Human Protein Reference Database—2009 update

Human Protein Reference Database (HPRD—http://www.hprd.org/), initially described in 2003, is a database of curated proteomic information pertaining to human proteins. We have recently added a number of new features in HPRD. These include PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest. Another new feature is a protein distributed annotation system—Human Proteinpedia (http://www.humanproteinpedia.org/)—through which laboratories can submit their data, which is mapped onto protein entries in HPRD. Over 75 laboratories involved in proteomics research have already participated in this effort by submitting data for over 15 000 human proteins. The submitted data includes mass spectrometry and protein microarray-derived data, among other data types. Finally, HPRD is also linked to a compendium of human signaling pathways developed by our group, NetPath (http://www.netpath.org/), which currently contains annotations for several cancer and immune signaling pathways. Since the last update, more than 5500 new protein sequences have been added, making HPRD a comprehensive resource for studying the human proteome

NetPath: a public resource of curated signal transduction pathways

NetPath, a novel community resource of curated human signaling pathways is presented and its utility demonstrated using immune signaling data

Investigating the Soft X-Ray Spectra of Solar Flare Onsets

In this study, we present the analysis of six solar flare events that occurred in 2022, using new data from the third-generation Miniature X-Ray Solar Spectrometer, also known as the Dual-zone Aperture X-ray Solar Spectrometer (DAXSS). The primary focus of this study is on the flare’s onset phase , which is characterized by elevated soft X-ray emissions even before the flare’s impulsive phase. We analyze the temporal evolution of plasma temperature, emission measure, and elemental abundance factors during the flare onset phase by fitting the DAXSS spectra with the Astrophysical Plasma Emission Code model. The model fitting results indicate that the flaring plasma is already at a high temperature (10–15 MK) during the onset period. The temperature rises during the onset phase, followed by a decrease and subsequent increase during the impulsive phase. Elemental abundance factors show a trend of falling below preflare values during the onset phase, with some recovery before the impulsive phase. During the impulsive phase, the abundance factors decrease from elevated coronal values to about photospheric values. We also analyze images from the 193 Å channel of the Atmospheric Imaging Assembly (AIA), highlighting the formation or brightening of coronal loop structures during the onset phase. Two distinct onset loop configurations are observed, which are referred to as one-loop and two-loop onsets. Both DAXSS and AIA observations indicate that the flare onset phase exhibits hot coronal plasma properties similar to those of the impulsive phase, suggesting that the onset phase may act as a preconditioning effect for some flares

NetSlim:High-confidence curated signaling maps

We previously developed NetPath as a resource for comprehensive manually curated signal transduction pathways. The pathways in NetPath contain a large number of molecules and reactions which can sometimes be difficult to visualize or interpret given their complexity. To overcome this potential limitation, we have developed a set of more stringent curation and inclusion criteria for pathway reactions to generate high-confidence signaling maps. NetSlim is a new resource that contains this ‘core’ subset of reactions for each pathway for easy visualization and manipulation. The pathways in NetSlim are freely available at http://www.netpath.org/netslim. Database URL: www.netpath.org/netsli