Graph Kernels and Applications in Bioinformatics

In recent years, machine learning has emerged as an important discipline. However, despite the popularity of machine learning techniques, data in the form of discrete structures are not fully exploited. For example, when data appear as graphs, the common choice is the transformation of such structures into feature vectors. This procedure, though convenient, does not always effectively capture topological relationships inherent to the data; therefore, the power of the learning process may be insufficient. In this context, the use of kernel functions for graphs arises as an attractive way to deal with such structured objects. On the other hand, several entities in computational biology applications, such as gene products or proteins, may be naturally represented by graphs. Hence, the demanding need for algorithms that can deal with structured data poses the question of whether the use of kernels for graphs can outperform existing methods to solve specific computational biology problems. In this dissertation, we address the challenges involved in solving two specific problems in computational biology, in which the data are represented by graphs. First, we propose a novel approach for protein function prediction by modeling proteins as graphs. For each of the vertices in a protein graph, we propose the calculation of evolutionary profiles, which are derived from multiple sequence alignments from the amino acid residues within each vertex. We then use a shortest path graph kernel in conjunction with a support vector machine to predict protein function. We evaluate our approach under two instances of protein function prediction, namely, the discrimination of proteins as enzymes, and the recognition of DNA binding proteins. In both cases, our proposed approach achieves better prediction performance than existing methods. Second, we propose two novel semantic similarity measures for proteins based on the gene ontology. The first measure directly works on the gene ontology by combining the pairwise semantic similarity scores between sets of annotating terms for a pair of input proteins. The second measure estimates protein semantic similarity using a shortest path graph kernel to take advantage of the rich semantic knowledge contained within ontologies. Our comparison with other methods shows that our proposed semantic similarity measures are highly competitive and the latter one outperforms state-of-the-art methods. Furthermore, our two methods are intrinsic to the gene ontology, in the sense that they do not rely on external sources to calculate similarities

Development of Novel Methods for Characterization of Complex Organic Mixtures By Liquid Chromatography and Raman Spectroscopy

ABSTRACT DEVELOPMENT OF NOVEL METHODS FOR CHARACTERIZATION OF COMPLEX ORGANIC MIXTURES BY LIQUID CHROMATOGRAPHY AND RAMAN SPECTROSCOPY by Veronica Marco Alvarez The University of Wisconsin-Milwaukee, 2014 Under the Supervision of Professor Joseph H. Aldstadt III The development of methods for the study of Humic Acids (HAs) and related substances is described. In the first part, a reversed-phase liquid chromatography (RP-LC) instrument was designed, fabricated, and a method for the separation of HAs was optimized for application as the second dimension in a two-dimensional LC (LCxLC) system. The optimized method for the RP-LC was used in the study of amino acid mixtures and HA standard solutions. The RP-LC used a monolithic disk in which the stationary phase was composed of butyl (C4) functional groups. The method had the following conditions: 100 µL injection volume, 1.0 mL/min flow rate, 30:70 acetonitrile:water (pH = 7.00) mobile phase, and fluorescence detection (λex = 257 nm, λex = 310 nm). Several HA fractions from solid-phase extraction separations were examined as a means to simplify the HA standard and their spectra were compared to the characteristic peaks found for HAs in the literature. The next step in this work is to integrate the RP-LC method into the LCxLC system. In the second part of this thesis, the characterization of two natural varnishes -- Linseed Oil and Chinawood Oil-- was studied by accelerated ageing experiments and Fourier Transform Raman Spectroscopy (FT Raman). An ageing chamber designed in our group for a previous investigation was modified to perform the ageing experiments. Two factors were studied over a range of time periods: heat and ultraviolet light. Thermal studies were conducted from 25ᵒC to 210ᵒC while the time periods ranged from 2 to 170 hr. A direct correlation was found between the changes in the vibrational bands that were observed in the FT Raman spectra and the observation of overt physical changes in the samples. Based upon these data, several reaction mechanisms for the decomposition of the varnishes were proposed. The FT Raman method may also be applied in the future to fractions collected from the LCxLC system for a more detailed off-line characterization of the molecular structures that are present

Genomic organization of nucleolin gene in carp fish: Evidence for several genes

http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602006000200017&lng=es&nrm=isoThe protein nucleolin, functionally involved in the main steps of ribosome biogenesis, is codified by a single copy gene in mammals. Here we report that at least three different genes codify for this protein in carp fish (Cyprinus carpio). This is the first description of the genomic organization of nucleolin in a teleost. The carp nucleolin gene includes 8.8 kb and contains 16 exons. Promoter cis regulatory elements are similar to constitutive genes, i.e., a putative TATA box, three G/C boxes, and three pyrimidine-rich boxes. As in other species, carp nucleolin gene introns host three snoRNA codifying sequences: U23 from the H/ACA family and two C/D box snoRNAs, U20 and U82. Both U20 and U82 span a complementary sequence with carp 18S rRNA. Additionally, we identified two cDNAs coding for nucleolin, confirming the existence of several nucleolin genes in carp. Amino acidderived sequence from carp cDNAs differ from mammal protein because they span additional acidic domains at the amino end, whose functional significance remains unclear. We performed amino acid sequence comparison and phylogenetic analyses showing that the three isoforms of carp nucleolin, which we describe herein, cluster in two groups. cNUC1 probably diverges from cNUC2 and cNUC3 as result of ancestral fish-specific genome duplication, indeed C. carpio is a tetraploid fish

The ventrolateral hypothalamic area and the parvafox nucleus: Role in the expression of (positive) emotions?

The lateral hypothalamus has been long suspected of triggering the expression of positive emotions, because stimulations of its tuberal portion provoke bursts of laughter. Electrophysiological studies in various species have indeed confirmed that the lateral hypothalamus contributes to reward mechanisms. However, only the rudiments of the neural circuit underlying the expression of positive emotions are known. The prefrontal cortex, the lateral hypothalamus, and the periaqueductal gray matter (PAG) are involved in these circuits; so, too, are the brainstem nuclei that control the laryngeal muscles and subserve mimicry, as well as the cardiovascular and respiratory systems. The implicated populations of hypothalamic neurons have not been defined either anatomically or molecularly. One promising candidate is the novel parvafox nucleus, which we recently described, in the murine medial forebrain bundle (mfb), which specifically expresses parvalbumin and Foxb1. With the molecularly defined parvafox nucleus as a centerpiece, the inputs from the prefrontal cortex and the projections to the PAG and brainstem can be studied with precision. By drawing on genetic approaches, it will be possible to manipulate the circuitry selectively with spatial and temporal exactitude and to evaluate the concomitant autonomic changes. These data will serve as a basis for imaging studies in humans using various paradigms to provoke the expression of positive emotions. In conclusion, studies of the hypothalamic parvafox nucleus will reveal whether this entity represents the fulcrum for positive emotions, as is the amygdala for fear and the insula for disgust

Anomalies and inflow on D-branes and O-planes

We derive the general form of the anomaly for chiral spinors and self-dual antisymmetric tensors living on D-brane and O-plane interesections, using both path-integral and index theorem methods. We then show that the anomalous couplings to RR forms of D-branes and O-planes in a general background are precisely those required to cancel these anomalies through the inflow mechanism. This allows, for instance, for local anomaly cancellation in generic orientifold models, the relevant Green-Schwarz term being given by the sum of the anomalous couplings of all the D-branes and O-planes in the model.Comment: 24 pages, LaTex file, no figure

Ethics and Aesthetics for Enhancing Design and Transforming Social Reality

Design is preponderant in the world economy; it allows competition and enhances the development of innovations in the market. The expansion of product offerings provides options to satisfy the user’s needs, which is an undeniable advance driven by design. However, this has led to a significant increase in the production of solid waste related to design, which generates environmental deterioration. Additionally, the supply of design products has been concentrated in the most economically favored sector, leaving out a large part of the world’s population which are not met because they are not a market of interest for the productive industry in general. The content of this paper is the result of a collective debate from the authors, based on the analysis of documentary sources and their own experience as academics. Our objective is to encourage discussion for the creation of a common front oriented towards a design practice focused simultaneously on social development and environmental care; a design practice based on ethics and commitment to the environment and society

The antiviral potential of algal lectins

Algae have emerged as fascinating subjects of study due to their vast potential as sources of valuable metabolites with diverse biotechnological applications, including their use as fertilizers, feed, food, and even pharmaceutical precursors. Among the numerous compounds found in algae, lectins have garnered special attention for their unique structures and carbohydrate specificities, distinguishing them from lectins derived from other sources. Here, a comprehensive overview of the latest scientific and technological advancements in the realm of algal lectins with a particular focus on their antiviral properties is provided. These lectins have displayed remarkable effectiveness against a wide range of viruses, thereby holding great promise for various antiviral applications. It is worth noting that several alga species have already been successfully commercialized for their antiviral potential. However, the discovery of a diverse array of lectins with potent antiviral capabilities suggests that the field holds immense untapped potential for further expansion. In conclusion, algae stand as a valuable and versatile resource, and their lectins offer an exciting avenue for developing novel antiviral agents, which may lead to the development of cutting-edge antiviral therapies.info:eu-repo/semantics/publishedVersio