Computational algorithms to predict Gene Ontology annotations

Background Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biological experiments and interpret their results. Despite their importance, these sources of information have some known issues. They are incomplete, since biological knowledge is far from being definitive and it rapidly evolves, and some erroneous annotations may be present. Since the curation process of novel annotations is a costly procedure, both in economical and time terms, computational tools that can reliably predict likely annotations, and thus quicken the discovery of new gene annotations, are very useful. Methods We used a set of computational algorithms and weighting schemes to infer novel gene annotations from a set of known ones. We used the latent semantic analysis approach, implementing two popular algorithms (Latent Semantic Indexing and Probabilistic Latent Semantic Analysis) and propose a novel method, the Semantic IMproved Latent Semantic Analysis, which adds a clustering step on the set of considered genes. Furthermore, we propose the improvement of these algorithms by weighting the annotations in the input set. Results We tested our methods and their weighted variants on the Gene Ontology annotation sets of three model organism genes (Bos taurus, Danio rerio and Drosophila melanogaster ). The methods showed their ability in predicting novel gene annotations and the weighting procedures demonstrated to lead to a valuable improvement, although the obtained results vary according to the dimension of the input annotation set and the considered algorithm. Conclusions Out of the three considered methods, the Semantic IMproved Latent Semantic Analysis is the one that provides better results. In particular, when coupled with a proper weighting policy, it is able to predict a significant number of novel annotations, demonstrating to actually be a helpful tool in supporting scientists in the curation process of gene functional annotations

Bridging the Flexibility Concepts in the Buildings and Multi-energy Domains

paper aims to stimulate a discussion on how to create a bridge between the concept of flexibility used in power and energy systems and the flexibility that buildings can offer for providing services to the electrical system. The paper recalls the main concepts and approaches considered in the power systems and multi-energy systems, and summarises some aspects of flexibility in buildings. The overview shows that there is room to strengthen the contacts among the scientists operating in these fields. The common aim is to identify the complementary aspects and provide inputs to enhance the methodologies and models to enable and support an effective energy and ecologic transition

Thermal energy storage for grid applications: Current status and emerging trends

Thermal energy systems (TES) contribute to the on-going process that leads to higher integration among different energy systems, with the aim of reaching a cleaner, more flexible and sustainable use of the energy resources. This paper reviews the current literature that refers to the development and exploitation of TES-based solutions in systems connected to the electrical grid. These solutions facilitate the energy system integration to get additional flexibility for energy management, enable better use of variable renewable energy sources (RES), and contribute to the modernisation of the energy system infrastructures, the enhancement of the grid operation practices that include energy shifting, and the provision of cost-effective grid services. This paper offers a complementary view with respect to other reviews that deal with energy storage technologies, materials for TES applications, TES for buildings, and contributions of electrical energy storage for grid applications. The main aspects addressed are the characteristics, parameters and models of the TES systems, the deployment of TES in systems with variable RES, microgrids, and multi-energy networks, and the emerging trends for TES applications

The Benefits of the Matthews Correlation Coefficient (MCC) Over the Diagnostic Odds Ratio (DOR) in Binary Classification Assessment

To assess the quality of a binary classification, researchers often take advantage of a four-entry contingency table called confusion matrix, containing true positives, true negatives, false positives, and false negatives. To recap the four values of a confusion matrix in a unique score, researchers and statisticians have developed several rates and metrics. In the past, several scientific studies already showed why the Matthews correlation coefficient (MCC) is more informative and trustworthy than confusion-entropy error, accuracy, F1 score, bookmaker informedness, markedness, and balanced accuracy. In this study, we compare the MCC with the diagnostic odds ratio (DOR), a statistical rate employed sometimes in biomedical sciences. After examining the properties of the MCC and of the DOR, we describe the relationships between them, by also taking advantage of an innovative geometrical plot called confusion tetrahedron, presented here for the first time. We then report some use cases where the MCC and the DOR produce discordant outcomes, and explain why the Matthews correlation coefficient is more informative and reliable between the two. Our results can have a strong impact in computer science and statistics, because they clearly explain why the trustworthiness of the information provided by the Matthews correlation coefficient is higher than the one generated by the diagnostic odds ratio

Ingesta de sacarosa durante la preñez y la lactancia: efectos sobre el metabolismo lipídico en la descendencia adulta

:La calidad nutricional en etapas tempranas de la vida influye sobre el desarrollo de patologías crónicas del adulto. Objetivo: examinar el efecto de la dieta rica en sacarosa (DRS) durante la preñez+lactancia sobre aspectos del metabolismo lipídico de la descendencia alimentada con dieta control (DC) o DRS desde el post-destete y hasta las 21 semanas de vida (grupos: DC-DC, DC-DRS, DRS-DRS y DRS-DC). Resultados: -En los grupos DC-DRS, DRS-DRS y DRS-DC observamos mayor adiposidad, peso corporal normal y dislipidemia. Esta última resulta de acelerada secreción hepática de VLDL-Tg y mayor contenido de triglicéridos hepáticos asociado a mayor actividad de enzimas lipogénicas hepáticas: acetil-CoA carboxilasa y enzima málica (p<0.05 vs DC-DC). La actividad Glucosa-6-P-deshidrogenasa hepática fue mayor solo en los grupos DC-DRS y DRS-DRS comparado a DRS-DC y DC-DC. Conclusión: la exposición temprana a DRS conlleva en la adultez a cambios desfavorables en el metabolismo lipídico independientemente que la dieta post-lactancia sea DC o DRS.Nutrition quality during the early steps of life has a high influence on the development of chronic adult diseases. The present study examined the effect of a sucrose-rich diet (SRD) fed to dams during pregnancy+lactation on the lipid metabolism of their adult progeny, fed a control diet (CD) or a SRD after weaning to 21 weeks of life (CD-CD, CD-SRD, SRD-SRD, SRD-CD groups). Results: Final body weight was similar between the groups although adiposity and plasma lipids were significantly higher in CD-SRD, SRD-SRD and SRD-CD vs CD-CD. The dyslipidemia was the result of an increased VLDL-Tg secretion rate and elevated liver triglyceride pool. The novo hepatic lipogenic enzymes acetyl-CoA carboxylase and malic enzyme were significantly higher in rats exposed to SRD at any period of life. On the other hand, the hepatic glucose-6-P-dehydrogenase activity was significantly higher (p<0.05) in DC-DRS and DRS-DRS compared to CD-CD and SRD-CD. Conclusion: An early life exposure to a SRD is associated with changes in lipid metabolism in the adult life regardless whether offspring consumed an SRD after weaning.Fil: D´Alessandro, M. E.. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas; ArgentinaFil: Rojido, M.. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas; ArgentinaFil: Chicco, Adriana Graciela. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas. Departamento de Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentin

Proof-of-concept Quantum Simulator based on Molecular Spin Qudits

The use of $d$-level qudits instead of two-level qubits can largely increase the power of quantum logic for many applications, ranging from quantum simulations to quantum error correction. Molecular Nanomagnets are ideal spin systems to realize these large-dimensional qudits. Indeed, their Hamiltonian can be engineered to an unparalleled extent and can yield a spectrum with many low-energy states. In particular, in the last decade intense theoretical, experimental and synthesis efforts have been devoted to develop quantum simulators based on Molecular Nanomagnets. However, this remarkable potential is practically unexpressed, because no quantum simulation has ever been experimentally demonstrated with these systems. Here we show the first prototype quantum simulator based on an ensemble of molecular qudits and a radiofrequency broadband spectrometer. To demonstrate the operativity of the device, we have simulated quantum tunneling of the magnetization and the transverse-field Ising model, representative of two different classes of problems. These results represent an important step towards the actual use of molecular spin qudits in quantum technologies

Blueprint of a Molecular Spin Quantum Processor

The implementation of a universal quantum processor still poses fundamental issues related to error mitigation and correction, which demand to investigate also platforms and computing schemes alternative to the main stream. A possibility is offered by employing multi-level logical units (qudits), naturally provided by molecular spins. Here we present the blueprint of a Molecular Spin Quantum Processor consisting of single Molecular Nanomagnets, acting as qudits, placed within superconducting resonators adapted to the size and interactions of these molecules to achieve a strong single spin to photon coupling. We show how to implement a universal set of gates in such a platform and to readout the final qudit state. Single-qudit unitaries (potentially embedding multiple qubits) are implemented by fast classical drives, while a novel scheme is introduced to obtain two-qubit gates via resonant photon exchange. The latter is compared to the dispersive approach, finding in general a significant improvement. The performance of the platform is assessed by realistic numerical simulations of gate sequences, such as Deutsch-Josza and quantum simulation algorithms. The very good results demonstrate the feasibility of the molecular route towards a universal quantum processor.Comment: 16 pages, 11 figures. Accepted in Physical Review Applie

Inter and intra-tumor somatostatin receptor 2 heterogeneity influences peptide receptor radionuclide therapy response

Patients with neuroendocrine tumors (NETs) can be treated with peptide receptor radionuclide therapy (PRRT). Here, the somatostatin analogue octreotate radiolabeled with lutetium-177 is targeted to NET cells by binding to the somatostatin receptor subtype 2 (SST2). During radioactive decay, DNA damage is induced, leading to NET cell death. Although the therapy proves to be effective, mortality rates remain high. To appropriately select more optimal treatment strategies, it is essential to first better understand the radiobiological responses of tumor cells to PRRT. Methods: We analyzed PRRT induced radiobiological responses in SST2 expressing cells and xenografted mice using SPECT/MRI scanning and histological and molecular analyses. We measured [177Lu]Lu-DOTA-TATE uptake and performed analyses to visualize induction of DNA damage, cell death and other cellular characteristics. Results: The highest accumulation of radioactivity was measured in the tumor and kidneys. PRRT induced DNA damage signaling and repair in a time-dependent manner. We observed intra-tumor heterogeneity of DNA damage and apoptosis, which was not attributed to proliferation or bioavailability. We found a strong correlation between high DNA damage levels and high SST2 expression. PRRT elicited a different therapeutic response between models with different SST2 expression levels. Heterogeneous SST2 expression levels were also confirmed in patient NETs. Conclusion: Hete