Dataset associated with “Bare Patches Created by Plateau Pikas Contribute to Warming Permafrost on the Tibet Plateau” submitted to GRL (2024)

This dataset is associated with Bare Patches Created by Plateau Pikas Contribute to Warming Permafrost on the Tibet Plateau submitted to GRL (2024), including (i) maps illustrating the difference in soil temperature (ST) between scenarios with and without pika disturbance; (ii) maps illustrating the difference in soil water content (SWC); (iii) a surface entrance density map of plateau pikas and (iv) a map depicting the fraction of bare patches induced by plateau pikas. All data are provided as GeoTIFF (.tif) files in a geographic coordinate system of WGS_1984.1. “ST_difference_soilayer[n]_[2.5cm, 66cm, 184cm, 370cm]_2015_2018_[June, July, August, September].tif” is the difference in soil temperature (°C) of the n-th layer at a certain depth with and without pika disturbance averaged from 2015-2018 in June, July, August and September, respectively. These values are derived from simulations by implementing scenarios with and without pika disturbance using the Noah-MP model.2. “SWC_difference_soilayer[n]_[2.5cm, 66cm, 184cm, 370cm]_2015_2018_[June, July, August, September].tif” is the difference in soil water content (m3/m3) of n-th layer at a certain depth with and without pika disturbance averaged from 2015-2018 in June, July, August and September, respectively. These values are derived from simulations by implementing scenarios with and without pika disturbance using the Noah-MP model.3. “pika_surface_entrance_density_1km.tif” is the surface entrance density map of plateau pikas, simulated using a stochastic model based on the habitat suitability of plateau pikas.4. “pika_induced_bare_patch_fraction_10km.tif” is the pika-induced bare patch fraction, estimated using an empirical model fitted from Unmanned Aerial Vehicle data.</p

GBM-BioDP overall architecture.

<p>The diagram represents a runtime view of the architecture of GBM-BioDP. The lower tier represents the sources of experimental and meta data, and external tools that are invoked to visualize the data. The middle tier represents how the data are processed, stored, and made available to the user. The right hand side of the middle tier represents the visualization “services” that are available at runtime to the user. These services are made available as web-services and are hosted on an Apache server. The higher tier represents the user interface, and is organized in a tabbed interface.</p

miRNAs module use case – mir-34a profile by survivorship stratification.

<p>We compare the expression levels of mir-34a in samples stratified by length of survival. Panels A–D shows comparison of 1–3 Quartiles (short survivors) versus 4th Quartile (long survivors). Panels E–H shows comparison of 1st Quartile (short survivors) versus 4th Quartile (long survivors). A, E show the histogram of expression distribution for all GBM patients. B, F show the p-values of the t-tests comparing expression of mir-34a in short and long survivors. C, G show the boxplots of expression for short and long survivors, and D, H show barplots of expressions mean-centered around the mean of the two groups. In both stratifications, long survivors (4th Quartile patients) express significantly lower levels of mir-34a compared to short survivors (p-val 0.041 when compared to 1–3 Quartile patients, and p-val 0.033 when compared to 1st Quartile patients).</p

Use case from miRNAs module – miRNA targets.

<p>Correlation of mir-34a predicted targets, and p53. Color red represent positive correlation, whereas blue color represent negative correlation. The cells are annotated with the correlation values. p53 and mir-34a expression are anti-correlated, which indicates a possible suppressor role of mir-34a.</p

Hypothesis generation – Molecular classification of GBM clinical data.

<p>A. Model depicting parallels between tumor subtypes and stages in neurogenesis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Phillips1" target="_blank">[28]</a>. B. Main features of tumor subtypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Verhaak1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Phillips1" target="_blank">[28]</a>. C. Random forest model “out of bag” error rates for training data using 201 samples from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Verhaak1" target="_blank">[6]</a> and the corresponding 768 gene expression measurements common between the training and validated data. D. Summary of error rates for the predicted subtypes of validated data. Abbreviations RF: random forest, C: classical, M: mesenchymal, N: neural, P: proneural.</p

RhNRG-1β Protects the Myocardium against Irradiation-Induced Damage via the ErbB2-ERK-SIRT1 Signaling Pathway

<div><p>Radiation-induced heart disease (RIHD), which is a serious side effect of the radiotherapy applied for various tumors due to the inevitable irradiation of the heart, cannot be treated effectively using current clinical therapies. Here, we demonstrated that rhNRG-1β, an epidermal growth factor (EGF)-like protein, protects myocardium tissue against irradiation-induced damage and preserves cardiac function. rhNRG-1β effectively ameliorated irradiation-induced myocardial nuclear damage in both cultured adult rat-derived cardiomyocytes and rat myocardium tissue via NRG/ErbB2 signaling. By activating ErbB2, rhNRG-1β maintained mitochondrial integrity, ATP production, respiratory chain function and the Krebs cycle status in irradiated cardiomyocytes. Moreover, the protection of irradiated cardiomyocytes and myocardium tissue by rhNRG-1β was at least partly mediated by the activation of the ErbB2-ERK-SIRT1 signaling pathway. Long-term observations further showed that rhNRG-1β administered in the peri-irradiation period exerts continuous protective effects on cardiac pump function, the myocardial energy metabolism, cardiomyocyte volume and interstitial fibrosis in the rats receiving radiation via NRG/ErbB2 signaling. Our findings indicate that rhNRG-1β can protect the myocardium against irradiation-induced damage and preserve cardiac function via the ErbB2-ERK-SIRT1 signaling pathway.</p></div

rhNRG-1β preserves mitochondrial function in irradiated cardiomyocyte via ERKs-SIRT1 pathway.

<p>(A-B) Western blots of SIRT1 in the adult rat cardiomyocyte cultures (A) and rat myocardial tissue (B). (C) Western analyses of the phosphorylation of ERK1/2, P38 and JNK in the adult rat cardiomyocyte cultures. (D) Western analyses of the phosphorylation of ERK1/2 in the rat myocardial tissue. β-actin expression was analyzed as an internal control. Abbreviation: F+NRG, FR180204 plus recombinant human neuregulin; H+NRG, Herceptin plus recombinant human neuregulin; M+NRG, Mubritinib plus recombinant human neuregulin; NRG, recombinant human neuregulin; ns, nonsignificant.</p

rhNRG-1β rescues radiation-induced myocardium injury via ErbB2 signaling.

<p>(A)&(C) Immunofluorescence images showing γH2AX (red) in the nuclei (blue) of cultured adult rat cardiomyocytes (A) and rat myocardial tissue (C). (B)&(D) Western blotting analyses of γH2AX levels in the adult rat cardiomyocyte cultures (B) and rat myocardial tissue (D). β-actin expression was analyzed as an internal control. For (B) and (D), data are expressed as mean ± SEM; statistical significance is determined by one-way ANOVA and the following Bonferroni’s multiple comparisons; bdi, below detectable limit; ***, P<0.001; n = 5 per group. Scale bar: (A) = 25 μm; (C) = 100 μm. Abbreviation: ANOVA, analysis of variance; bdi, below detectable limit; DAPI, 4′,6′-diamidino-2-phenylindole; ErbB2, human epidermal growth factor receptor-2; H+NRG, Herceptin plus recombinant human neuregulin; M+NRG, Mubritinib plus recombinant human neuregulin; NRG, recombinant human neuregulin; SEM, standard error of mean.</p

rhNRG-1β exerts long-term protective effects on the function of irradiated myocardium.

<p>(A) Representative M-mode images of left ventricles of the irradiated rats at Weeks 10 and 20 post-irradiation. (B) Quantitative analysis of LVFS of the irradiated rats at Week 1 pre-irradiation and Weeks 1, 5, 10, 15 and 20 post-irradiation. (C) Quantitative analysis of the relative ATP level in myocardial tissue of the irradiated rats at Week 1 pre-irradiation and Weeks 1, 5, 10, 15 and 20 post-irradiation. For (B) and (C), data are expressed as mean ± SEM; statistical significance is determined by two-way ANOVA and the following Bonferroni’s multiple comparisons; ns, nonsignificant; *, P<0.05; #, P<0.001; n = 4 per group per time point. Abbreviation: ANOVA, analysis of variance; ATP, adenosine triphosphate; H+NRG, Herceptin plus recombinant human neuregulin; LVFS, left ventricular fractional shortening; M+NRG, Mubritinib plus recombinant human neuregulin; NRG, recombinant human neuregulin; ns, nonsignificant; SEM, standard error of the mean.</p

Example of a workflow initiated from the Arrays module.

<p>The Arrays workflow typically starts with 1) inspection of available arrays and selection of a study of interest, 2) viewing of experimental conditions and selection of a p-value threshold for significance of gene expression differentiation, and 3) study of expressions heatmap. Comparison of several arrays can also be initiated from the overview page.</p