The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.

Abstract:The plant hormone auxin plays pivotal roles in many aspects of plant growth and development. The auxin/indole-3-acetic acid (Aux/IAA) gene family encodes short-lived nuclear proteins acting on auxin perception and signaling, but the evolutionary history of this gene family remains to be elucidated. In this study, the Aux/IAA gene family in 17 plant species covering all major lineages of plants is identified and analyzed by using multiple bioinformatics methods. A total of 434 Aux/IAA genes was found among these plant species, and the gene copy number ranges from three (Physcomitrella patens) to 63 (Glycine max). The phylogenetic analysis shows that the canonical Aux/IAA proteins can be generally divided into five major clades, and the origin of Aux/IAA proteins could be traced back to the common ancestor of land plants and green algae. Many truncated Aux/IAA proteins were found, and some of these truncated Aux/IAA proteins may be generated from the C-terminal truncation of auxin response factor (ARF) proteins. Our results indicate that tandem and segmental duplications play dominant roles for the expansion of the Aux/IAA gene family mainly under purifying selection. The putative nuclear localization signals (NLSs) in Aux/IAA proteins are conservative, and two kinds of new primordial bipartite NLSs in P. patens and Selaginella moellendorffii were discovered. Our findings not only give insights into the origin and expansion of the Aux/IAA gene family, but also provide a basis for understanding their functions during the course of evolution.

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BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize the software containers including the metadata, versions, licenses, and/or software dependencies. BioContainers supports multiple packaging and containers technologies such as Conda, Docker, and Singularity. Here, we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). BioContainers registry provides a fast and convenient way to find and retrieve bioinformatics tools packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.

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The uniaxial cyclic loading tests have been conducted to study the mechanical behavior of dry and water saturated igneous rock with acoustic emission (AE) monitoring. The igneous rock samples are dried, naturally immersed, and boiled to get specimens with different water contents for the testing. The mineral compositions and the microstructures of the dry and water saturated igneous rock are also presented. The dry specimens present higher strength, fewer strains, and rapid increase of AE count subjected to the cyclic loading, which reflects the hard and brittle behavior and strong burst proneness of igneous rock. The water saturated specimens have lower peak strength, more accumulated strains, and increase of AE count during the cyclic loading. The damage of the igneous rocks with different water contents has been identified by the Felicity Ratio Analysis. The cyclic loading and unloading increase the dislocation between the mineral aggregates and the water-rock interactions further break the adhesion of the clay minerals, which jointly promote the inner damage of the igneous rock. The results suggest that the groundwater can reduce the burst proneness of the igneous rock but increase the potential support failure of the surrounding rock in igneous invading area. In addition, the results inspire the fact that the water injection method is feasible for softening the igneous rock and for preventing the dynamic disasters within the roadways and working faces located in the igneous intrusion area.

Overlapped residual coal pillars, together with the surrounding rock strata, play a combined bearing role in ultra-close multiple seam mining. Global stability of the whole bearing system is significant for the mining design, construction, and operation. Laboratory uniaxial compressive experiments for different kinds of sandwiched coal-rock specimens are carried out to investigate the progressive failure characteristics and mechanisms. Results show that: (1) The mechanical behavior of the sandwiched coal-rock specimen is mainly divided into four stages during the failure process. The response of the electrical resistivity and the evolution of acoustic emission (AE) energy are in good agreement with the mechanical behaviors at different stages, which are a reflection of the global failure characteristics of sandwiched specimens. (2) The distribution of AE events and the development of local strain can provide further insight into the local failure characteristics of coal elements or rock elements in sandwiched specimens. AE events are more likely to be generated in coal elements, which can propagate across coal-rock interfaces and induce damage to rock elements in a certain area. Similarly, the unbalanced deformation characteristics of coal elements and rock elements are apparently revealed in the progressive failure process. (3) Progressive failure of a sandwiched coal-rock specimen is closely associated with the interactions between the coal elements and rock elements. Initial failure usually appears in the coal elements. At this process, the recovery of elastic deformation and the output of strain energy are observed in the rock elements, which can accelerate the rupture of coal elements. In turn, the dynamic fracture energy generated in the rupture process of coal elements can propagate into rock elements and induce damage to rock elements a certain area. (4) The experimental results are helpful for maintaining the long-term stability of a sandwiched coal-rock system in ultra-close multiple seam mining.