Omics Data Preprocessing for Machine Learning: A Case Study in Childhood Obesity.

The use of machine learning techniques for the construction of predictive models of disease outcomes (based on omics and other types of molecular data) has gained enormous relevance in the last few years in the biomedical field. Nonetheless, the virtuosity of omics studies and machine learning tools are subject to the proper application of algorithms as well as the appropriate pre-processing and management of input omics and molecular data. Currently, many of the available approaches that use machine learning on omics data for predictive purposes make mistakes in several of the following key steps: experimental design, feature selection, data pre-processing, and algorithm selection. For this reason, we propose the current work as a guideline on how to confront the main challenges inherent to multi-omics human data. As such, a series of best practices and recommendations are also presented for each of the steps defined. In particular, the main particularities of each omics data layer, the most suitable preprocessing approaches for each source, and a compilation of best practices and tips for the study of disease development prediction using machine learning are described. Using examples of real data, we show how to address the key problems mentioned in multi-omics research (e.g., biological heterogeneity, technical noise, high dimensionality, presence of missing values, and class imbalance). Finally, we define the proposals for model improvement based on the results found, which serve as the bases for future work.

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research.

Until date, several machine learning approaches have been proposed for the dynamic modeling of temporal omics data. Although they have yielded impressive results in terms of model accuracy and predictive ability, most of these applications are based on "Black-box" algorithms and more interpretable models have been claimed by the research community. The recent eXplainable Artificial Intelligence (XAI) revolution offers a solution for this issue, were rule-based approaches are highly suitable for explanatory purposes. The further integration of the data mining process along with functional-annotation and pathway analyses is an additional way towards more explanatory and biologically soundness models. In this paper, we present a novel rule-based XAI strategy (including pre-processing, knowledge-extraction and functional validation) for finding biologically relevant sequential patterns from longitudinal human gene expression data (GED). To illustrate the performance of our pipeline, we work on in vivo temporal GED collected within the course of a long-term dietary intervention in 57 subjects with obesity (GSE77962). As validation populations, we employ three independent datasets following the same experimental design. As a result, we validate primarily extracted gene patterns and prove the goodness of our strategy for the mining of biologically relevant gene-gene temporal relations. Our whole pipeline has been gathered under open-source software and could be easily extended to other human temporal GED applications.

The AMPA receptor positive allosteric modulator S 47445 rescues in vivo CA3-CA1 long-term potentiation and structural synaptic changes in old mice.

Positive allosteric modulators of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are small molecules that decrease deactivation of AMPARs via an allosteric site. These molecules keep the receptor in an active state. Interestingly, this type of modulator has been proposed for treating cognitive decline in ageing, dementias, and Alzheimer's disease (AD). S 47445 (8-cyclopropyl-3-[2-(3-fluorophenyl)ethyl]-7,8-dihydro-3H-[1,3]oxazino[6,5-g][1,2,3]benzotriazine-4,9-dione) is a novel AMPAR positive allosteric modulator (AMPA-PAM). Here, the mechanisms by which S 47445 could improve synaptic strength and connectivity were studied and compared between young and old mice. A single oral administration of S 47445 at 10 mg/kg significantly increased long-term potentiation (LTP) in CA3-CA1 hippocampal synapses in alert young mice in comparison to control mice. Moreover, chronic treatment with S 47445 at 10 mg/kg in old alert animals significantly counteracted the deficit of LTP due to age. Accordingly, chronic treatment with S 47445 at 10 mg/kg seems to preserve synaptic cytoarchitecture in old mice as compared with young control mice. It was shown that the significant decreases in number and size of pre-synaptic buttons stained for VGlut1, and post-synaptic dendritic spines stained for spinophilin, observed in old mice were significantly prevented after chronic treatment with 10 mg/kg of S 47445. Altogether, by its different effects on LTP, VGlut1-positive particles, and spinophilin, S 47445 is able to modulate both the structure and function of hippocampal excitatory synapses known to be involved in learning and memory processes. These results open a new window for the treatment of specific age-dependent cognitive decline and dementias such as AD.

Modeling of racetrack-resonator add-drop filters with arbitrary nonlinear directional couplers.

In this Letter we employ the general coupled-mode equations of the nonlinear directional coupler and demonstrate that the switching characteristics of prototypical nonlinear racetrack-resonator structures may differ considerably from those obtained when the standard, generally incorrect, coupled-mode equations are used.

In situ photopolymerization of biomaterials by thiol-yne click chemistry.

The thiol-yne click chemistry reaction has been used for the in situ photocrosslinking of an aliphatic hyperbranched polyester. The biocompatibility of the resulting networks has been studied and marked cytotoxicity was not found for HeLa (human cervical carcinoma) tumoral cells and COS7 fibroblasts. The photoinduced thiol-yne process allows the generation of patterned structures with different geometries in films by DLW and these materials can be used as substrates for cell adhesion. The influence of the substrate geometry on cell adhesion has been studied by culturing cells onto these substrates and a preference for the photopatterned polymeric material can be seen in some of the structures by contrast phase microscopy. Actin and vinculin fluorescent staining revealed different adhesion behavior for HeLa cells and COS7 fibroblasts and this could be assigned to the different motility of cells. The thiol-yne photoreaction has proven to be an attractive approach for the preparation of micropatterned biomaterials.

Tuning first molecular hyperpolarizabilities through the use of proaromatic spacers.

In this paper, we describe the second-order nonlinear optical properties of a series of 1,3-dithiole-based electron donor-acceptor systems incorporating proaromatic donor and spacer groups. Modification of the proaromaticity of the quinoid spacer gives rise to NLO-phores with mubeta values ranging from -2000 x 10(-)(48) esu to +3000 x 10(-)(48) esu. Quite surprisingly, compounds with a p-benzoquinoid spacer and a strong acceptor group show negative mubeta values, usually associated to zwitterionic ground states, and yet they are largely quinoid, as evidenced by crystallographic data and theoretical calculations. Progressive benzoannulation of the spacer and introduction of alkylsulfanyl substituents on the dithiole donor unit result in a shift to more positive mubeta values. DFT and ab initio calculations verify these empirical trends.

Experimental and DFT studies of the conversion of ethanol and acetic acid on PtSn-based catalysts.

Reaction kinetics studies were conducted for the conversions of ethanol and acetic acid over silica-supported Pt and Pt/Sn catalysts at temperatures from 500 to 600 K. Addition of Sn to Pt catalysts inhibits the decomposition of ethanol to CO, CH4, and C2H6, such that PtSn-based catalysts are active for dehydrogenation of ethanol to acetaldehyde. Furthermore, PtSn-based catalysts are selective for the conversion of acetic acid to ethanol, acetaldehyde, and ethyl acetate, whereas Pt catalysts lead mainly to decomposition products such as CH4 and CO. These results are interpreted using density functional theory (DFT) calculations for various adsorbed species and transition states on Pt(111) and Pt3Sn(111) surfaces. The Pt3Sn alloy slab was selected for DFT studies because results from in situ (119)Sn Mössbauer spectroscopy and CO adsorption microcalorimetry of silica-supported Pt/Sn catalysts indicate that Pt-Sn alloy is the major phase present. Accordingly, results from DFT calculations show that transition-state energies for C-O and C-C bond cleavage in ethanol-derived species increase by 25-60 kJ/mol on Pt3Sn(111) compared to Pt(111), whereas energies of transition states for dehydrogenation reactions increase by only 5-10 kJ/mol. Results from DFT calculations show that transition-state energies for CH3CO-OH bond cleavage increase by only 12 kJ/mol on Pt3Sn(111) compared to Pt(111). The suppression of C-C bond cleavage in ethanol and acetic acid upon addition of Sn to Pt is also confirmed by microcalorimetric and infrared spectroscopic measurements at 300 K of the interactions of ethanol and acetic acid with Pt and PtSn on a silica support that had been silylated to remove silanol groups.

Electronic and structural effects on the nonlinear optical behavior in push-pull TTF/tricarbonyl chromiun arene complexes.

A novel D-pi-A system in which tetrathiafulvalene (TTF) and pi-extended TTFs as strong electron donors are covalently connected to a tricarbonyl (eta(6)-arene)chromium complex as the acceptor moiety through a systematically increased conjugated bridge of vinylene units (12a-c, 16a-c) have been synthesized by Wittig-Horner olefination reaction. The electronic spectra as well as the electrochemical data reveal a different behavior of TTF derivatives (12a-c) and of exTTF derivatives (16a-c). Cyclic voltammetry shows the influence of the tricarbonylchromium arene on the oxidation potentials in compounds 12a-c, and no remarkable effect is observed for exTTFs (16a-c). The nonlinear optical properties of 12a-c and 16a-c have been calculated by using the ab initio CPHF/6-31G//B3P86/6-31G model, and the time-dependent density functional theory (TD-DFT) method has been used for the calculation of the electronic transitions. The calculations reveal that an intraligand charge-transfer transition (ILCT) and the metal to ligand charge-transfer transition (MLCT) are responsible for the nonlinear response. In addition, the large angles formed by the ground-state dipole moment and the vectorial hyperpolarizability are responsible for the mubeta values determined experimentally by the EFISH technique.

Novel NLO-phores with proaromatic donor and acceptor groups.

[reaction: see text] Novel D-pi-A NLO-phores based on the 1,3-dithiol-2-ylidene donor and the thiobarbituric acceptor moieties have been prepared. Modification of the length and rigidity of the pi-spacer allows the first systematic study of the second-order nonlinear optical properties of doubly proaromatic merocyanines. The pi-electron donor efficiency of the 1,3-dithiol-2-ylidene group is superior to that of the tetrathiafulvalenyl group.

Necrosis avascular en pacientes con infección por el VIH / Avascular esteonecrosis in HIV infected patients

La necrosis avascular ósea u osteonecrosis era una rara entidad en pacientes con infección por el VIH. La incidencia de esta asociación está aumentando en los últimos años, especialmente en pacientes que reciben tratamiento antirretroviral de alta eficacia con inhibidores de la proteasa. Presentamos tres casos (dos varones y una mujer) de osteonecrosis en pacientes con infección por el VIH. En dos casos, la osteonecrosis afectó a rodillas y el tercero a la cadera. Los tres pacientes recibían tratamiento antirretroviral de alta eficacia desde hacía más de un año, en ningún caso se detectó hiperlipemia, anticuerpos antifosfolipídicos, ni ningún otro factor clásico de riesgo para la osteonecrosis. Creemos que la osteonecrosis debe ser una complicación a tener en cuenta en los pacientes con VIH especialmente aquellos con tratamiento antirretroviral de alta eficacia. (AU)