Examining the influence of picture format on children’s naming responses
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.
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
Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection
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 the nuclear pore complex protein 93 (Nup93, E2RSV7), which is associated with nuclear–cytoplasmic transport. In addition, Western blot experiments confirmed that the expression of Nup93 was significantly downregulated in lycorine treatment but induced after viral infection. Our results may provide new insights into how lycorine may trap vRNPs in the nucleus and suggest new potential therapeutic targets for influenza virus.
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
Variation of 13C and 15N enrichments in different plant components of labeled winter wheat (Triticum aestivum L.)
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.
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
Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture
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/.
Environmental Contamination and Remediation
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
Trans-oral robotic surgery versus coblation tongue base reduction for obstructive sleep apnea syndrome
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.
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
Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders
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 aggregates with histones and cathepsin B identified as novel cast components. Apart from the proteomic composition of the casts, also the formation of the light chains and aggregates is of relevance. Dimerized light chains, which are typical for lambda paraproteins, might be less dialyzable than monomeric forms and may therefore identify patients less responsive to high cut-off dialysis.
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
Clinical implications of aberrant neurovascular structures coursing through the submandibular gland
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.
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
Cooperation in bottlenose dolphins: bidirectional coordination in a rope-pulling task
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.
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
Extensive plastome reduction and loss of photosynthesis genes in Diphelypaea coccinea, a holoparasitic plant of the family Orobanchaceae
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.
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
Increased expression of RUNX1 in clear cell renal cell carcinoma predicts poor prognosis
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 multivariate Cox analysis. GSEA showed that the apoptosis, B cell receptor signalling pathway, calcium signalling pathway, chemokine signalling pathway, JAK/STAT signalling pathway, MAPK signalling pathway, p53 signalling pathway, pathways in cancer, T cell receptor signalling pathway, Toll-like receptor signalling pathway, VEGF signalling pathway, and Wnt signalling pathway were significantly enriched in the RUNX1 high-expression phenotype. In conclusion, RUNX1 can be used as a novel prognostic factor and therapeutic target in ccRCC.
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