A contribution to the study of the German treasury bills market

We study the yields in the German treasury bills market. We take a detailed look at the yield banks require to buy treasury bills in the primary market, and we also examine the yield households and nonbank firms demand to buy these bills in the secondary market. We use data from real world tenders to show that the bids set by banks are in accordance with the predictions of our theoretical framework. In particular, we show that current monetary policy and the market's expectations regarding the future path of monetary policy can be used to define an interval in which the bids from banks lie. Our theoretical predictions for the secondary market also match the data.info:eu-repo/semantics/publishedVersio

Determinant factors of bank customers' demand for liquidity

In contexts of economic instability investors show an increase in aversion to risk and prefer high liquidity and low-risk financial products. In this paper, we study the reasons behind bank customers holding wealth in the form of immediate liquidity. Using micro data on clients’ portfolios of a Portuguese bank, we ask whether there is a relationship between the bank’s capital ratio and the proportion of wealth that clients allocate to demand deposits, which is a relatively unexplored topic in the literature. Special attention is also paid to the impact of investors' financial knowledge by looking at professional group and age. Results indicate that when banks’ capital ratio decreases, savers put a larger fraction of their investment into demand deposits, especially savers with greater risk aversion and knowledge. Finally, we find evidence of an “age effect” and also that investors belonging to professional groups with more skills follow more sophisticated investment strategies.FC

Towards the integration of regulatory networks with metabolic models

Metabolism is present in every living being and for that reason understanding the mechanisms behind it is essential for comprehending the phenotypical behaviour of the organisms. Metabolic models reconstructed at genome scale level can provide in-depth comprehension of the metabolic processes within an organism, therefore emerging as one of the best strategies for studying these systems. Genome-scale metabolic models can be enriched with information from regulatory networks, such as gene expression data. Merging regulatory networks with metabolic models can help uncovering information that can be used for many applications, for example identifying potential drug targets. In this work we propose developing bioinformatics tools capable of merging a genome-scale metabolic models with regulatory networks. A tool named CORAMI (Combination Of Regulatory And Metabolic Information) is being developed as a plugin for merlin software. A genome-scale metabolic model of Saccharomyces cerevisiae will be imported into merlin in order to collect the necessary metabolic data for CORAMI. Also, annotation data for metabolic genes will be integrated with regulatory genes in order to validate the integration and establish a correlation between these two models. Additionally, the regulatory network of S. cerevisiae chosen to be merged with the metabolic model was manual curated. Here we present the strategy for merging the two networks, which together can provide unique insights into S. cerevisiaes phenotypical behaviour. In the future, several tools which will allow the user to explore the total potential of the plugin and retrieve more results for their studies will be developed.info:eu-repo/semantics/publishedVersio

BSA-PEG Hydrogel: A Novel Protein-Ligand Binding 3D Matrix

Hydrogel materials have good biomimetic properties and high potential for biomedical and bioanalytical applications. In this work, a hydrogel of serum albumin crosslinked with poly-(ethylene glycol) was prepared and characterized for its water content, protein structure and stability. The ability of the hydrogel to bind small molecule ligands with different hydrophobicity was evaluated using a homologous series of amphiphiles (NBD-Cn, n = 4, 6 and 8) and the calculated binding affinities were similar to that of free protein in solution. Overall, the results indicate this type of hydrogel system as a convenient tool for studying the binding of xenobiotics to tissue proteins.info:eu-repo/semantics/publishedVersio

Towards a genome-wide transport systems encoding genes tracker

[Excerpt] Introduction: TRIAGE, is a tool currently embedded in merlin , which performs the identification of transport systems and automatically generates transport reactions for every metabolite transported by those carriers. Reactions generated by TRIAGE can be directly integrated in GSM models, as all metabolites involved have KEGG and/or ChEBI identifiers. Up to our knowledge, this is the only tool capable of identifying and generating such reactions. [...]by FCT under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorteoperation (NORTE -01-0145-FEDER- 000004) funded by the European Regional Development Fund under the scope of Norte2020 -Programa Operacional Regional do Norteinfo:eu-repo/semantics/publishedVersio

merlin v4: an updated platform for reconstructing genome-scale metabolic models

The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) software is an open source user-friendly Java application developed for Windows and Unix, aimed towards the reconstruction of genome-scale metabolic models. The development of merlin follows a design philosophy of automating time-consuming steps in the reconstruction of genome-scale metabolic models, while allowing users to control the parameters of operations and manually curate the results. All major steps involved in the reconstruction of a metabolic model are implemented in merlin, including genome retrieval and its functional annotation, construction of the reactions set and associated entities, model compartmentalization and conversion to standard SBML formats. The fourth iteration of merlin includes a major overhaul of the user interface, implementation of new features, improvements to existing features, and most notably, the implementation of the object-relational mapping framework Hibernate. The graphical layout has been significantly streamlined, while supporting the latest version of AiBench, providing users with an intuitive and responsive interface. Development was also focused at new quality of life improvements, aimed mainly towards importing, exporting and duplicating merlin user projects. The development of the latest version of merlin followed a modular approach, culminating in the implementation of a plugin manager which simplifies and hastens the process of updating and debugging the various features of merlin. In addition, TranSyT, a state-of-the-art genome-wide transmembrane transport system annotation tool has been implemented to overcome the limitations of the previously available TRIAGE module. Finally, it is noteworthy to mention the implementation of BioISO, a tool aimed at evaluating a genome-scale metabolic network or biomass formulation, based on the previously available COBRA and FBA frameworks.info:eu-repo/semantics/publishedVersio

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.Centre of Biological Engineering (CEB, UMinho); Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit; this work is a result of the project 22231/01/SAICT/2016: Biodata.pt Infraestrutura Portuguesa de Dados Biologicos, supported by the ´ PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); FCT for providing PhD scholarships [DFA/BD/08789/2021 J.C, DFA/BD/8076/2020 E.C., SFRH/BD/139198/2018 to F.C., SFRH/BD/131916/2017 R. Rodrigues]; FCT for the Assistant Research contract of Oscar Dias obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersio