Semantic Similarity in Cheminformatics

Similarity in chemistry has been applied to a variety of problems: to predict biochemical properties of molecules, to disambiguate chemical compound references in natural language, to understand the evolution of metabolic pathways, to predict drug-drug interactions, to predict therapeutic substitution of antibiotics, to estimate whether a compound is harmful, etc. While measures of similarity have been created that make use of the structural properties of the molecules, some ontologies (the Chemical Entities of Biological Interest (ChEBI) being one of the most relevant) capture chemistry knowledge in machine-readable formats and can be used to improve our notions of molecular similarity. Ontologies in the biomedical domain have been extensively used to compare entities of biological interest, a technique known as ontology-based semantic similarity. This has been applied to various biologically relevant entities, such as genes, proteins, diseases, and anatomical structures, as well as in the chemical domain. This chapter introduces the fundamental concepts of ontology-based semantic similarity, its application in cheminformatics, its relevance in previous studies, and future potential. It also discusses the existing challenges in this area, tracing a parallel with other domains, particularly genomics, where this technique has been used more often and for longer

Exploiting disjointness axioms to improve semantic similarity measures

Motivation: Representing domain knowledge in biology has traditionally been accomplished by creating simple hierarchies of classes with textual annotations. Recently, expressive ontology languages, such as Web Ontology Language, have become more widely adopted, supporting axioms that express logical relationships other than class-subclass, e.g. disjointness. This is improving the coverage and validity of the knowledge contained in biological ontologies. However, current semantic tools still need to adapt to this more expressive information. In this article, we propose a method to integrate disjointness axioms, which are being incorporated in real-world ontologies, such as the Gene Ontology and the chemical entities of biological interest ontology, into semantic similarity, the measure that estimates the closeness in meaning between classes. Results: We present a modification of the measure of shared information content, which extends the base measure to allow the incorporation of disjointness information. To evaluate our approach, we applied it to several randomly selected datasets extracted from the chemical entities of biological interest ontology. In 93.8% of these datasets, our measure performed better than the base measure of shared information content. This supports the idea that semantic similarity is more accurate if it extends beyond the hierarchy of classes of the ontology. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Creating shared value in Rock in Rio business model: case study

This discourse will attempt to discuss `Creation of Shared Value' (CSV) through the case study of the music festival "Rock in Rio" (RIR) in order to further understand the company's sustainability program. The main goal is to clearly recognize if RIR uses a genuine practice of CSV to accomplish their social policies. To commence, we started with the State of Art, studying the CSV theory created by Porter and Kramer, as well as the authors that were either in support of, or against, the strategy. Qualitative Research Method was used, thus focusing the enterprise case study, by analysing media interviews given by the managerial staff of RIR. Content analysis was used to process data and deliver results. The main limitation of the study was the lack of institutional information, due to an absence of responses, to the survey in sufficient time by RIR's managers, subsequently a triangulation of the information acquired could not be achieved.info:eu-repo/semantics/acceptedVersio

Parallelizing superFine

The estimation of the Tree of Life, a rooted binary tree representing how all extant species evolved from a common ancestor, is one of the grand challenges of modern biology. Research groups around the world are attempting to estimate evolutionary trees on particular sets of species (typically clades, or rooted subtrees), in the hope that a final "supertree" can be produced from these smaller estimated trees through the addition of a "scaffold" tree of randomly sampled taxa from the tree of life. However, supertree estimation is itself a computationally challenging problem, because the most accurate trees are produced by running heuristics for NP-hard problems. In this paper we report on a study in which we parallelize SuperFine, the currently most accurate and efficient supertree estimation method. We explore performance of these parallel implementations on simulated data-sets with 1000 taxa and biological data-sets with up to 2,228 taxa. Our study reveals aspects of SuperFine that limit the speed-ups that are possible through the type of outer-loop parallelism we exploit.(undefined

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources

BACKGROUND: Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic annotation of epidemiology resources is a cornerstone to effectively support such activities. Although several ontologies cover some of the subdomains of epidemiology, we identified a lack of semantic resources for epidemiology-specific terms. This paper addresses this need by proposing the Epidemiology Ontology (EPO) and by describing its integration with other related ontologies into a semantic enabled platform for sharing epidemiology resources. RESULTS: The EPO follows the OBO Foundry guidelines and uses the Basic Formal Ontology (BFO) as an upper ontology. The first version of EPO models several epidemiology and demography parameters as well as transmission of infection processes, participants and related procedures. It currently has nearly 200 classes and is designed to support the semantic annotation of epidemiology resources and data integration, as well as information retrieval and knowledge discovery activities. CONCLUSIONS: EPO is under active development and is freely available at https://code.google.com/p/epidemiology-ontology/. We believe that the annotation of epidemiology resources with EPO will help researchers to gain a better understanding of global epidemiological events by enhancing data integration and sharing

Colonization of rice and Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae) larvae by genetically modified endophytic Methylobacterium mesophilicum

The colonization of Spodoptera frugiperda J.E. Smith larvae and rice seedlings by genetically modified endophytic bacterium Methylobacterium mesophilicum, and also the possible transfer of this bacterium to inside the larva's body during seedlings consumption were studied. The data obtained by bacterial reisolation and fluorescence microscopy showed that the bacterium colonized the rice seedlings, the larva's body and that the endophytic bacteria present in seedlings could be acquired by the larvae. In that way, the transference of endophytic bacterium from plants to insect can be a new and important strategy to insect control using engineered microorganisms.CNPq National Council of Researc

An Evaluation System for University-Industry Partnership Sustainability: Enhancing Options for Entrepreneurial Universities

The concept of university–industry partnership sustainability (UIPS) stands for well-adjusted progress among key players from universities and industry by sustaining their welfare, both in the present and in the future. This paper sought to develop an evaluation system for UIPS. The need for such a system is justified at three levels: the micro level (i.e., research and innovation performance, transfer and absorptive capability, and technology development), the meso level (i.e., institutional arrangements, communication networks, and local and indigenous rules) and the macro level (i.e., supply and demand, regulations, financing, taxes, culture, traditions, market, climate, politics, demographics, and technology). The UIPS evaluation system developed in this study offers the possibility of calculating a fair value of UIPS and providing recommendations for improving university–industry (U–I) partnerships. This can be of great importance for entrepreneurial universities that would like to strengthen their corporate links and/or reduce/reverse the “hollowing effect” of globalisation in disadvantaged regions. Additionally, this paper also contains discussions on the advantages, limitations, and managerial implications of this proposal.info:eu-repo/semantics/publishedVersio

Prescription and Effects of Cardiorespiratory Training in Individuals with Intellectual Disability: a Systematic Review

This study aims to systematize effects of cardiorespiratory training (CT) programs in individuals with intellectual disability (ID) and identifying the fundamental and structuring aspects for the prescription of CT. This systematic review was carried out through four databases (Pubmed, Web of Science, Scopus, and SPORTDiscus), considering data from the period between 2013 and 2022. From 257 studies, 12 studies were included in this systematic review. Three studies used interval CT, while seven used continuous CT. Seven were carried out in the population with Down syndrome, while only three were carried out with participants with ID. The CT programs had the following characteristics: duration of 8 to 12 weeks, weekly frequency of three sessions, for 20 to 60 min, the intensity of 50% to 80% of maximal heart rate or 70% to 80% of peak oxygen consumption, using an ergometer cycle or an outdoor walking. The studies reported improvements in cardiorespiratory function, lipid, hemodynamic and metabolic profile, body composition, and neuromuscular and cognitive capacity. This review presents characteristics and recommendations that technicians can follow when structuring, prescribing, and implementing CT programs to individuals with ID.info:eu-repo/semantics/publishedVersio

Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products

Accurate detection and quantification of microbiological contaminations remains an issue mainly due the lack of rapid and precise analytical techniques. Standard methods are expensive and time-consuming being associated to high economic losses and public health threats. In the context of pharmaceutical industry, the development of fast analytical techniques able to overcome these limitations is crucial and spectroscopic techniques might constitute a reliable alternative. In this work we proved the ability of Fourier transform near infrared spectroscopy (FT-NIRS) to detect and quantify bacteria (Bacillus subtilis, Escherichia coli, Pseudomonas fluorescens, Salmonella enterica, Staphylococcus epidermidis) from 10-108 CFUs/mL in sterile saline solutions (NaCl 0.9%). Partial least squares discriminant analysis (PLSDA) models showed that FT-NIRS was able to discriminate between sterile and contaminated solutions for all bacteria as well as to identify contaminant bacteria. Partial least squares (PLS) models allowed bacterial quantification with limits of detection ranging from 5.1 to 9CFU/mL for E. coli and B. subtilis, respectively. This methodology was successfully validated in three pharmaceutical preparations (contact lens solution, cough syrup and topic anti-inflammatory solution) proving that this technique possess a high potential to be routinely used for the detection and quantification of bacterial contaminations.This work was funded by Fundacao para a Ciencia e a Tecnologia (FCT) under the project UID/QUI/50006/2013. The authors also thank the FCT Strategic Project of UID/BIO/04469/2013 unit, the project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and the project "BioInd-Biotechnology and Bioengineering for improved Industrial and Agro-Food processes", REF. NORTE-07-0124-FEDER-000028 co-funded by the Programa Operacional Regional do Norte (ON. 2-O Novo Norte), QREN, FEDER. Daniela Mesquita (SFRH/BPD/82558/2011) and Cristina Quintelas were funded by post-doctoral grants from FCT and ON.2. Clara Sousa was funded by a CIENCIA2008 contract from FCT

Creation of a vehicular delay-tolerant network prototype

Vehicular Delay-Tolerant Network (VDTN) is a new disruptive network architecture where vehicles act as the communication infrastructure. VDTN follows a layered architecture based on control and data planes separation, and positioning the bundle layer under the network layer. VDTN furnishes low-cost asynchronous communications coping with intermittent and sparse connectivity, variable delays and even no end-to-end connection. This paper presents a VDTN prototype (testbed) proposal, which implements and validates the VDTN layered architecture considering the proposed out-of-band signaling. The main goals of the prototype are emulation, demonstration, performance evaluation, and diagnose of protocol stacks and services, proving the applicability of VDTNs over a wide range of environments.Part of this work has been supported by the Instituto de Telecomunicações, Next Generation Networks and Applications Group (NetGNA), Covilhã Delegation, Portugal in the framework of the VDTN@Lab Project, and by the Euro-NF Network of Excellence from the Seventh Framework Programme of EU