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ShareScore release 0.9.0
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2 results for “library event”
Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis
<p><em>Mycobacterium avium</em> is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. <em>M. avium</em> has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of <em>M. avium</em> with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for <em>Mycobacterium tuberculosis,</em> and a genome six-frame translated database and a variant protein database of <em>M. avium</em>. A search of mass spectrometry data analysis against <em>M. avium</em> protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of <em>M. avium</em> proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the <em>M. avium</em> proteome. Thus, we present a <em>M. avium </em>spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.</p>
Heat wave and cold snap event library under various technical choices for NERC subregions in the conterminous U.S. (1980 - 2024)
<p>This <strong>Extreme Thermal Event Library</strong> provides comprehensive records of heat wave and cold snap events from 1980 to 2024, aggregated at the North American Electric Reliability Corporation (NERC) subregion level for the conterminous United States. A map of NERC subregions with county-level mean temperatures is included in the file <strong>'NERC_subregions_with_mean_temperature.tif'</strong>.</p> <p>The heat wave and cold snap events were identified using temperature data simulated by the Thermodynamic Global Warming (TGW) model. The raw TGW hourly temperature data (at a 12-km resolution) was aggregated to the county level using spatial averaging within county boundaries. Daily mean, maximum, and minimum temperatures were then derived from the hourly surface air temperature data for each county. Subsequently, the county-level daily temperatures were spatially aggregated to the NERC subregion level using three distinct spatial aggregation methods:</p> <ol> <li><strong>Simple Mean (SM)</strong>: A simple average of county-level temperatures.</li> <li><strong>Area-Weighted Mean (MWA)</strong>: Weighted by the area of each county.</li> <li><strong>Population-Weighted Mean (MWP)</strong>: Weighted by the population of each county.</li> </ol> <p>The database includes separate zipped files for each spatial aggregation method:</p> <ul> <li><strong>"heat_wave_library_NERC_average.zip"</strong> and <strong>"cold_snap_library_NERC_average.zip"</strong> contain events based on the SM method.</li> <li><strong>"heat_wave_library_NERC_average_area.zip"</strong> and <strong>"cold_snap_library_NERC_average_area.zip"</strong> contain events based on the MWA method.</li> <li><strong>"heat_wave_library_NERC_average_pop.zip"</strong> and <strong>"cold_snap_library_NERC_average_pop.zip"</strong> contain events based on the MWP method.</li> </ul> <p>Each zipped file includes 12 event libraries, corresponding to 12 different event definitions. Details about these definitions are provided in the file <strong>'Event definitions.docx'</strong>.</p> <p> </p> <h3><strong>Event Library Structure</strong></h3> <p>Each row in an event library represents one detected thermal event. The columns in the library are defined as follows:</p> <ul> <li><strong>start_date</strong>: Start date of the event.</li> <li><strong>end_date</strong>: End date of the event.</li> <li><strong>centroid_date</strong>: The centroid date, calculated as the midpoint between the start and end dates.</li> <li><strong>highest_temperature / lowest_temperature</strong>: The highest daily maximum temperature (for heat waves) or lowest daily minimum temperature (for cold snaps), in Kelvin.</li> <li><strong>duration</strong>: Duration of the event in days.</li> <li><strong>NERC_ID</strong>: Identifier for the NERC subregion.</li> <li><strong>spatial_coverage</strong>: The spatial coverage of the event within the NERC subregion, expressed as the percentage of counties experiencing the event relative to the total number of counties in the subregion.</li> </ul>
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