  family name: Gao
  given name: Shaowei
author list: Agent
  family name: Zhou
  given name: Huaqiang
author list: Agent
  family name: Tan
  given name: Wulin
author list: Agent
  family name: Cao
  given name: Minghui
author list: Agent
  family name: Huang
  given name: Wenqi
doi: 10.7717/peerj.4062
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-17
copyright: ©2017 Qiu et al.
attribution name: Qiu et al.

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