Design of Machine Learning Models for the Prediction of Transcription Factor Binding Regions in Bacterial DNA

Presented at the 4th XoveTIC Conference, A Coruña, Spain, 7–8 October 2021.[Abstract] Transcription Factors (TFs) are proteins that regulate the expression of genes by binding to their promoter regions. There is great interest in understanding in which regions TFs will bind to the DNA sequence of an organism and the possible genetic implications that this entails. Occasionally, the sequence patterns (motifs) that a TF binds are not well defined. In this work, machine learning (ML) models were applied to TF binding data from ChIP-seq experiments. The objective was to detect patterns in TF binding regions that involved structural (DNAShapeR) and compositional (kmers) characteristics of the DNA sequence. After the application of random forest and Glmnet ML techniques with both internal and external validation, it was observed that two types of generated descriptors (HelT and tetramers) were significantly better than the others in terms of prediction, achieving values of more than 90%.This work has received financial support from the Xunta de Galicia and the European Union (European Social Fund (ESF)). This project was also supported by the General Directorate of Culture, Education and University Management of Xunta de Galicia (Ref. ED431G/01, ED431D 2017/16).Xunta de Galicia; ED431G/01Xunta de Galicia; ED431D 2017/1

First order formulation of unimodular gravity

First order Lagrangians for the Weyl invariant formulation of unimodular gravity are proposed. Several alternatives are examined; in some of them, first and second order are equivalent in a certain gauge onlyThis work has been partially supported by the European Union FP7 ITN INVISIBLES (Marie Curie Actions, PITN- GA-2011- 289442) and (HPRN-CT-200-00148), COST action MP1405 (Quantum Structure of Spacetime), COST action MP1210 (The String Theory Universe) as well as by FPA2012-31880 (MINECO, Spain) and S2009ESP-1473 (CA Madrid). The authors acknowledge the support of the Spanish MINECO Centro de Excelencia Severo Ochoa Programme under grant SEV-2012-024

HIV-1 and Alzheimer: a real conection?

La infección por el virus de inmunodeficiencia humana (VIH) causa alteraciones neurológicas que son más graves y frecuentes como consecuenia del envejecimieno de la población. Este daño se asocia a la disfunción neuronal, que patológicamente se caracteriza como una pérdida de sinapsis, acortamiento de neuritas, anormalidades dendríticas, así comon pérdida neuronal. A este respecto, varios estudios han observado un aumento significativo de placas amiloides en cerebros de individuos infectados por el VIH en comparación con controles sanos, así como en individuos VIH positivos que habían estado expuestos a la terapia antirretroviral. En este trabajo se ha investigado el efecto de la combinación del péptido β-amiloide e infección por VIH-1 en diferentes células del sistema nervioso. El pretratamiento de las células gliales y neuronales provoca un incremento en la replicación viral, así como el tratamiento combinado virus y formas de oligómeros y fibrillas producen un incremento en las especies reactivas de oxígeno y de la forma activa de la enzima proapoptótica caspasa-3, en astrocitos. Lo que podría traducirse como un incremento de neurotoxicidad y depositos de β-amiloide en el cerebro infectado.Infection by human immunodeficiency virus (HIV) promotes neurological alterations which are more severe and frequents, due to the aging of the population. This dementia is associated to neuronal disfunction, and is pathologicaly characterized as sinapse lose, dendritic abnormalities and neuronal death. Supporting this, several studies have shown a significant increase of the amyloid plaques in infected HIV brains compared to healthy controls as well as HIV positive individuals which were exposed to antiretroviral therapy. In the present study we have investigated the combined effect of amyloid-β and HIV-1 infection in diferent nervous cells. When we pretreated glial cells and neurons we found an increased viral replication, as well as the combined treatment of HIV and oligomeric and fibrils forms of amyloid-β which produce glial increased levels of oxygen reactive species and the proapoptotic enzyme caspase-3. These observations could be traduced in an increased neurotoxicity and amyloid-β deposits in infected brains

Aplicación del análisis dedrocronológico de Retama sphaerocarpa L. (Boiss) para datar el abandono agrícola

Abandonment of agricultural land leads to changes in soil characteristics that may result in better or worse soil conditions. These changes are slow therefore the use of indicators for dating the time of abandonment is particularly useful. This study was carried out in Madrid, Spain with the aim to establish for the first time the use of Retama sphaerocarpa L. (Boiss) as a dendrochronological tool for dating land abandonment. This offers the possibility to take into consideration a period of time long enough for changes in soil to be determined. Such changes can be indicated by fluctuations in soil organic carbon content (SOC), porosity or water availability. Three different situations resulted from the dendrochronological analysis: soil currently tilled; soil recently abandoned (less than 5 years), and prolonged abandonment (in average 10 years). In addition the influence of Retama sphaerocarpa L. (Boiss) on soils was checked for these periods of abandonment. The rate of SOC gain can be considered fast. Tilled soils accounted for 0.48% SOC, and reached 1% in less than 5 years, although with wide standard deviations. Due to prolonged abandonment SOC reached 1.41%, (P = 0.09). Total soil porosity under tillage was 49%, and decreased to 38% after 4-5 years, but recovered to 41% under prolonged abandonment. Water availability (volumetric soil moisture between field capacity and permanent wilting point) remained the same, ranging from 7.7 to 8.5% along the whole period of time. The presence of R. sphaerocarpa L. (Boiss) accelerates soil changes as SOC in prolonged abandonment increased to 2.65%, porosity was 41% and water availability 10.3

Osteoblastoma del sacro. A propósito de dos casos clínicos.

El osteoblastoma es un tumor óseo primitivo de frecuente localización en los elementos posteriores de la columna vertebral, aunque raro en el sacro. Se presentan dos osteoblastomas del sacro, con un seguimiento medio de ocho años, tratados mediante resección intralesional que, sin morbilidad, deparó un excelente resultado. El curetaje sería un procedimiento de resección válido en osteoblastomas sacros no agresivos, si bien obliga a un seguimiento prolongado del paciente para vigilar la posibilidad de recidivas locales.Osteoblastoma is a primary neoplasm of bone fre- quently located in the posterior elements of the spine, alt- hough rarely affecting the sacrum. Two cases in this location are reported, with a mean follow-up of eight years, treated with an intralesional resection that, without any morbidity, has provided an excellent result. Curettage should be a valid re- section procedure for nonagressive osteoblastomas of the sacrum, although it makes necessary a long follow-up in or- der to watch over the possibility of a local recurrence

Use of Multiple Astrocytic Configurations within an Artificial Neuro-Astrocytic Network

[Abstract] The artificial neural networks used in a multitude of fields are achieving good results. However, these systems are inspired in the vision of classical neuroscience where neurons are the only elements that process information in the brain. Advances in neuroscience have shown that there is a type of glial cell called astrocytes that collaborate with neurons to process information. In this work, a connectionist system formed by neurons and artificial astrocytes is presented. The astrocytes can have different configurations to achieve a biologically more realistic behaviour. This work indicates that the use of different artificial astrocytes behaviours is beneficial.Xunta de Galicia; ED431G/01Xunta de Galicia; ED431D 2017/16Xunta de Galicia; ED431D 2017/23Ministerio de Economía y Competitividad; UNLC08-1E-002Ministerio de Economía y Competitividad; UNLC13-13-350

Influence of relative humidity on the carbonation of calcium hydroxide nanoparticles and the formation of calcium carbonate polymorphs

A consolidating product based on nanoparticles of slaked lime (Ca(OH)2) dispersed in isopropyl alcohol was exposed under different relative humidities (RH), 33%, 54%, 75% and 90% during 7, 14, 21 and 28days. The characterization of the calcium hydroxide nanoparticles and the formed calcium carbonate polymorphs have been performed by Micro Raman spectroscopy, Transmission Electron Microscopy (TEM), Environmental Scanning Electron Microscopy (ESEM) with Energy Dispersive X-ray Spectroscopy (EDS) and X-ray Diffraction (XRD). Precipitation and transformation of calcium carbonate polymorphs strongly depend on the relative humidity (RH). Higher RH (75%-90% RH) gives rise to amorphous calcium carbonate and monohydrocalcite, calcite, aragonite and vaterite, faster carbonation and larger particles sizes with higher crystallinity compared to lower RH (33%-54% RH) that gives rise mainly to portlandite and vaterite, slower carbonation and smaller particle sizes with lower crystallinity. © 2010 Elsevier B.V.This study was funded by the Government of the Community of Madrid by GEOMATERIALES (S2009/MAT-1629) and CONSOLIDERTCP (CSD2007-0058) and to the JAE-Doc CSIC contracts for supporting P. López-Arce and L.S. Gómez-Villalba to develop this work.Peer Reviewe

Análisis exergético de escenarios integrados de producción de etanol y otros productos a partir de la caña de azúcar

Se realiza el análisis exergético de seis escenarios parala producción conjunta de alcohol y otros productos derivados de la caña de azúcar, con el objetivo de identificar y localizar las principales fuentes generadoras de irreversibilidades en estos esquemas. En los esquemas integrados se considera la caña de azúcar como materia prima principal para la generación de productos y coproductos. Los seis escenarios de integración evaluados incluyen la producción de azúcar, alcohol de primera y segunda generación y coproductos tales como: furfural y lignina, la obtención de levadura torula y la recuperacióndel CO2. Se realizaron los balances de masa y energía para cada proceso, determinando los flujos de las corrientes que intervienen en el análisis exergético. Para el análisis exergético el esquema integrado fue dividido en diez subsistemas. Los subsistemas extracción de jugo, cristalización y cocción, fermentación y destilación resultaron los mayores generadores de pérdidas exergéticas. Para los primeros cinco escenarios la eficiencia exergética total se encuentra entre 71-80% y para el escenario de tiempo de no zafra en un 59%

Validation of an Aesthetic Assessment System for Commercial Tasks

[Abstract] Automatic prediction of the aesthetic value of images has received increasing attention in recent years. This is due, on the one hand, to the potential impact that predicting the aesthetic value has on practical applications. Even so, it remains a difficult task given the subjectivity and complexity of the problem. An image aesthetics assessment system was developed in recent years by our research group. In this work, its potential to be applied in commercial tasks is tested. With this objective, a set of three portals and three real estate agencies in Spain were taken as case studies. Images of their websites were taken to build the experimental dataset and a validation method was developed to test their original order with another proposed one according to their aesthetic value. So, in this new order, the images that have the high aesthetic score by the AI system will occupy the first positions of the portal. Relevant results were obtained, with an average increase of 52.54% in the number of clicks on the ads, in the experiment with Real Estate portals. A statistical analysis prove that there is a significant difference in the number of clicks after selecting the images with the AI system.This work is supported by the General Directorate of Culture, Education and University Management of Xunta de Galicia (Ref. ED431D 201716), Competitive Reference Groups (Ref. ED431C 201849) and Ministry of Science and Innovation project Society challenges (Ref. PID2020-118362RB-I00). We also wish to acknowledge the support received from the Centro de Investigación de Galicia “CITIC”, funded by Xunta de Galicia and the European Union (European Regional Development Fund- Galicia 2014-2020 Program), by grant ED431G 2019/01Xunta de Galicia; ED431D 201716Xunta de Galicia; ED431C 201849Xunta de Galicia; ED431G 2019/0

First Multiplatform Application for Pharmacies in Spain, Which Guides the Prescription of Probiotics According to Pathology

[Abstract] The study of the intestinal microbiota is one of the biggest challenges in the current clinical environment. In this context, probiotics have been a focus of interest to achieve the stability of the intestinal microbiota, due to probiotics’ key role in its regulation. The development of an automated system that allows practitioners to easily search for the optimal probiotic is the main objective of this study. Although it is true that there have been previous attempts of applications with this purpose, only authorized probiotics available in the countries of origin, Canada and the USA, were included. This event was a limitation when looking for those endorsed in other countries such as Spain. Thus, a system has been developed from free and multiplatform technologies that allow its use without any cost, finding, in a simple way, those probiotics that would be ideal for each pathology, either from a browser or from a cell phone.This work was supported by the “Collaborative Project in Genomic Data Integration (CICLOGEN)” PI17/01826 funded by the Carlos III Health Institute from the Spanish National plan for Scientific and Technical Research and Innovation 2013–2016, the European Regional Development Funds (ERDF)—“A way to build Europe.”, the General Directorate of Culture, Education and University Management of Xunta de Galicia (Ref. ED431D 2017/16), the “Galician Network for Colorectal Cancer Research” (Ref. ED431D 2017/23) and Competitive Reference Groups (Ref. ED431C 2018/49). The funding body did not have a role in the experimental design, data collection, analysis and interpretation, and writing of this manuscript. CITIC, as a Research Center accredited by Galician University System, is funded by “Consellería de Cultura, Educación e Universidades” of Xunta de Galicia, 80% co-financed by the ERDF Funds, ERDF Operational Programme Galicia 2014-2020, and the remaining 20% by “Secretaría Xeral de Universidades” (Grant ED431G 2019/01)Xunta de Galicia; ED431D 2017/16Xunta de Galicia; ED431D 2017/23Xunta de Galicia; ED431C 2018/49Xunta de Galicia; ED431G 2019/0