PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Examining the influence of picture format on children’s naming responses
items: Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection
items: Variation of 13C and 15N enrichments in different plant components of labeled winter wheat (Triticum aestivum L.)
items: Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture
items: Trans-oral robotic surgery versus coblation tongue base reduction for obstructive sleep apnea syndrome
items: Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders
items: Clinical implications of aberrant neurovascular structures coursing through the submandibular gland
items: Cooperation in bottlenose dolphins: bidirectional coordination in a rope-pulling task
items: Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae
items: Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis

Examining the influence of picture format on children’s naming responses
type: item
type: AcademicArticle
description: Digital photography has facilitated the use of more ecological stimuli than line drawings as experimental stimuli. However, there is lack of evidence regarding the effect of the picture format on children’s naming agreement. The present work investigated whether the format of presentation of the pictures (line drawing or photograph) affects naming task performance in children. Two naming task experiments are reported using 106 concepts depicted both as a photograph and as a matched drawing delineated directly from the photograph. Thirty-eight and thirty-four Spanish-speaking children from 8 to 10 years old participated in Experiment 1 and Experiment 2, respectively. We examined name agreement measures (H index, percentage of modal name, and alternative responses) and subjective scales (familiarity and visual complexity). The results revealed a significant main effect of format in all of the variables except for familiarity, indicating better name agreement indices and higher visual complexity values for the photograph format than for the line drawing format. Additionally, line drawings were more likely to produce alternative incorrect names. The implications of these findings for psychoeducational research and practice are discussed.
format: application/pdf
format: text/html
creator: Naroa Martínez
creator: Helena Matute
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7692
publisher: PeerJ Inc.
rights: © 2019 Martínez and Matute
abstract: Digital photography has facilitated the use of more ecological stimuli than line drawings as experimental stimuli. However, there is lack of evidence regarding the effect of the picture format on children’s naming agreement. The present work investigated whether the format of presentation of the pictures (line drawing or photograph) affects naming task performance in children. Two naming task experiments are reported using 106 concepts depicted both as a photograph and as a matched drawing delineated directly from the photograph. Thirty-eight and thirty-four Spanish-speaking children from 8 to 10 years old participated in Experiment 1 and Experiment 2, respectively. We examined name agreement measures (H index, percentage of modal name, and alternative responses) and subjective scales (familiarity and visual complexity). The results revealed a significant main effect of format in all of the variables except for familiarity, indicating better name agreement indices and higher visual complexity values for the photograph format than for the line drawing format. Additionally, line drawings were more likely to produce alternative incorrect names. The implications of these findings for psychoeducational research and practice are discussed.
bibliographic citation: Martínez et al. (2019) Examining the influence of picture format on children’s naming responses. PeerJ 7:e7692 https://doi.org/10.7717/peerj.7692
date submitted: 2019-02-19
date accepted: 2019-08-19
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez
  given name: Naroa
author list: Agent
  family name: Matute
  given name: Helena
doi: 10.7717/peerj.7692
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Martínez and Matute
attribution name: Martínez and Matute

Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection
type: item
type: AcademicArticle
description: Highly pathogenic H5N1 influenza viruses (HPAIV) cause rapid systemic illness and death in susceptible animals, leading to a disease with high morbidity and mortality rates. Although vaccines and drugs are the best solution to prevent this threat, a more effective treatment for H5 strains of influenza has yet to be developed. Therefore, the development of therapeutics/drugs that combat H5N1 influenza virus infection is becoming increasingly important. Lycorine, the major component of Amaryllidaceae alkaloids, exhibits better protective effects against A/CK/GD/178/04 (H5N1) (GD178) viruses than the commercial neuraminidase (NA) inhibitor oseltamivir in our prior study. Lycorine demonstrates outstanding antiviral activity because of its inhibitory activity against the export of viral ribonucleoprotein complexes (vRNPs) from the nucleus. However, how lycorine affects the proteome of AIV infected cells is unknown. Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Three groups were designed: mock infection group (M), virus infection group (V), and virus infection and lycorine-treated after virus infection group (L). The multiplexed tandem mass tag (TMT) approach was employed to analyze protein level in this study. In total, 5,786 proteins were identified from the three groups of cells by using TMT proteomic analysis. In the V/M group, 1,101 proteins were identified, of which 340 differentially expressed proteins (DEPs) were determined during HPAIV infection; among the 1,059 proteins identified from the lycorine-treated group, 258 proteins presented significant change. Here, 71 proteins showed significant upregulation or downregulation of expression in the virus-infected/mock and virus-infected/lycorine-treated comparisons, and the proteins in each fraction were functionally classified further. Interestingly, lycorine treatment decreased the levels of th…
format: application/pdf
format: text/html
creator: Li Yang
creator: Jia Hao Zhang
creator: Xiao Li Zhang
creator: Guang Jie Lao
creator: Guan Ming Su
creator: Lei Wang
creator: Yao Lan Li
creator: Wen Cai Ye
creator: Jun He
subject: Molecular Biology
subject: Evidence Based Medicine
subject: Infectious Diseases
description: doi:10.7717/peerj.7697
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Highly pathogenic H5N1 influenza viruses (HPAIV) cause rapid systemic illness and death in susceptible animals, leading to a disease with high morbidity and mortality rates. Although vaccines and drugs are the best solution to prevent this threat, a more effective treatment for H5 strains of influenza has yet to be developed. Therefore, the development of therapeutics/drugs that combat H5N1 influenza virus infection is becoming increasingly important. Lycorine, the major component of Amaryllidaceae alkaloids, exhibits better protective effects against A/CK/GD/178/04 (H5N1) (GD178) viruses than the commercial neuraminidase (NA) inhibitor oseltamivir in our prior study. Lycorine demonstrates outstanding antiviral activity because of its inhibitory activity against the export of viral ribonucleoprotein complexes (vRNPs) from the nucleus. However, how lycorine affects the proteome of AIV infected cells is unknown. Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Three groups were designed: mock infection group (M), virus infection group (V), and virus infection and lycorine-treated after virus infection group (L). The multiplexed tandem mass tag (TMT) approach was employed to analyze protein level in this study. In total, 5,786 proteins were identified from the three groups of cells by using TMT proteomic analysis. In the V/M group, 1,101 proteins were identified, of which 340 differentially expressed proteins (DEPs) were determined during HPAIV infection; among the 1,059 proteins identified from the lycorine-treated group, 258 proteins presented significant change. Here, 71 proteins showed significant upregulation or downregulation of expression in the virus-infected/mock and virus-infected/lycorine-treated comparisons, and the proteins in each fraction were functionally classified further. Interestingly, lycorine treatment decreased the levels of th…
bibliographic citation: Yang et al. (2019) Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection. PeerJ 7:e7697 https://doi.org/10.7717/peerj.7697
date submitted: 2019-03-08
date accepted: 2019-08-19
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Li
author list: Agent
  family name: Zhang
  given name: Jia Hao
author list: Agent
  family name: Zhang
  given name: Xiao Li
author list: Agent
  family name: Lao
  given name: Guang Jie
author list: Agent
  family name: Su
  given name: Guan Ming
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Li
  given name: Yao Lan
author list: Agent
  family name: Ye
  given name: Wen Cai
author list: Agent
  family name: He
  given name: Jun
doi: 10.7717/peerj.7697
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Variation of 13C and 15N enrichments in different plant components of labeled winter wheat (Triticum aestivum L.)
type: item
type: AcademicArticle
description: Information on the homogeneity and distribution of 13carbon (13C) and nitrogen (15N) labeling in winter wheat (Triticum aestivum L.) is limited. We conducted a dual labeling experiment to evaluate the variability of 13C and 15N enrichment in aboveground parts of labeled winter wheat plants. Labeling with 13C and 15N was performed on non-nitrogen fertilized (−N) and nitrogen fertilized (+N, 250 kg N ha−1) plants at the elongation and grain filling stages. Aboveground parts of wheat were destructively sampled at 28 days after labeling. As winter wheat growth progressed, δ13C values of wheat ears increased significantly, whereas those of leaves and stems decreased significantly. At the elongation stage, N addition tended to reduce the aboveground δ13C values through dilution of C uptake. At the two stages, upper (newly developed) leaves were more highly enriched with 13C compared with that of lower (aged) leaves. Variability between individual wheat plants and among pots at the grain filling stage was smaller than that at the elongation stage, especially for the −N treatment. Compared with those of 13C labeling, differences in 15N excess between aboveground components (leaves and stems) under 15N labeling conditions were much smaller. We conclude that non-N fertilization and labeling at the grain filling stage may produce more uniformly 13C-labeled wheat materials, whereas the materials were more highly 13C-enriched at the elongation stage, although the δ13C values were more variable. The 15N-enriched straw tissues via urea fertilization were more uniformly labeled at the grain filling stage compared with that at the elongation stage.
format: application/pdf
format: text/html
creator: Zhaoan Sun
creator: Shuxia Wu
creator: Biao Zhu
creator: Yiwen Zhang
creator: Roland Bol
creator: Qing Chen
creator: Fanqiao Meng
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.7738
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Information on the homogeneity and distribution of 13carbon (13C) and nitrogen (15N) labeling in winter wheat (Triticum aestivum L.) is limited. We conducted a dual labeling experiment to evaluate the variability of 13C and 15N enrichment in aboveground parts of labeled winter wheat plants. Labeling with 13C and 15N was performed on non-nitrogen fertilized (−N) and nitrogen fertilized (+N, 250 kg N ha−1) plants at the elongation and grain filling stages. Aboveground parts of wheat were destructively sampled at 28 days after labeling. As winter wheat growth progressed, δ13C values of wheat ears increased significantly, whereas those of leaves and stems decreased significantly. At the elongation stage, N addition tended to reduce the aboveground δ13C values through dilution of C uptake. At the two stages, upper (newly developed) leaves were more highly enriched with 13C compared with that of lower (aged) leaves. Variability between individual wheat plants and among pots at the grain filling stage was smaller than that at the elongation stage, especially for the −N treatment. Compared with those of 13C labeling, differences in 15N excess between aboveground components (leaves and stems) under 15N labeling conditions were much smaller. We conclude that non-N fertilization and labeling at the grain filling stage may produce more uniformly 13C-labeled wheat materials, whereas the materials were more highly 13C-enriched at the elongation stage, although the δ13C values were more variable. The 15N-enriched straw tissues via urea fertilization were more uniformly labeled at the grain filling stage compared with that at the elongation stage.
bibliographic citation: Sun et al. (2019) Variation of 13C and 15N enrichments in different plant components of labeled winter wheat (Triticum aestivum L.). PeerJ 7:e7738 https://doi.org/10.7717/peerj.7738
date submitted: 2018-11-12
date accepted: 2019-08-25
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhaoan
author list: Agent
  family name: Wu
  given name: Shuxia
author list: Agent
  family name: Zhu
  given name: Biao
author list: Agent
  family name: Zhang
  given name: Yiwen
author list: Agent
  family name: Bol
  given name: Roland
author list: Agent
  family name: Chen
  given name: Qing
author list: Agent
  family name: Meng
  given name: Fanqiao
doi: 10.7717/peerj.7738
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Sun et al.
attribution name: Sun et al.

Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture
type: item
type: AcademicArticle
description: Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, “DCMF”, was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
format: application/pdf
format: text/html
creator: Sophie I. Holland
creator: Richard J. Edwards
creator: Haluk Ertan
creator: Yie Kuan Wong
creator: Tonia L. Russell
creator: Nandan P. Deshpande
creator: Michael J. Manefield
creator: Matthew Lee
subject: Genomics
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.7775
publisher: PeerJ Inc.
rights: © 2019 Holland et al.
abstract: Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, “DCMF”, was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.
bibliographic citation: Holland et al. (2019) Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PeerJ 7:e7775 https://doi.org/10.7717/peerj.7775
date submitted: 2019-05-09
date accepted: 2019-08-27
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holland
  given name: Sophie I.
author list: Agent
  family name: Edwards
  given name: Richard J.
author list: Agent
  family name: Ertan
  given name: Haluk
author list: Agent
  family name: Wong
  given name: Yie Kuan
author list: Agent
  family name: Russell
  given name: Tonia L.
author list: Agent
  family name: Deshpande
  given name: Nandan P.
author list: Agent
  family name: Manefield
  given name: Michael J.
author list: Agent
  family name: Lee
  given name: Matthew
doi: 10.7717/peerj.7775
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Holland et al.
attribution name: Holland et al.

Trans-oral robotic surgery versus coblation tongue base reduction for obstructive sleep apnea syndrome
type: item
type: AcademicArticle
description: Objectives To compare the efficacy of trans-oral robotic surgery (TORS) with that of coblation assisted tongue base reduction surgery in patients with obstructive sleep apnea syndrome (OSAS). Subjects and Methods The medical charts were retrospectively reviewed for all OSAS patients admitted to one institution for surgical intervention between 2012 and 2017. We analyzed 33 cases; 16 patients received TORS and 17 received coblation surgery for tongue base reduction. Both groups received concomitant uvulopalatoplasty. Surgical outcomes were evaluated by comparing the initial polysomnography (PSG) parameters with the follow-up PSG data (at least 3 months after the surgery). Epworth sleepiness scale (ESS) and complications were also compared between the 2 groups. Results The success rate (≥50% reduction of pre-operative AHI and post-operative AHI <20) in the TORS group and coblation group were 50% and 58%, respectively, and there was no significant difference (p = .611). The AHI (mean ± SD) reduction in the TORS and coblation groups were 24.9 ± 26.5 events/h and 19.4 ± 24.8 events/h, respectively; the between-group difference was not significant (p = .631). ESS improvement did not differ significantly between the TORS and coblation groups (3.8 ± 6.6 and 3.1 ± 9.2, respectively, p = .873). The rates of minor complication were higher in the TORS group (50%) than that of the coblation group (35.3%) without statistical significance (p = .393). Conclusion TORS achieved comparable surgical outcomes compared to coblation assisted tongue base reduction surgery in OSAS patients. Multilevel surgery using either TORS or coblation tongue base reduction combined with uvulopalatoplasty is an effective approach for the management of OSAS.
format: application/pdf
format: text/html
creator: Wei-Che Lan
creator: Wen-Dien Chang
creator: Ming-Hsui Tsai
creator: Yung-An Tsou
subject: Otorhinolaryngology
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7812
publisher: PeerJ Inc.
rights: © 2019 Lan et al.
abstract: Objectives To compare the efficacy of trans-oral robotic surgery (TORS) with that of coblation assisted tongue base reduction surgery in patients with obstructive sleep apnea syndrome (OSAS). Subjects and Methods The medical charts were retrospectively reviewed for all OSAS patients admitted to one institution for surgical intervention between 2012 and 2017. We analyzed 33 cases; 16 patients received TORS and 17 received coblation surgery for tongue base reduction. Both groups received concomitant uvulopalatoplasty. Surgical outcomes were evaluated by comparing the initial polysomnography (PSG) parameters with the follow-up PSG data (at least 3 months after the surgery). Epworth sleepiness scale (ESS) and complications were also compared between the 2 groups. Results The success rate (≥50% reduction of pre-operative AHI and post-operative AHI <20) in the TORS group and coblation group were 50% and 58%, respectively, and there was no significant difference (p = .611). The AHI (mean ± SD) reduction in the TORS and coblation groups were 24.9 ± 26.5 events/h and 19.4 ± 24.8 events/h, respectively; the between-group difference was not significant (p = .631). ESS improvement did not differ significantly between the TORS and coblation groups (3.8 ± 6.6 and 3.1 ± 9.2, respectively, p = .873). The rates of minor complication were higher in the TORS group (50%) than that of the coblation group (35.3%) without statistical significance (p = .393). Conclusion TORS achieved comparable surgical outcomes compared to coblation assisted tongue base reduction surgery in OSAS patients. Multilevel surgery using either TORS or coblation tongue base reduction combined with uvulopalatoplasty is an effective approach for the management of OSAS.
bibliographic citation: Lan et al. (2019) Trans-oral robotic surgery versus coblation tongue base reduction for obstructive sleep apnea syndrome. PeerJ 7:e7812 https://doi.org/10.7717/peerj.7812
date submitted: 2019-04-02
date accepted: 2019-09-01
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lan
  given name: Wei-Che
author list: Agent
  family name: Chang
  given name: Wen-Dien
author list: Agent
  family name: Tsai
  given name: Ming-Hsui
author list: Agent
  family name: Tsou
  given name: Yung-An
doi: 10.7717/peerj.7812
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Lan et al.
attribution name: Lan et al.

Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders
type: item
type: AcademicArticle
description: Background Monoclonal overproduction of kappa and/or lambda light chains might result in renal light chain deposition disease. Light chain associated cast nephropathy and renal AL-amyloidosis represent two further pathologies going along with monoclonal gammopathy of renal significance and multiple myeloma. While cast nephropathy often manifests with acute kidney injury, AL-amyloidosis is rather accompanied with chronic kidney disease. Methods Urine samples were collected from 17 patients with multiple myeloma or monoclonal gammopathy. The urine sediment was stained for cast morphology by H/E and light chain immunofluorescence. Following micro-selection of casts under microscope, proteomic analysis of casts was performed by mass spectrometry. Sucrose gradient sedimentation was employed and light chain architecture examined by immunoblotting. Uromodulin was measured by ELISA in sucrose gradient fractions. Results Urinary casts were observed of about 30 µm in diameter by H/E staining and under immunofluorescence microscopy. Casts with a diameter of 20 µm were observed as a novel variant. Proteome analysis showed that in addition to the expected light chain variants produced by the malignant clone of plasma cells, also histones such as H2B and cathepsin B were contained. Uromodulin was not detectable in urinary casts of all patients. All eleven patients with lambda light chains showed predominant dimerized light chains in the urine immunoblot. Six patients with kappa light chains presented with predominantly monomeric forms of light chains in the immunoblot. The densitometric evaluated ratio of lambda dimers vs. monomers was significantly higher (2.12 ± 0.75) when compared with the ratio of kappa dimers vs. monomers (0.64 ± 0.47), p = 0.00001. Aggregates of light chains separated in part into denser sucrose fractions. Conclusion This work on urinary casts and light chains demonstrates that hyaline tubular casts represent a complex formation of protein-protein aggregate…
format: application/pdf
format: text/html
creator: Thomas Reiter
creator: Daniela Knafl
creator: Hermine Agis
creator: Karl Mechtler
creator: Ludwig Wagner
creator: Wolfgang Winnicki
subject: Internal Medicine
subject: Nephrology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.7819
publisher: PeerJ Inc.
rights: © 2019 Reiter et al.
abstract: Background Monoclonal overproduction of kappa and/or lambda light chains might result in renal light chain deposition disease. Light chain associated cast nephropathy and renal AL-amyloidosis represent two further pathologies going along with monoclonal gammopathy of renal significance and multiple myeloma. While cast nephropathy often manifests with acute kidney injury, AL-amyloidosis is rather accompanied with chronic kidney disease. Methods Urine samples were collected from 17 patients with multiple myeloma or monoclonal gammopathy. The urine sediment was stained for cast morphology by H/E and light chain immunofluorescence. Following micro-selection of casts under microscope, proteomic analysis of casts was performed by mass spectrometry. Sucrose gradient sedimentation was employed and light chain architecture examined by immunoblotting. Uromodulin was measured by ELISA in sucrose gradient fractions. Results Urinary casts were observed of about 30 µm in diameter by H/E staining and under immunofluorescence microscopy. Casts with a diameter of 20 µm were observed as a novel variant. Proteome analysis showed that in addition to the expected light chain variants produced by the malignant clone of plasma cells, also histones such as H2B and cathepsin B were contained. Uromodulin was not detectable in urinary casts of all patients. All eleven patients with lambda light chains showed predominant dimerized light chains in the urine immunoblot. Six patients with kappa light chains presented with predominantly monomeric forms of light chains in the immunoblot. The densitometric evaluated ratio of lambda dimers vs. monomers was significantly higher (2.12 ± 0.75) when compared with the ratio of kappa dimers vs. monomers (0.64 ± 0.47), p = 0.00001. Aggregates of light chains separated in part into denser sucrose fractions. Conclusion This work on urinary casts and light chains demonstrates that hyaline tubular casts represent a complex formation of protein-protein aggregate…
bibliographic citation: Reiter et al. (2019) Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders. PeerJ 7:e7819 https://doi.org/10.7717/peerj.7819
date submitted: 2019-07-03
date accepted: 2019-09-03
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reiter
  given name: Thomas
author list: Agent
  family name: Knafl
  given name: Daniela
author list: Agent
  family name: Agis
  given name: Hermine
author list: Agent
  family name: Mechtler
  given name: Karl
author list: Agent
  family name: Wagner
  given name: Ludwig
author list: Agent
  family name: Winnicki
  given name: Wolfgang
doi: 10.7717/peerj.7819
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Reiter et al.
attribution name: Reiter et al.

Clinical implications of aberrant neurovascular structures coursing through the submandibular gland
type: item
type: AcademicArticle
description: Background Variation within the submandibular triangle, including variant paths of facial neurovasculature, could increase risk of neurovascular derangement during submandibular gland (SMG) dysfunction, enlargement, interventions, or removal. Methods Frequency of anatomical variants enveloped within or piercing the SMG, including facial artery, vein, or branches of CN VII, were assessed in 70 cadaveric submandibular glands (39M/31F). Results Eighteen of 70 SMGs (25.7%) were pierced by at least one aberrant neurovasculature structure: Facial artery most frequently (n = 13), followed by facial vein (n = 2), inferior labial artery and vein (n = 1), and CN VII cervical branch (n = 1). This study demonstrated the high variability of neurovasculature within submandibular parenchyma. These aberrant neurovascular structures, especially facial artery, are in danger of compromise during surgical and other medical procedures on the SMG. To avoid potential neurovascular compromise, ultrasonographic or other imaging is recommended prior to procedures involving the SMG.
format: application/pdf
format: text/html
creator: Kelsey J. Eaton
creator: Heather F. Smith
subject: Anatomy and Physiology
subject: Dentistry
subject: Diabetes and Endocrinology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7823
publisher: PeerJ Inc.
rights: © 2019 Eaton and Smith
abstract: Background Variation within the submandibular triangle, including variant paths of facial neurovasculature, could increase risk of neurovascular derangement during submandibular gland (SMG) dysfunction, enlargement, interventions, or removal. Methods Frequency of anatomical variants enveloped within or piercing the SMG, including facial artery, vein, or branches of CN VII, were assessed in 70 cadaveric submandibular glands (39M/31F). Results Eighteen of 70 SMGs (25.7%) were pierced by at least one aberrant neurovasculature structure: Facial artery most frequently (n = 13), followed by facial vein (n = 2), inferior labial artery and vein (n = 1), and CN VII cervical branch (n = 1). This study demonstrated the high variability of neurovasculature within submandibular parenchyma. These aberrant neurovascular structures, especially facial artery, are in danger of compromise during surgical and other medical procedures on the SMG. To avoid potential neurovascular compromise, ultrasonographic or other imaging is recommended prior to procedures involving the SMG.
bibliographic citation: Eaton et al. (2019) Clinical implications of aberrant neurovascular structures coursing through the submandibular gland. PeerJ 7:e7823 https://doi.org/10.7717/peerj.7823
date submitted: 2019-07-23
date accepted: 2019-09-03
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eaton
  given name: Kelsey J.
author list: Agent
  family name: Smith
  given name: Heather F.
doi: 10.7717/peerj.7823
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Eaton and Smith
attribution name: Eaton and Smith

Cooperation in bottlenose dolphins: bidirectional coordination in a rope-pulling task
type: item
type: AcademicArticle
description: In comparison with terrestrial animals, such as primates, there is limited empirical evidence for cooperative behavior in marine mammals under experimental conditions. In this study, we used a cooperative rope-pulling task to investigate how bottlenose dolphins (Tursiops truncatus) coordinate their behavior with a partner. Dolphins successfully learned and were able to perform the task, even when one subject started after the other. In the no-delay condition (i.e., both subjects sent at the same time), one pair of dolphins showed coordinated behaviors. When pairs were successful in solving the task in the delay condition (i.e., one individual sent later than the other), the initiators (i.e., first individual sent) were likely to wait for the follower to arrive, and the follower was likely to swim faster when the initiator did not wait and started pulling the rope alone. These coordinated behaviors might help resolve the given cooperative task. Our results suggest that bottlenose dolphins learn to coordinate their behaviors via trial and error and recognize the necessity of performing simultaneous actions with a partner to successfully accomplish cooperative tasks. In addition, both partners showed behavioral changes over many trials of no-delay and delay conditions, suggesting that bidirectional coordination occurred in the cooperative task.
format: application/pdf
format: text/html
creator: Chisato Yamamoto
creator: Nobuyuki Kashiwagi
creator: Mika Otsuka
creator: Mai Sakai
creator: Masaki Tomonaga
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.7826
publisher: PeerJ Inc.
rights: © 2019 Yamamoto et al.
abstract: In comparison with terrestrial animals, such as primates, there is limited empirical evidence for cooperative behavior in marine mammals under experimental conditions. In this study, we used a cooperative rope-pulling task to investigate how bottlenose dolphins (Tursiops truncatus) coordinate their behavior with a partner. Dolphins successfully learned and were able to perform the task, even when one subject started after the other. In the no-delay condition (i.e., both subjects sent at the same time), one pair of dolphins showed coordinated behaviors. When pairs were successful in solving the task in the delay condition (i.e., one individual sent later than the other), the initiators (i.e., first individual sent) were likely to wait for the follower to arrive, and the follower was likely to swim faster when the initiator did not wait and started pulling the rope alone. These coordinated behaviors might help resolve the given cooperative task. Our results suggest that bottlenose dolphins learn to coordinate their behaviors via trial and error and recognize the necessity of performing simultaneous actions with a partner to successfully accomplish cooperative tasks. In addition, both partners showed behavioral changes over many trials of no-delay and delay conditions, suggesting that bidirectional coordination occurred in the cooperative task.
bibliographic citation: Yamamoto et al. (2019) Cooperation in bottlenose dolphins: bidirectional coordination in a rope-pulling task. PeerJ 7:e7826 https://doi.org/10.7717/peerj.7826
date submitted: 2019-04-09
date accepted: 2019-09-03
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamamoto
  given name: Chisato
author list: Agent
  family name: Kashiwagi
  given name: Nobuyuki
author list: Agent
  family name: Otsuka
  given name: Mika
author list: Agent
  family name: Sakai
  given name: Mai
author list: Agent
  family name: Tomonaga
  given name: Masaki
doi: 10.7717/peerj.7826
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Yamamoto et al.
attribution name: Yamamoto et al.

Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae
type: item
type: AcademicArticle
description: Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.
format: application/pdf
format: text/html
creator: Eugeny V. Gruzdev
creator: Vitaly V. Kadnikov
creator: Alexey V. Beletsky
creator: Andrey V. Mardanov
creator: Nikolai V. Ravin
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7830
publisher: PeerJ Inc.
rights: © 2019 Gruzdev et al.
abstract: Background Parasitic plants have the ability to obtain nutrients from their hosts and are less dependent on their own photosynthesis or completely lose this capacity. The reduction in plastid genome size and gene content in parasitic plants predominantly results from loss of photosynthetic genes. Plants from the family Orobanchaceae are used as models for studying plastid genome evolution in the transition from an autotrophic to parasitic lifestyle. Diphelypaea is a poorly studied genus of the Orobanchaceae, comprising two species of non-photosynthetic root holoparasites. In this study, we sequenced the plastid genome of Diphelypaea coccinea and compared it with other Orobanchaceae, to elucidate patterns of plastid genome evolution. In addition, we used plastid genome data to define the phylogenetic position of Diphelypaea spp. Methods The complete nucleotide sequence of the plastid genome of D. coccinea was obtained from total plant DNA, using pyrosequencing technology. Results The D. coccinea plastome is only 66,616 bp in length, and is highly rearranged; however, it retains a quadripartite structure. It contains only four rRNA genes, 25 tRNA genes and 25 protein-coding genes, being one of the most highly reduced plastomes among the parasitic Orobanchaceae. All genes related to photosynthesis, including the ATP synthase genes, had been lost, whereas most housekeeping genes remain intact. The plastome contains two divergent, but probably intact clpP genes. Intron loss had occurred in some protein-coding and tRNA genes. Phylogenetic analysis yielded a fully resolved tree for the Orobanchaceae, with Diphelypaea being a sister group to Orobanche sect. Orobanche.
bibliographic citation: Gruzdev et al. (2019) Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae. PeerJ 7:e7830 https://doi.org/10.7717/peerj.7830
date submitted: 2019-05-16
date accepted: 2019-09-04
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gruzdev
  given name: Eugeny V.
author list: Agent
  family name: Kadnikov
  given name: Vitaly V.
author list: Agent
  family name: Beletsky
  given name: Alexey V.
author list: Agent
  family name: Mardanov
  given name: Andrey V.
author list: Agent
  family name: Ravin
  given name: Nikolai V.
doi: 10.7717/peerj.7830
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Gruzdev et al.
attribution name: Gruzdev et al.

Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis
type: item
type: AcademicArticle
description: Background Runt-related transcription factor 1 (RUNX1) was previously reported to play a dual role in promoting or suppressing tumorigenesis in various malignancies. A public dataset from The Cancer Genome Atlas (TCGA) was used to evaluate the role of RUNX1 in clear cell renal cell carcinoma (ccRCC). Methods The Wilcoxon signed-rank test was used to compare the expression of RUNX1 in ccRCC tissues and normal tissues. The Wilcoxon signed-rank test and logistic regression were utilized to investigate the relationship between clinicopathological factors and RUNX1 expression. Additionally, we analysed the differences in prognosis between patients with high and low expression of RUNX1 via the Kaplan–Meier method and Cox regression. Gene set enrichment analysis (GSEA) was performed to explore the mechanisms of RUNX1 in ccRCC. Results The expression of RUNX1 in ccRCC tissues was significantly higher than that in normal tissues. High expression of RUNX1 was significantly associated with gender (p = 0.003), clinical stage (p < 0.001), tissue infiltration (p < 0.001), lymph node metastasis (p = 0.037) and histological grade (p < 0.001). Logistic regression analysis showed that high RUNX1 expression was significantly correlated with gender (OR = 1.71 for male vs. female, p = 0.004), histological grade (OR = 11.61 for grade IV vs. I, p < 0.001), clinical stage (OR = 1.55 for stage III/IV vs. I/II, p = 0.014) and tissue infiltration (OR = 1.54 for positive vs. negative, p = 0.018). Kaplan–Meier survival curves revealed that the prognosis of patients with ccRCC with high RUNX1 expression was worse than that of patients with ccRCC with low RUNX1 expression (p < 0.001). Univariate Cox regression analysis showed that high RUNX1 expression was strongly correlated with poor prognosis (HR = 1.60, 95% CI [1.31–1.97], p < 0.001). In addition, high expression of RUNX1 was an independent prognostic factor for poor overall survival (OS), with an HR of 1.50 (95% CI [1.20–1.87], p < 0.001) in…
format: application/pdf
format: text/html
creator: Yang Fu
creator: Shanshan Sun
creator: Xiaojun Man
creator: Chuize Kong
subject: Bioinformatics
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.7854
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Background Runt-related transcription factor 1 (RUNX1) was previously reported to play a dual role in promoting or suppressing tumorigenesis in various malignancies. A public dataset from The Cancer Genome Atlas (TCGA) was used to evaluate the role of RUNX1 in clear cell renal cell carcinoma (ccRCC). Methods The Wilcoxon signed-rank test was used to compare the expression of RUNX1 in ccRCC tissues and normal tissues. The Wilcoxon signed-rank test and logistic regression were utilized to investigate the relationship between clinicopathological factors and RUNX1 expression. Additionally, we analysed the differences in prognosis between patients with high and low expression of RUNX1 via the Kaplan–Meier method and Cox regression. Gene set enrichment analysis (GSEA) was performed to explore the mechanisms of RUNX1 in ccRCC. Results The expression of RUNX1 in ccRCC tissues was significantly higher than that in normal tissues. High expression of RUNX1 was significantly associated with gender (p = 0.003), clinical stage (p < 0.001), tissue infiltration (p < 0.001), lymph node metastasis (p = 0.037) and histological grade (p < 0.001). Logistic regression analysis showed that high RUNX1 expression was significantly correlated with gender (OR = 1.71 for male vs. female, p = 0.004), histological grade (OR = 11.61 for grade IV vs. I, p < 0.001), clinical stage (OR = 1.55 for stage III/IV vs. I/II, p = 0.014) and tissue infiltration (OR = 1.54 for positive vs. negative, p = 0.018). Kaplan–Meier survival curves revealed that the prognosis of patients with ccRCC with high RUNX1 expression was worse than that of patients with ccRCC with low RUNX1 expression (p < 0.001). Univariate Cox regression analysis showed that high RUNX1 expression was strongly correlated with poor prognosis (HR = 1.60, 95% CI [1.31–1.97], p < 0.001). In addition, high expression of RUNX1 was an independent prognostic factor for poor overall survival (OS), with an HR of 1.50 (95% CI [1.20–1.87], p < 0.001) in…
bibliographic citation: Fu et al. (2019) Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis. PeerJ 7:e7854 https://doi.org/10.7717/peerj.7854
date submitted: 2019-07-02
date accepted: 2019-09-08
issued: 2019-10-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Yang
author list: Agent
  family name: Sun
  given name: Shanshan
author list: Agent
  family name: Man
  given name: Xiaojun
author list: Agent
  family name: Kong
  given name: Chuize
doi: 10.7717/peerj.7854
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-02
copyright: ©2019 Fu et al.
attribution name: Fu et al.

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