The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across different database resources, experimental modalities and levels of mechanistic detail. The STRING database (https://string-db.org/) systematically collects and integrates protein-protein interactions-both physical interactions as well as functional associations. The data originate from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources. All of these interactions are critically assessed, scored, and subsequently automatically transferred to less well-studied organisms using hierarchical orthology information. The data can be accessed via the website, but also programmatically and via bulk downloads. The most recent developments in STRING (version 12.0) are: (i) it is now possible to create, browse and analyze a full interaction network for any novel genome of interest, by submitting its complement of encoded proteins, (ii) the co-expression channel now uses variational auto-encoders to predict interactions, and it covers two new sources, single-cell RNA-seq and experimental proteomics data and (iii) the confidence in each experimentally derived interaction is now estimated based on the detection method used, and communicated to the user in the web-interface. Furthermore, STRING continues to enhance its facilities for functional enrichment analysis, which are now fully available also for user-submitted genomes

Demand-Orientated Power Production from Biogas: Modeling and Simulations under Swedish Conditions

The total share of intermittent renewable electricity is increasing, intensifying the need for power balancing in future electricity systems. Demand-orientated combined heat and power (CHP) production from biogas has potential for this purpose. An agricultural biogas plant, using cattle manure and sugar beet for biogas and CHP production, was analyzed here. The model Dynamic Biogas plant Model (DyBiM) was developed and connected to the Anaerobic Digestion Model No. 1 (ADM1). Flexible scenarios were simulated and compared against a reference scenario with continuous production, to evaluate the technical requirements and economic implications of demand-orientated production. The study was set in Swedish conditions regarding electricity and heat price, and the flexibility approaches assessed were increased CHP and gas storage capacity and feeding management. The results showed that larger gas storage capacity was needed for demand-orientated CHP production but that feeding management reduced the storage requirement because of fast biogas production response to feeding. Income from electricity increased by 10%, applying simple electricity production strategies to a doubled CHP capacity. However, as a result of the currently low Swedish diurnal electricity price variation and lack of subsidies for demand-orientated electricity production, the increase in income was too low to cover the investment costs. Nevertheless, DyBiM proved to be a useful modeling tool for assessing the economic outcome of different flexibility scenarios for demand-orientated CHP production

A Guide to Conquer the Biological Network Era Using Graph Theory

Networks are one of the most common ways to represent biological systems as complex sets of binary interactions or relations between different bioentities. In this article, we discuss the basic graph theory concepts and the various graph types, as well as the available data structures for storing and reading graphs. In addition, we describe several network properties and we highlight some of the widely used network topological features. We briefly mention the network patterns, motifs and models, and we further comment on the types of biological and biomedical networks along with their corresponding computer- and human-readable file formats. Finally, we discuss a variety of algorithms and metrics for network analyses regarding graph drawing, clustering, visualization, link prediction, perturbation, and network alignment as well as the current state-of-the-art tools. We expect this review to reach a very broad spectrum of readers varying from experts to beginners while encouraging them to enhance the field further. © Copyright © 2020 Koutrouli, Karatzas, Paez-Espino and Pavlopoulos

Reusable Defense Components for Online Reputation Systems

Attacks on trust and reputation systems (TRS) as well as defense strategies against certain attacks are the subject of many research papers. Although proposing valuable ideas, they all exhibit at least one of the following major shortcomings. Firstly, many researchers design defense mechanisms from scratch and without reusing approved ideas. Secondly, most proposals are limited to naming and theoretically describing the defense mechanisms. Another issue is the inconsistent denomination of attacks with similar characteristics among different researchers. To address these shortcomings, we propose a novel taxonomy of attacks on TRS focusing on their general characteristics and symptomatology. We use this taxonomy to assign reusable, clearly described and practically implemented components to different classes of attacks. With this work, we aim to provide a basis for TRS designers to experiment with numerous defense mechanisms and to build more robust systems in the end

Inter-species spin-noise correlations in hot atomic vapors

We report an experimental and theoretical study of spin noise correlations in a $^{87}$Rb-$^{133}$Cs unpolarized alkali-metal vapor dominated by spin-exchange collisions. We observe strong unequal-time inter-species correlations and account for these with a first-principles theoretical model. Since the two atomic species have different spin precession frequencies, the dual-species vapor enables the use of an additional experimental handle, the applied magnetic field, for untangling various sub-types of spin correlations. In particular, the measured cross-correlation and auto-correlation spectra shed light on a number of spin-dynamic effects involving intra-atom, inter-atom, intra-species and inter-species correlations. Cross-correlation coefficients exceeding $60\%$ have been observed at low-magnetic fields, where the two spin species couple strongly via spin-exchange collisions. The understanding of such spontaneously generated correlations can motivate the design of quantum-enhanced measurements with single or multi-species spin-polarized alkali-metal vapors used in quantum sensing applications