title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1276 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Nomogram for predicting cancer specific survival in inflammatory breast carcinoma: a SEER population-based study link: https://peerj.com/articles/7659 last-modified: 2019-09-16 description: The clinicopathological features of inflammatory breast carcinoma (IBC), the effect of therapeutic options on survival outcome and the identification of prognostic factors were investigated in this study. Information on IBC patients were extracted from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015. Cox proportional hazard regression was used to determine potential significant prognostic factors of IBC. A nomogram was then constructed to evaluate patient survival based on certain variables. Univariate and multivariate analyses revealed that race (p < 0.001), M stage (p < 0.001), surgery (p = 0.010), chemotherapy (CT) (p < 0.001), tumor size (p = 0.010), estrogen receptor (p < 0.001), progesterone receptor (p = 0.04), and human epidermal growth factor receptor 2 (p < 0.001) were all independent risk factors. The concordance index (C-index) of the nomogram was 0.735, which showed good predictive efficiency. Survival analysis indicated that IBC patients without CT had poorer survival than those with CT (p < 0.001). Stratified analyses showed that modified radical mastectomy (MRM) had significant survival advantages over non-MRM in patients with stage IV IBC (p = 0.031). Patients treated with or without CT stratified by stage III and stage IV showed better survival than those without stage III and IV (p < 0.001). Trimodality therapy resulted in better survival than surgery combined with CT or CT alone (p < 0.001). Competing risk analysis also showed the same results. The nomogram was effectively applied to predict the 1, 3 and 5-year survival of IBC. Our nomogram showed relatively good accuracy with a C-index of 0.735 and is a visualized individually predictive tool for prognosis. Treatment strategy greatly affected the survival of patients. Trimodality therapy was the preferable therapeutic strategy for IBC. Further prospective studies are needed to validate these findings. creator: Haige Zhang creator: Guifen Ma creator: Shisuo Du creator: Jing Sun creator: Qian Zhang creator: Baoying Yuan creator: Xiaoyong Luo uri: https://doi.org/10.7717/peerj.7659 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Land use management based on multi-scenario allocation and trade-offs of ecosystem services in Wafangdian County, Liaoning Province, China link: https://peerj.com/articles/7673 last-modified: 2019-09-16 description: Developing effective methods to coordinate the trade-offs among ecosystem services (ES) is important for achieving inclusive growth and sustainable development, and has been the focus of scholars and ecosystem managers globally. Using remote sensing and geographic information system (GIS) data, our study examined Wafangdian County of Liaoning Province as a case study to reveal the spatiotemporal evolution of four ES (food supply [FS], net primary productivity [NPP], water yield [WY], and soil conservation [SC]) and changes among their interactions. Then, an ordered weighted averaging model was introduced to simulate the optimal scenario of ES allocation. Results showed that: (1) the spatial and temporal changes in ES were significant over 14 years. All ES presented an inverted U-shaped growth curve from 2000–2014. (2) Synergies were observed within provisioning services, and there were trade-offs between provisioning services and regulating services, as well as provisioning services and supporting services. (3) The optimal scenario for Wafangdian was scenario 5 (trade-off coefficient, 0.68). The allocation of FS, NPP, WY, and SC in scenario 5 were 0.187, 0.427, 0.131, and 0.063, respectively. Implementing each ES weight of optimal scenario in land use management contributed to achieving intercoordination of ES. We propose to coordinate land and sea management to restore natural habitats that were expanded into in the high ES area. It is our anticipation that this study could provide a scientific basis for optimizing the allocation of ES and improving land use structure of coastal zones in the future. creator: Wenzhen Zhao creator: Zenglin Han creator: Xiaolu Yan creator: Jingqiu Zhong uri: https://doi.org/10.7717/peerj.7673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhao et al. title: Why the long face? Comparative shape analysis of miniature, pony, and other horse skulls reveals changes in ontogenetic growth link: https://peerj.com/articles/7678 last-modified: 2019-09-16 description: BackgroundMuch of the shape variation found in animals is based on allometry and heterochrony. Horses represent an excellent model to investigate patterns of size-shape variation among breeds that were intentionally bred for extreme small and large sizes.MethodsWe tested whether ponies (wither height < 148 cm) have a diverging size-shape relationship in skull shape as compared to regular-sized horse breeds (wither height > 148 cm, here-after called horses) during ontogenetic growth. We used a dataset of 194 specimens from 25 horse and 13 pony breeds, two of which are miniature breeds (wither height < 96.5 cm)—Falabella, Shetland. We applied three-dimensional geometric morphometrics, linear measurements, and multivariate analyses (Procrustes ANOVAs) to quantitatively examine and compare the ontogenetic trajectories between pony and horse breeds with an emphasis on the miniature breeds as an extreme case of artificial selection on size. Additionally, we tested for juvenile characteristics in adult horse and miniature breeds that could resemble “paedomorphosis”—retention of juvenile characteristics in adult stage; e.g. large eyes, large braincase-to-face-relationship, and large head-to-body relationship.ResultsAllometric regression of size on shape revealed that 42% of shape variation could be explained by variation in size in all breeds. The ontogenetic trajectories of ponies and horses vary in slope and therefore in rate of change per unit size, and length. The differences in trajectory lengths and slopes result in ponies having a similar skull shape in an older age stage than horses of the same size in a younger age stage. This pattern could cause the generally perceived “paedomorphic” appearance of ponies. Miniature breeds have larger heads in relation to wither height compared to horses, a non-paedomorphic feature in horses specifically. Also, rostra (faces) are longer in adult individuals than in juveniles across all kinds of breeds. This pattern can be explained by the long-face hypothesis for grazing ungulates and could possibly be caused by the mismatch of selection by humans for shorter rostra and the dentition of ruminants.ConclusionsMiniature breed specimens do not exhibit any of the classical mammalian “paedomorphic” features (large orbits, large heads), except for the adult Falabella that has enlarged orbits, possibly because they are herbivorous ungulates that are affected by functional and metabolic constraints related to low nutrient-food consumption. Instead ponies, including miniature breeds, have faster and shorter ontogenetic growth compared to horses, resulting in adult pony skulls looking in part like juvenile horse skulls. creator: Laura Heck creator: Marcelo R. Sanchez-Villagra creator: Madlen Stange uri: https://doi.org/10.7717/peerj.7678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Heck et al. title: Effects of Lecanicillium lecanii strain JMC-01 on the physiology, biochemistry, and mortality of Bemisia tabaci Q-biotype nymphs link: https://peerj.com/articles/7690 last-modified: 2019-09-16 description: BackgroundLecanicillium lecanii is an entomopathogenic fungi, which was isolated from insects suffering from disease. Now, it is an effective bio-control resource that can control agricultural pests such as whitefly and aphids. There are many studies on the control of various agricultural pests by L. lecanii, but no report on its control of Bemisia tabaci biotype-Q exists. In this work, we studied the susceptibility of B. tabaci Q-biotype (from Ningxia, China) to L. lecanii JMC-01 in terms of nymph mortality and the changes in detoxifying protective enzymes activities.MethodsB. tabaci nymphs were exposed to L. lecanii JMC-01 conidia by immersion with the host culture. Mortality was assessed daily for all nymph stages. The detoxifying and protective enzyme activity changes, weight changes, and fat, and water contents of the nymphs were determined spectrophotometrically.ResultsAll instars of B. tabaci died after being infested with 1 × 108 conidia/mL. The 2nd-instar nymphs were the most susceptible, followed by the 3rd-instar nymphs. The corrected cumulative mortality of the 2nd- and 3rd-instar nymphs was 82.22% and 75.55%, respectively. The levels of detoxifying and protective enzymes initially increased and then decreased. The highest activities of carboxylesterase, acetylcholinesterase, peroxidase, and catalase occurred on the 3rd day, reaching 10.5, 0.32, 20, and 6.3 U/mg prot, respectively. These levels were 2.2-, 4.3-, 2.4-, and 1.4-fold the control levels, respectively. The highest activities of glutathione-S transferase and superoxide dismutase on the 2nd day were, respectively, 64 and 43.5 U/mg prot. These levels were, respectively, 2.7 and 1.1-fold that of the control level. The water and fat content in the infected B. tabaci nymphs decreased and differed significantly from the control levels. The weight increased continuously in the first 24 h, decreasing thereafter. At 72 h, the infestation level was about 0.78-fold that of the control level.ConclusionsThe studied L. lecanii JMC-01 strain is pathogenic to the B. tabaci Q-biotype. This strain interferes with the normal functioning of detoxifying and protective enzymes, and is also involved in the disruption of normal physiological metabolism in B. tabaci. creator: Ting Xie creator: Ling Jiang creator: Jianshe Li creator: Bo Hong creator: Xinpu Wang creator: Yanxia Jia uri: https://doi.org/10.7717/peerj.7690 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xie et al. title: The mineralization characteristics of organic carbon and particle composition analysis in reconstructed soil with different proportions of soft rock and sand link: https://peerj.com/articles/7707 last-modified: 2019-09-16 description: The organic carbon mineralization process reflects the release intensity of soil CO2. Therefore, the study of organic carbon mineralization and particle composition analysis of soft rock and sand compound soil can provide technical support and a theoretical basis for soil organic reconstruction (soil structure, materials and biological nutrition). Based on previous research, four treatments were selected: CK (soft rock:sand=0:1), C1 (soft rock:sand=1:5), C2 (soft rock:sand=1:2) and C3 (soft rock:sand=1:1), respectively. Specifically, we analyzed the organic carbon mineralization process and soil particle composition by lye absorption, laser granulometer, and scanning electron microscope. The results showed that there was no significant difference in organic carbon content between C1, C2 , and C3 treatments, but they were significantly higher than in the CK treatment (P < 0.05). The organic carbon mineralization rate in each treatment accords with a logarithmic function throughout the incubation period (P < 0.01), which can be divided into a rapid decline phase in days 1 to 11 followed by a steady decline phase in days 11 to 30. The cumulative mineralization on the 11th day reached 54.96%–74.44% of the total mineralization amount. At the end of the incubation, the cumulative mineralization and potential mineralizable organic carbon content of the C1, C2 and C3 treatments were significantly higher than those of the CK treatment. The cumulative mineralization rate was also the lowest in the C1 and C2 treatment. The turnover rate constant of soil organic carbon in each treatment was significantly lower than that of the CK treatment, and the residence time increased. With the increase of volume fraction of soft rock, the content of silt and clay particles increased gradually, the texture of soil changed from sandy soil to sandy loam, loam , and silty loam, respectively. With the increase of small particles, the structure of soil appear ed to collapse when the volume ratio of soft rock was 50%. A comprehensive mineralization index and scanning electron microscopy analysis, when the ratio of soft rock to sand volume was 1:5–1:2, this can effectively increase the accumulation of soil organic carbon. Then, the distribution of soil particles was more uniform, the soil structure was stable (not collapsed), and the mineralization level of unit organic carbon was lower. Our research results have practical significance for the large area popularization of soft rock and sand compound technology. creator: Zhen Guo creator: Jichang Han creator: Yan Xu creator: Yangjie Lu creator: Chendi Shi creator: Lei Ge creator: Tingting Cao creator: Juan Li uri: https://doi.org/10.7717/peerj.7707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guo et al. title: AURKB: a promising biomarker in clear cell renal cell carcinoma link: https://peerj.com/articles/7718 last-modified: 2019-09-16 description: BackgroundAurora kinase B (AURKB) is an important carcinogenic factor in various tumors, while its role in clear cell renal cell carcinoma (ccRCC) still remains unclear. This study aimed to investigate its prognostic value and mechanism of action in ccRCC.MethodsGene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. R software was utilized to analyze the expression and prognostic role of AURKB in ccRCC. Gene set enrichment analysis (GSEA) was used to analyze AURKB related signaling pathways in ccRCC.ResultsAURKB was expressed at higher levels in ccRCC tissues than normal kidney tissues. Increased AURKB expression in ccRCC correlated with high histological grade, pathological stage, T stage, N stage and distant metastasis (M stage). Kaplan-Meier survival analysis suggested that high AURKB expression patients had a worse prognosis than patients with low AURKB expression levels. Multivariate Cox analysis showed that AURKB expression is a prognostic factor of ccRCC. GSEA indicated that genes involved in autoimmune thyroid disease, intestinal immune network for IgA production, antigen processing and presentation, cytokine-cytokine receptor interaction, asthma, etc., were differentially enriched in the AURKB high expression phenotype.ConclusionsAURKB is a promising biomarker for predicting prognosis of ccRCC patients and a potential therapeutic target. In addition, AURKB might regulate progression of ccRCC through modulating intestinal immune network for IgA production and cytokine-cytokine receptor interaction, etc. signaling pathways. However, more research is necessary to validate the findings. creator: Bangbei Wan creator: Yuan Huang creator: Bo Liu creator: Likui Lu creator: Cai Lv uri: https://doi.org/10.7717/peerj.7718 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wan et al. title: Prediction model for patients with acute respiratory distress syndrome: use of a genetic algorithm to develop a neural network model link: https://peerj.com/articles/7719 last-modified: 2019-09-16 description: BackgroundAcute respiratory distress syndrome (ARDS) is associated with significantly increased risk of death, and early risk stratification may help to choose the appropriate treatment. The study aimed to develop a neural network model by using a genetic algorithm (GA) for the prediction of mortality in patients with ARDS.MethodsThis was a secondary analysis of two multicenter randomized controlled trials conducted in forty-four hospitals that are members of the National Heart, Lung, and Blood Institute, founded to create an acute respiratory distress syndrome Clinical Trials Network. Model training and validation were performed using the SAILS and OMEGA studies, respectively. A GA was employed to screen variables in order to predict 90-day mortality, and a neural network model was trained for the prediction. This machine learning model was compared to the logistic regression model and APACHE III score in the validation cohort.ResultsA total number of 1,071 ARDS patients were included for analysis. The GA search identified seven important variables, which were age, AIDS, leukemia, metastatic tumor, hepatic failure, lowest albumin, and FiO2. A representative neural network model was constructed using the forward selection procedure. The area under the curve (AUC) of the neural network model evaluated with the validation cohort was 0.821 (95% CI [0.753–0.888]), which was greater than the APACHE III score (0.665; 95% CI [0.590–0.739]; p = 0.002 by Delong’s test) and logistic regression model, albeit not statistically significant (0.743; 95% CI [0.669–0.817], p = 0.130 by Delong’s test).ConclusionsThe study developed a neural network model using a GA, which outperformed conventional scoring systems for the prediction of mortality in ARDS patients. creator: Zhongheng Zhang uri: https://doi.org/10.7717/peerj.7719 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang title: CeRNA network analysis and functional enrichment of salt sensitivity of blood pressure by weighted-gene co-expression analysis link: https://peerj.com/articles/7534 last-modified: 2019-09-13 description: BackgroundSalt sensitivity of blood pressure (SSBP) is an independent risk factor for cardiovascular disease. The pathogenic mechanisms of SSBP are still uncertain. This study aimed to construct the co-regulatory network of SSBP and data mining strategy based on the competitive endogenous RNA (ceRNA) theory.MethodsLncRNA and mRNA microarray was performed to screen for candidate RNAs. Four criteria were used to select the potential differently expressed RNAs. The weighted correlation network analysis (WGCNA) package of R software and target miRNA and mRNA prediction online databases were used to construct the ceRNA co-regulatory network and discover the pathways related to SSBP. Gene ontology enrichment, gene set enrichment analysis (GSEA) and KEGG pathway analysis were performed to explore the functions of hub genes in networks.ResultsThere were 274 lncRNAs and 36 mRNAs that differently expressed between salt-sensitive and salt-resistant groups (P < 0.05). Using WGCNA analysis, two modules were identified (blue and turquoise). The blue module had a positive relationship with salt-sensitivity (R = 0.7, P < 0.01), high-density lipoprotein (HDL) (R = 0.53, P = 0.02), and total cholesterol (TC) (R = 0.55, P = 0.01). The turquoise module was positively related with triglyceride (TG) (R = 0.8, P < 0.01) and low-density lipoprotein (LDL) (R = 0.54, P = 0.01). Furthermore, 84 ceRNA loops were identified and one loop may be of great importance for involving in pathogenesis of SSBP. KEGG analysis showed that differently expressed mRNAs were mostly enriched in the SSBP-related pathways. However, the enrichment results of GSEA were mainly focused on basic physical metabolic processes.ConclusionThe microarray data mining process based on WGCNA co-expression analysis had identified 84 ceRNA loops that closely related with known SSBP pathogenesis. The results of our study provide implications for further understanding of the pathogenesis of SSBP and facilitate the precise diagnosis and therapeutics. creator: Han Cao creator: Han Qi creator: Zheng Liu creator: Wen-Juan Peng creator: Chun-Yue Guo creator: Yan-Yan Sun creator: Christine Pao creator: Yu-Tao Xiang creator: Ling Zhang uri: https://doi.org/10.7717/peerj.7534 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cao et al. title: Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies link: https://peerj.com/articles/7543 last-modified: 2019-09-13 description: Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation. creator: Bruna Trevisan creator: Daniel M.C. Alcantara creator: Denis Jacob Machado creator: Fernando P.L. Marques creator: Daniel J.G. Lahr uri: https://doi.org/10.7717/peerj.7543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Trevisan et al. title: Biochar application significantly affects the N pool and microbial community structure in purple and paddy soils link: https://peerj.com/articles/7576 last-modified: 2019-09-13 description: BackgroundThe increasing demand for food production has resulted in the use of large quantities of chemical fertilizers. This has created major environmental problems, such as increased ammonia volatilization, N2O emission, and nitrogen (N) leaching from agricultural soil. In particular, the utilization rate of N fertilizer is low in subtropical southern parts of China due to high rainfall. This causes not only large financial losses in agriculture, but also serious environmental pollution.MethodsIn this study, 16S rDNA-based analysis and static-chamber gas chromatography were used to elucidate the effects of continuous straw biochar application on the N pool and bacteria environment in two typical soil types, purple and paddy soils, in southern China.ResultsStraw biochar application (1) improved the soil N pool in both rhizosphere and non-rhizosphere soils; (2) significantly reduced the emission of N2O, with no difference in emission between 1 and 2 years of application; (3) increased the abundance of N-processing bacteria in the soil and altered the bacterial community structure; and (4) improved the tobacco yield and N use efficiency in paddy soil. These findings suggest that, in southern China, the application of straw biochar can promote N transformation in purple and paddy soils and reduce the emission of the greenhouse gas N2O. creator: Shen Yan creator: Zhengyang Niu creator: Haitao Yan creator: Fei Yun creator: Guixin Peng creator: Yongfeng Yang creator: Guoshun Liu uri: https://doi.org/10.7717/peerj.7576 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al.