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36 results for “SOM”
Рис. 3. Гусеница коΛьчатого шеΛкопря- Δа, пораженная вирусом яΔерного поΛиэΔроза. УПН, 2019 г. (фото автора) Fig. 3. Caterpillar of the Lackey moth, killed by the nuclear polyhedrosis virus. SOM, 2019 (photo by author) in Lackey Moth (Malacosoma Neustria L., Lasiocampidae, Lepidoptera) Population During The Eruptive Phase
Рис. 3. Гусеница коΛьчатого шеΛкопря- Δа, пораженная вирусом яΔерного поΛиэΔроза. УПН, 2019 г. (фото автора) Fig. 3. Caterpillar of the Lackey moth, killed by the nuclear polyhedrosis virus. SOM, 2019 (photo by author)
High frequency soil sensor data for SOM input - Complex drivers of riparian soil oxygen variability revealed using self-organizing maps
The provided datasets contain the original (non-normalized) high-frequency soil and meteorological observations that were fed to the Self-Organizing Map (SOM) in order to identify ranges of values associated with low and high soil O2 conditions. For the Champlain Valley (CV) site we used the natural breaks algorithm to subset the data into high and low O2 datasets. O2 values were consistently low at the Green Mountains (GM) site, so we ran a single SOM for all O2 values at this site. The original values were then range-normalized before they were fed to the SOM.
SOM density fractions beneath trees of different mycorrhizal types in New England forests
Recent work suggests mycorrhizal fungi are important drivers of soil organic matter dynamics; however, whether this is a result of the fungi themselves or related traits of their host trees remains unclear. We evaluated how tree mycorrhizal associations and foliar chemistry influence mineral-associated organic matter (MAOM) and particulate organic matter (POM) in temperate forests of northern New England, USA. We measured carbon (C) and nitrogen (N) concentrations and C:N of three soil density fractions beneath six tree species that vary in both mycorrhizal association and foliar chemistry. We found a significant decline in the concentration of MAOM C and N with increasing foliar C:N in soil beneath tree species with arbuscular mycorrhizal (AM), but not ectomycorrhizal (ECM) fungi. The C:N of POM and MAOM was positively associated with the foliar C:N of the dominant tree species in a forest, and MAOM C:N was also higher beneath ECM- rather than AM-associated tree species. These results add to the growing body of support for mycorrhizal fungi as predictors of soil C and N dynamics, and suggest that C concentration in the MAOM fraction is more sensitive to organic matter chemistry beneath AM-associated tree species. Because MAOM decomposition is thought to be less responsive than POM decomposition to changes in soil temperature and moisture, differences in the tendency of AM- vs. ECM-dominated forests to support MAOM formation and persistence may lead to systematic differences in the response of these forest types to ongoing climate change. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.
Tropical North Atlantic phases: A Self-Organizing Maps (SOM) approach.
<p>Data from SOM analysis</p>
PSF-SOM full results
<p>This archive contains full results generated with PSF-SOM algorithm.</p> <p>Analysis was performed using oposSOM R package (see main article for details).</p> <p>The most convenient way to browse the results is starting from <em><strong>"Summary.html"</strong></em> file from <strong><em>"Autoimmunity_PSF-SOM"</em></strong> folder. </p> <p><strong><em>"Autoimmunity_PSF-SOM.RData"</em></strong> file contains all variables produced during the analysis. </p> <p> </p>
Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets
<p>This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes". </p> <p>The archive contains three folders:</p> <p>1. "Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data. </p> <p>2. "IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets.</p> <p>3. "BC" - folder contains data, scripts, and results of analysis of breast cancer datasets.</p>
CESM1-SOM Climatologies used for "Climate Sensitivity is Sensitive to Changes in Ocean Heat Transport" (published in Journal of Climate, Mar 2022)
<p>CESM1-SOM climatologies.</p> <p>Pre-industrial control run = SOM_Control.cam5.0030-0059.ann.nc</p> <p>CO2-doubling experiments:</p> <ul> <li>OHT + 30% = SOM_OHFC_P30_2XCO2_032019.cam5.0030-0059.ann.nc</li> <li>OHT + 15% = SOM_OHFC_P15_2XCO2_032019.cam5.0030-0059.ann.nc</li> <li>Control OHT = SOM_2XCO2_032019.cam5.0030-0059.ann.nc</li> <li>OHT - 15% = SOM_OHFC_M15_2XCO2_032019.cam5.0030-0059.ann.nc</li> <li>OHT - 30% = SOM_OHFC_M30_2XCO2_032019.cam5.0030-0059.ann.nc</li> </ul>
Soil C saturation in tropical agricultural systems: soil fertility, climate, texture and N controls on SOM fractions
<p><span>Nature-based solutions for C sequestration in tropical croplands are paramount strategies in a changing climate. Soybean-maize-forage intercropped systems associated with soil acidity alleviation and nitrogen (N) fertilization effectively accumulate carbon (C) in weathered soils. However, the soil saturation status and the controls of C stabilization up to 40 cm soil depth into particulate (POM) and mineral-associated organic matter (MAOM) fractions are poorly understood in tropical croplands. This study tested the hypothesis of C saturation in the MAOM fraction by comparing field and published data focused on Brazilian tropical soils. We assessed the N fertilization effect on C stabilization in POM and MAOM pools, and climate, soil texture, and chemical attributes controls on POM and MAOM formation in tropical croplands using a machine-learning Random Forest (RF) modeling approach. Our findings do not support C saturation in the MAOM regardless of contrasting soil contents of silt plus clay and depths. C in the MAOM and POM fractions were not affected by N fertilizer. However, legume inclusion in the system resulted in higher total soil C and lower soil C:N ratio compared with N fertilization, which indicates that C dynamics differ whether synthetic or organic-N forms are applied to tropical croplands. Our RF model showed robust predictive performance for the MAOM but poorer for the POM fraction. Total organic carbon (TOC), total N, silt plus clay, phosphorus (P) and soil depth, zinc (Zn), cation exchange capacity, and TOC covariates were the most important variables for predicting MAOM and POM fractions, respectively. Our findings show, besides the well-known effect of calcium, that other nutrients such as P, Zn, manganese and copper play a key role in either MAOM or POM formation. Our work provides key insights on C saturation status in tropical croplands and land-management C sequestering potential, and N, climate, soil chemical attributes and texture controls on C distribution into MAOM and POM fractions up to 40 cm soil depth in tropical conservation agricultural systems. We advocate for upscaling C saturation concept nationally and further research investigating the role of climate and micronutrients contribution on MAOM and POM formation in broad scenarios and N fertilizer responsiveness for C stabilization in tropical croplands.</span></p>
Biologics repositioning: ml-SOM analysis raw results
<p><strong>Summary</strong></p> <p>This dataset contains raw result files for multiple-layer SOM (ml-SOM) repositioning analysis of infliximab and brodalumab. </p> <p><strong>Infliximab_results.zip</strong> archive contains the results of ml-SOM repositioning analysis of infliximab (T1) as a potential therapeutics for ulcerative colitis (D1), Crohn’s disease (D2), COPD (R1) and sarcoidosis (R2).</p> <p>Data is organized in the archive as follows:</p> <ol> <li>inflixmab_UC_CD_COPD_SARC021018_results+.RData - R data file that contains ml-SOM environment</li> <li>folder "inflixmab_UC_CD_COPD_SARC021018_results+ - Results" - comprises of various PDF and CSV files representing the a ml-SOM analysis results. It also contains the separate layer-level SOM analysis results for all datasets: <ul> <li>folder "1" - SOM analysis of infliximab dataset</li> <li>folder "2" - SOM analysis for ulcerative colitis and Crohn's disease dataset</li> <li>folder "3" - SOM analysis for COPD dataset</li> <li>folder "4" - SOM analysis for sarcoidosis dataset.</li> </ul> </li> </ol> <p><strong>Brodalumab_results.zip</strong> archive contains the results of ml-SOM repositioning analysis of brodalumab (T1) as a potential therapeutics for psoriasis (D1), Crohn’s disease (R1), and systemic juvenile idiopathic arthritis (R2).</p> <p>Data is organized in the archive as follows:</p> <ol> <li>brodalumab_CD_SJIA_301218_results+.RData - R data file that contains ml-SOM environment</li> <li>folder "brodalumab_CD_SJIA_301218_results+ - Results" - comprises of various PDF and CSV files representing the a ml-SOM analysis results. It also contains the separate layer-level SOM analysis results for all datasets: <ul> <li>folder "1" - SOM analysis of brodalumab and psoriasis dataset</li> <li>folder "2" - SOM analysis for Crohn's disease dataset</li> <li>folder "3" - SOM analysis for systemic juvenile idiopathic arthritis dataset</li> </ul> </li> </ol> <p>For detailed instructions on browsing the results and their interpretation please refer to the oposSOM package manual [1], as well as original publications [2-4]. </p> <p><strong>References</strong></p> <ol> <li>Henry Loeffler-Wirth, Hoang Thanh Le and Martin KalcheroposSOM.Comprehensive analysis of transcriptome data. DOI: <a href="https://doi.org/doi:10.18129/B9.bioc.oposSOM">10.18129/B9.bioc.oposSOM</a> </li> <li>Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor.Bioinformatics. 2015 Oct 1;31(19):3225-7. DOI: 10.1093/bioinformatics/btv342. Epub 2015 Jun 10.</li> <li>Wirth H, von Bergen M, Binder H. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012 Oct 8;5(1):18. DOI: 10.1186/1756-0381-5-18.</li> <li>Wirth H, Löffler M, von Bergen M, Binder H. Expression cartography of human tissues using self organizing maps. BMC Bioinformatics. 2011 Jul 27;12:306. DOI: 10.1186/1471-2105-12-306.</li> </ol> <p> </p>
Siwiec et al 2024 - RAW full microscopic images; DG PV-SOM-GFP staining in Htr7-GFP mice
<p>The archive contains raw microscopic images in Zeiss (.czi) format obtained during the Siwiec 2024 study (https://www.biorxiv.org/content/10.1101/2024.09.17.613425v1). Datafiles contain Z-stacks of microscopic images with metadata and four image channels (immunostaining for parvalbumin, somatostatin and GFP, with DAPI nuclear counterstain; see describing work for technical details) of transverse hippocampal sections from transgenic Htr7-GFP mice Tg(Htr7-EGFP)ST29Gsat.</p> <p> </p> <p>Example open software supporting .czi files: FIJI, Bio-Formats, ZEISS libczi C++ library (github.com/ZEISS/libczi) and its implementations (e.g. aicspylibczi in Python).</p>
PS+ SOM_prototype
<p>PS+ SOM_prototype</p>
PS+ SOM_datasheet
<p>PS+ SOM_datasheet</p>
Supporting CESM1-SOM Output for "Regional Precipitation Sensitivity is Sensitive to Changes in Cross-Equatorial Ocean Heat Transport"
<p>Supporting CESM1-SOM experiment output.</p>
SOM 230 and Gemcitabine in Advanced Pancreatic Cancer
ClinicalTrials.gov study NCT01385956. IPD Sharing: Not stated. Countries: 1. Publications: 1.
BRCA1- and BRCA2- mutation associated transcriptome landscapes in breast and ovarian cancers: ml-SOM results
<p>This is the submission accompanying raw result files for multiple-layer SOM (ml-SOM) analysis for the paper "Transcriptome patterns of BRCA1- and BRCA2- mutated breast and ovarian cancers".</p> <p>The dataset contains the results of the ml-SOM analysis of RNA-sequencing data from TCGA-OV (ovarian cancer) and TCGA-BRCA (breast cancer) projects. </p> <p>The dataset is organized as follows:</p> <ul> <li>Folder <strong>"12.BC.40 - Results" </strong>- ml-SOM analysis of TCGA-BRCA (breast cancer) dataset</li> <li>Folder <strong>"12.OV.40 - Results"</strong> - ml-SOM analysis of TCGA-OV (ovarian cancer) dataset</li> <li>File <strong>"12.BC.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> <li>File <strong>"12.OV.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> </ul> <p>For detailed instructions on browsing the results and their interpretation please refer to the oposSOM package manual [1], as well as original publications [2-4]. </p> <p><strong>References</strong></p> <ol> <li>Henry Loeffler-Wirth, Hoang Thanh Le and Martin Kalcheropos. SOM.Comprehensive analysis of transcriptome data. DOI: <a href="https://doi.org/doi:10.18129/B9.bioc.oposSOM">10.18129/B9.bioc.oposSOM</a> </li> <li>Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on Bioconductor. Bioinformatics. 2015 Oct 1;31(19):3225-7. DOI: 10.1093/bioinformatics/btv342. Epub 2015 Jun 10.</li> <li>Wirth H, von Bergen M, Binder H. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012 Oct 8;5(1):18. DOI: 10.1186/1756-0381-5-18.</li> <li>Wirth H, Löffler M, von Bergen M, Binder H. Expression cartography of human tissues using self-organizing maps. BMC Bioinformatics. 2011 Jul 27;12:306. DOI: 10.1186/1471-2105-12-306.</li> </ol>
Рис. 4. Àинамика гибеΛи гусениц коΛьчатого шеΛкопряΔа, собранных в районе УПН, соΔержащихся в Λабораторных усΛовиях. ВертикаΛьно: коΛичество погибших гусениц (% от чисΛа собранных за весь периоΔ иссΛеΔований в 2019 г. гусениц). ГоризонтаΛьно: Δата осмотра в Λаборатории. В правом верхнем угΛу графика: Δата сбора гусениц в районе УПН. — гибеΛь от вируса яΔерного поΛиэΔроза; — гибеΛь от бактериоза Fig. 4. Dynamics of death of the Lackey moth caterpillars collected at the SOM and kept in the laboratory, 2019. Vertical: number of deaths (percentage from the total number of caterpillars collected in 2019 (578 caterpillars)); horizontal: dates of laboratory controls. Upper right corner: collection date. — death from NPV; — death from bacteriosis in Lackey Moth (Malacosoma Neustria L., Lasiocampidae, Lepidoptera) Population During The Eruptive Phase
Рис. 4. Àинамика гибеΛи гусениц коΛьчатого шеΛкопряΔа, собранных в районе УПН, соΔержащихся в Λабораторных усΛовиях. ВертикаΛьно: коΛичество погибших гусениц (% от чисΛа собранных за весь периоΔ иссΛеΔований в 2019 г. гусениц). ГоризонтаΛьно: Δата осмотра в Λаборатории. В правом верхнем угΛу графика: Δата сбора гусениц в районе УПН. — гибеΛь от вируса яΔерного поΛиэΔроза; — гибеΛь от бактериоза Fig. 4. Dynamics of death of the Lackey moth caterpillars collected at the SOM and kept in the laboratory, 2019. Vertical: number of deaths (percentage from the total number of caterpillars collected in 2019 (578 caterpillars)); horizontal: dates of laboratory controls. Upper right corner: collection date. — death from NPV; — death from bacteriosis
Supplementary material 2 from: Phimmachak S, Richards SJ, Sivongxay N, Seateun S, Chuaynkern Y, Makchai S, Som HE, Stuart BL (2019) A new caruncle-bearing fanged frog (Limnonectes, Dicroglossidae) from Laos and Thailand. ZooKeys 846: 133-156. https://doi.org/10.3897/zookeys.846.33200
: Data type: species data
Supplementary material 1 from: Phimmachak S, Richards SJ, Sivongxay N, Seateun S, Chuaynkern Y, Makchai S, Som HE, Stuart BL (2019) A new caruncle-bearing fanged frog (Limnonectes, Dicroglossidae) from Laos and Thailand. ZooKeys 846: 133-156. https://doi.org/10.3897/zookeys.846.33200
: Data type: species data
Figure 9 from: Phimmachak S, Richards SJ, Sivongxay N, Seateun S, Chuaynkern Y, Makchai S, Som HE, Stuart BL (2019) A new caruncle-bearing fanged frog (Limnonectes, Dicroglossidae) from Laos and Thailand. ZooKeys 846: 133-156. https://doi.org/10.3897/zookeys.846.33200
Figure 9 Comparisons of males of four similar, caruncle-bearing species of Limnonectes in preservative: Dorsal (above) and ventral (below) views of AL.savan sp. nov. holotype male (NCSM 76288) BL.dabanus (MVZ 258200) with high-profiled caruncle from Ratanakiri Province, Cambodia CL.dabanus (MVZ 258202) with low-profiled caruncle from Ratanakiri Province, Cambodia DL.macrognathus (FMNH 174526) from Nakhon Si Thammarat Province, Thailand EL.gyldenstolpei topotype (ZMKU AM 01143) from Lampang Province, Thailand.
Figure 7 from: Phimmachak S, Richards SJ, Sivongxay N, Seateun S, Chuaynkern Y, Makchai S, Som HE, Stuart BL (2019) A new caruncle-bearing fanged frog (Limnonectes, Dicroglossidae) from Laos and Thailand. ZooKeys 846: 133-156. https://doi.org/10.3897/zookeys.846.33200
Figure 7 Localities of studied specimens of Limnonectessavan sp. nov. at the holotype locality at Savannakhet Province, Vilabouli District, Laos (star) and the paratype localities at Khammouan Province, Boualapha District, Laos (square), Champasak Province, Pakxong District, Laos (asterisk), Ubon Ratchathani Province, Sirindhorn District, Thailand (circle), and Ubon Ratchathani Province, Na Chaluai and Buntharik Districts, Thailand (triangle).
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