Semantic Similarity for Automatic Classification of Chemical Compounds

With the increasing amount of data made available in the chemical field, there is a strong need for systems capable of comparing and classifying chemical compounds in an efficient and effective way. The best approaches existing today are based on the structure-activity relationship premise, which states that biological activity of a molecule is strongly related to its structural or physicochemical properties. This work presents a novel approach to the automatic classification of chemical compounds by integrating semantic similarity with existing structural comparison methods. Our approach was assessed based on the Matthews Correlation Coefficient for the prediction, and achieved values of 0.810 when used as a prediction of blood-brain barrier permeability, 0.694 for P-glycoprotein substrate, and 0.673 for estrogen receptor binding activity. These results expose a significant improvement over the currently existing methods, whose best performances were 0.628, 0.591, and 0.647 respectively. It was demonstrated that the integration of semantic similarity is a feasible and effective way to improve existing chemical compound classification systems. Among other possible uses, this tool helps the study of the evolution of metabolic pathways, the study of the correlation of metabolic networks with properties of those networks, or the improvement of ontologies that represent chemical information

Anticholinesterase and Antioxidant Activities of Spilanthes filicaulis Whole Plant Extracts for the Management of Alzheimer’s Disease

Background: Spilanthes filicaulis is a tropical herb implicated as a memory enhancer in ethnomedicine. Objective: The study investigated acetyl/butyryl cholinesterase inhibitory and antioxidant activities of different extracts of S. filicaulis whole plant and correlated them to its phytochemical constituents. Methods: The powdered whole plant was successively extracted with n-hexane, ethyl acetate and methanol. Acetyl cholinesterase (AChE) and Butyryl cholinesterase (BuChE) inhibitory activity were evaluated by Ellman colorimetry assay. Antioxidant activity was tested using 1, 1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, ferric reducing power and nitric oxide scavenging assays. Total phenolic, flavonoid and tannin were estimated using standard methods. Correlation was determined using Quest Graph™ Regression Calculator. Results: Various extracts exhibited concentration-dependent AChE and BuChE inhibitory activity with ethyl acetate extract being the highest with IC50 of 0.77 μg/mL and 0.92 μg/mL for AChE and BuChE respectively. The ethyl acetate extract also showed the highest reducing power when compared with the other extracts. The methanol extract had slightly higher phenolic and flavonoid content and showed the highest DPPH radical scavenging effect. DPPH scavenging, AChE and BuChE inhibition had high correlation with the total flavonoid content with R2 values of 1.00, 0.800 and 0.992 respectively while nitric oxide scavenging had high correlation with phenolics and tannins with R2 = 0.942 and 0.806 respectively. Conclusion: These results show that the extracts of the whole plant of S. filicaulis possess significant AChE/BuChE inhibitory and antioxidant properties, mostly due to its flavonoid content, suggesting the possible use of the plant in neurodegenerative diseases such as AD

Effects of Yeast Enzymatic Hydrolyzate on in vitro Fermentation of Low Quality Tropical Forages

Trabajo presentado al 2nd World Conference on Innovative Animal Nutrition and Feeding . (October 18-20, 2017. Budapest, Hungary).Peer Reviewe

Nitrogen metabolism of diets differing in forage type and forage to concentrate ratio in sheep and goats

2 páginas.-- Energy and protein metabolism and nutrition. 3rd EAAP International Symposium on Energy and Protein Metabolism and Nutrition (Parma, Italy, 6-10 September, 2010).--EAAP Publication No. 127The aim of this study was to compare the nitrogen (N) utilization in sheep and goats fed 4 medium-good quality diets at similar levels of intake. The diet ingredients were selected to represent those most frequently used under practical feeding conditions of both animal species in Spain. Four rumen-fistulated Granadina goats and 4 Merino sheep were used in 4 experimental periods. Four total mixed diets were formulated according to a 2 × 2 factorial arrangement of treatments. The diets had forage:concentrate (FC; dry matter (DM) basis) ratios of 70:30 (H) or 30:70 (L) with either lucerne hay (A) or grass hay (G) as forage and were designated as HA, LA, HG and LG. Nitrogen contents were 26.9, 28.3, 19.4 and 25.6 g/kg DM and neutral detergent fibre contents were 426, 374, 499 and 401 g/kg DM for the HA, LA, HG and LG diets, respectively. No difference was observed between animal species (AS) in N intake. The percentage of N intake excreted in urine was higher in goats than in sheep, but the percentage of N intake in faeces was lower in goats compared with sheep. Protein digestibility was greater in goats than in sheep, which was consistent with the greater ammonia nitrogen (NH3-N) concentrations observed in the rumen of goats. A significant AS × FC interaction was detected for N digestibility and ruminal NH3-N concentrations, but there were no AS × type or forage (FOR) interactions for any parameter. Goats showed lower N retention than sheep for all diets either expressed in absolute terms (g/day) or as g per kg of digestible organic matter intake (DOMI). These results indicated different N utilization in goats and sheep with similar N intakes. The interspecies differences in N digestibility and ruminal ammonia concentrations seemed to be modulated by the composition of the diet.Peer reviewe

An efficient and scalable block parallel algorithm of Neville elimination as a tool for the CMB maps problem

Abstract This paper analyses the performance of several versions of a block parallel algorithm in order to apply Neville elimination in a distributed memory parallel computer. Neville elimination is a procedure to transform a square matrix A into an upper triangular one. This analysis must take into account the algorithm behaviour as far as execution time, efficiency and scalability are concerned. Special attention has been paid to the study of the scalability of the algorithms trying to establish the relationship existing between the size of the block and the performance obtained in this metric. It is important to emphasize the high efficiency achieved in the studied cases and that the experimental results confirm the theoretical approximation. Therefore, we have obtained a high predicting ability tool of analysis. Finally, we will present the elimination of Neville as an efficient tool in detecting point sources in cosmic microwave background maps.© Springer Science+Business Media, LLC 2010This work has been partially supported by the Spanish Research Grants TIN2007-61273, TIN2008-06570-C04-02 and TIN2010-14971, and by Valencia Regional Government Grant PRO-METEO/2009/013. Also, we would like to give special thanks to Professor Francisco Argueso of University of Oviedo for his help.Alonso, P.; Cortina, R.; Ranilla, J.; Vidal Maciá, AM. (2012). An efficient and scalable block parallel algorithm of Neville elimination as a tool for the CMB maps problem. Journal of Mathematical Chemistry. 50(2):345-358. https://doi.org/10.1007/s10910-010-9769-0S345358502Alonso P., Cortina R., Díaz I., Ranilla J.: Analyzing scalability of Neville elimination. J. Math. Chem. 40(1), 49 (2006)Alonso P., Cortina R., Díaz I., Ranilla J.: Scalability of Neville elimination using checkerboard partitioning. Int. J. Comput. Math. 85(3–4), 309 (2008)Alonso P., Cortina R., Díaz I., Ranilla J.: Blocking Neville elimination algorithm for exploiting cache memories. Appl. Math. Comput. 209, 2 (2009)Ando T.: Totally positive matrices. Linear Algebra Appl. 90, 165 (1987)Gasca M., Michelli C.A.: Total Positivity and its Applications. Kluwer, Dordrecht (1996)Gasca M., Peña J.M.: Total positivity and Neville elimination. Linear Algebra Appl. 165, 25 (1992)Gemignani L.: Neville elimination for rank-structured matrices. Linear Algebra Appl. 428(4), 978 (2008)Grama A., Gupta A., Karypis G., Kumar V.: Introduction to Parallel Computing. Pearson Education Limited, London (2003)Lin H., Bao H., Wang G.: Totally positive bases and progressive iteration approximation. Comput. Math. Appl. 50, 575 (2005)Lopez-Caniego M. et al.: Comparison of filters for the detection of point sources in Planck simulations. Mon. Not. Roy. Astron. Soc. 370, 2047 (2006)Peña J.M.: Shape Preserving Representations in Computer Aided–Geometric Design. Nova Science Publishers, New York (1999)Penzias A.A., Wilson R.W.: A measurement of excess antenna temperature at 4080 Mc/s. Astrophys. J. 142, 419 (1965)Prieto M., Montero R.S., Llorente I.M., Tirado F.: A parallel multigrid solver for viscous flows on anisotropic structured grids. Parallel Comput. 29, 907 (2003)Smoot G. et al.: Structure in the COBE differential microwave radiometer first-year maps. Astrophys. J. 396, L1 (1992)Spergel D.N. et al.: First-year Wilkinson microwave anisotropy probe (WMAP) observations: determination of cosmological parameters. Astrophys. J. Suppl. 148, 175 (2003)J.A. Tauber, The Planck mission, in New Cosmological Data and the Values of the Fundamental Parameters. Proceedings of IAU Symposium vol. 201 (2005), p. 86, eds. by A. Lasenby, A. WilkinsonToffolatti L. et al.: Extragalactic source counts and contributions to the anisotropies of the cosmic microwave background: predictions for the Planck Surveyor mission. Mon. Not. Roy. Astron. Soc. 297, 117 (1998