Mapping networks of anti-HIV drug cocktails vs. AIDS epidemiology in the US counties

[Abstract] The implementation of the highly active antiretroviral therapy (HAART) and the combination of anti-HIV drugs have resulted in longer survival and a better quality of life for the people infected with the virus. In this work, a method is proposed to map complex networks of AIDS prevalence in the US counties, incorporating information about the chemical structure, molecular target, organism, and results in preclinical protocols of assay for all drugs in the cocktail. Different machine learning methods were trained and validated to select the best model. The Shannon information invariants of molecular graphs for drugs, and social networks of income inequality were used as input. The nodes in molecular graphs represent atoms weighed by Pauling electronegativity values, and the links correspond to the chemical bonds. On the other hand, the nodes in the social network represent the US counties and have Gini coefficients as weights. We obtained the data about anti-HIV drugs from the ChEMBL database and the data about AIDS prevalence and Gini coefficient from the AIDSVu database of Emory University. Box–Jenkins operators were used to measure the shift with respect to average behavior of drugs from reference compounds assayed with/in a given protocol, target, or organism. To train/validate the model and predict the complex network, we needed to analyze 152,628 data points including values of AIDS prevalence in 2310 counties in the US vs. ChEMBL results for 21,582 unique drugs, 9 viral or human protein targets, 4856 protocols, and 10 possible experimental measures. The best model found was a linear discriminant analysis (LDA) with accuracy, specificity, and sensitivity above 0.80 in training and external validation series.Ministerio de Educación, Cultura y Deportes; AGL2011-30563-C03-0

DISEÑO DE ALGORITMO BASADO EN EL PROCESAMIENTO DE TERMOGRAMAS PARA RECONOCIMIENTO FACIAL EN HUMANOS QUE HAN CONSUMIDO TABACO (ALGORITHM DESIGN BASED ON THE PROCESSING OF THERMOGRAMS FOR FACIAL RECOGNITION IN HUMANS WHO HAVE USED TOBACCO)

Resumen Los sistemas de reconocimiento de personas es uno de los temas de mayor auge dentro de los sistemas de visión por computadora y principalmente aquellos que pretenden medir la forma de los patrones que son obtenidos a partir de tejidos biológicos. Sin embargo, estos patrones pueden ser modificados debido al consumo de sustancias que alteran el sistema termorregulatorio del individuo y por consecuencia afectan los porcentajes de reconocimiento de personas. En este estudio, se estudian los efectos que provoca el consumo de tabaco en un sistema de reconocimiento sin restricciones, diseñado para analizar los termogramas en una base de datos generada con individuos que consumieron cigarrillos. Se utilizó el modelo de perfusión sanguínea como método de preprocesamiento de los termogramas y el método de patrones binarios locales como método de extracción de la información capturada en los termogramas de rostro. En el experimento, los conjuntos de imágenes se representaron denotándoles como "Clase 1", el caso en el que el participante consumió 1 cigarrillo y "Clase 2 "," Clase 3 "y" Clase 4 "para los casos en los que se consumieron 2, 3 y 4 cigarros respectivamente. El método propuesto obtuvo un 75% para la “Clase 1” por lo que resulta más eficaz ante estas condiciones en comparación con las otras clases analizados porque obtuvieron porcentajes de 47% para “Clase 2”, 66% para “Clase 3” y 54% para “Clase 4”. Palabras Clave: patrones binarios locales, perfusión sanguínea, termogramas. Abstract People recognition systems is one of the most popular topics within computer vision systems and mainly those that seek to measure the shape of the patterns that are obtained from biological tissues. However, these patterns can be modified due to the consumption of substances that affect the thermoregulatory system of the individual and consequently affect the percentages of recognition of people. In this study, the effects caused by tobacco use are analyzed in an unrestricted recognition system, designed to analyze face thermograms in a database generated from individuals who consumed cigarettes. The blood perfusion model was used as the preprocessing method for the thermograms and the local binary patterns method as a method for extracting the information captured in the face thermograms. In the experiment, the sets of images were represented denoting as "Class 1", the case where the participant consumed 1 cigarette and "Class 2", "Class 3" and "Class 4" for the cases where 2, 3 and 4 were consumed. cigarettes respectively. The proposed method obtained 75% for “Class 1”, which is why it is more effective under these conditions compared to the other classes analyzed because they obtained percentages of 47% for “Class 2”, 66% for “Class 3” and 54% for “Class 4”. Keywords: local binary patterns, blood perfusion, thermograms

Rapid enhanced MM3-COPRO ELISA for detection of fasciola coproantigens

ELISA-based methods of detecting Fasciola cathepsins in feces are powerful techniques for diagnosing infections by F. hepatica and F. gigantica. In the last decade, the in-house MM3-COPRO ELISA and its commercial version BIO K 201 (BIO X Diagnostics, Belgium) have been recognized as useful tools for detecting early infections by such trematodes and for monitoring the efficacy of anthelmintic treatments in human and animal species, as they provide some advantages over classic fecal egg counts. However, the sensitivity of MM3- COPRO ELISA can sometimes be compromised by the high variability in the concentration of cathepsins in fecal samples throughout the biological cycle of Fasciola (mainly in cattle) and by differences in the between-batch performance of peroxidase-labeled anti-mouse IgG polyclonal antibodies. To prevent such problems, we investigated whether the incorporation of a commercial streptavidin-polymerized horseradish peroxidase conjugate, in order to reveal bound biotinylated monoclonal antibody MM3, can improve the sensitivity of the MM3-COPRO ELISA. We observed that inclusion of this reagent shifted the previous detection limit of the assay from 0.6 ng/mL to 150 pg/mL and that the modified test is able to identify infection in cows harboring only one fluke. Moreover, we demonstrated that maximal OD values can be achieved with short incubations (30 min each step) at RT with shaking, rather than standard incubations, which significantly accelerates the diagnostic procedure. Finally, we did not find a significant correlation between coproantigen concentration and parasite burden in cattle, which may be due to the low parasite burden (1–10 adult flukes) of the animals used in the present study. As the usefulness of the classic MM3-COPRO test for detecting animal and human infections has already been demonstrated, it is expected that the improvements reported in this study will add new insights into the diagnosis and control of fasciolosisWe have previously reported how the combined use of mAb MM3 with polyclonal antibodies obtained from rabbit immunized with Fasciola hepatica excretory-antigens led to the development of the in-house MM3-COPRO ELISA and its commercial version BIO K 201 (BIO X Diagnostics, Belgium), which are widely used to detect human and animal infections caused by F. hepatica. After more than a decade in use, both tests have proven to be useful tools for specifically detecting Fasciola infections, although it has also been found that: i) the conditions of use of the commercial test in some field studies did not enable the sensitivity obtained with the in-house test to be reached, and ii) the batches of the secondary reagent (peroxidase-labeled anti-mouse antibodies) currently available for use in the in-house test do not perform the same as previous batches. To solve these problems, we provide data showing that the incorporation of an enhancement system consisting of streptavidin-polymerized horseradish peroxidase conjugate greatly improved the sensitivity of the MM3-COPRO ELISA and enabled reduction of the incubation time. These modifications enabled the detectability of the assay to be 150 pg/mL, thus enabling detection of infection in animals harboring only one flukeThis work was funded by Ministerio de Ciencia e Innovación, Spain, Grants AGL2011- 30563-C02/C03; Xunta de Galicia, Spain, Grant GPC2014/058; and the European Fund for Regional Development (FEDER). VMS holds a predoctoral fellowship from the Spanish Ministerio de Educación, Cultura y Deporte (Programa de Formación del Profesorado Universitario, AP2010-5808) and RAOM is recipient of a fellowship from the Spanish Ministerio de Economía y Competitividad (Programa de Formación de Personal Investigador, BES-2012- 060270)S

Mapping chemical structure-activity information of HAART-drug cocktails over complex networks of AIDS epidemiology and socioeconomic data of U.S. counties

[Abstract] Using computational algorithms to design tailored drug cocktails for highly active antiretroviral therapy (HAART) on specific populations is a goal of major importance for both pharmaceutical industry and public health policy institutions. New combinations of compounds need to be predicted in order to design HAART cocktails. On the one hand, there are the biomolecular factors related to the drugs in the cocktail (experimental measure, chemical structure, drug target, assay organisms, etc.); on the other hand, there are the socioeconomic factors of the specific population (income inequalities, employment levels, fiscal pressure, education, migration, population structure, etc.) to study the relationship between the socioeconomic status and the disease. In this context, machine learning algorithms, able to seek models for problems with multi-source data, have to be used. In this work, the first artificial neural network (ANN) model is proposed for the prediction of HAART cocktails, to halt AIDS on epidemic networks of U.S. counties using information indices that codify both biomolecular and several socioeconomic factors. The data was obtained from at least three major sources. The first dataset included assays of anti-HIV chemical compounds released to ChEMBL. The second dataset is the AIDSVu database of Emory University. AIDSVu compiled AIDS prevalence for >2300 U.S. counties. The third data set included socioeconomic data from the U.S. Census Bureau. Three scales or levels were employed to group the counties according to the location or population structure codes: state, rural urban continuum code (RUCC) and urban influence code (UIC). An analysis of >130,000 pairs (network links) was performed, corresponding to AIDS prevalence in 2310 counties in U.S. vs. drug cocktails made up of combinations of ChEMBL results for 21,582 unique drugs, 9 viral or human protein targets, 4856 protocols, and 10 possible experimental measures. The best model found with the original data was a linear neural network (LNN) with AUROC > 0.80 and accuracy, specificity, and sensitivity ≈ 77% in training and external validation series. The change of the spatial and population structure scale (State, UIC, or RUCC codes) does not affect the quality of the model. Unbalance was detected in all the models found comparing positive/negative cases and linear/non-linear model accuracy ratios. Using synthetic minority over-sampling technique (SMOTE), data pre-processing and machine-learning algorithms implemented into the WEKA software, more balanced models were found. In particular, a multilayer perceptron (MLP) with AUROC = 97.4% and precision, recall, and F-measure >90% was found

Assessment of the Canary current upwelling system in a regionally coupled climate model

The Canary current upwelling is one of the major eastern boundary coastal upwelling systems in the world, bearing a high productive ecosystem and commercially important fisheries. The Canary current upwelling system (CCUS) has a large latitudinal extension, usually divided into upwelling zones with different characteristics. Eddies, filaments and other mesoscale processes are known to have an impact in the upwelling productivity, thus for a proper representation of the CCUS and high horizontal resolution are required. Here we assess the CCUS present climate in the atmosphere-ocean regionally coupled model. The regional coupled model presents a global oceanic component with increased horizontal resolution along the northwestern African coast, and its performance over the CCUS is assessed against relevant reanalysis data sets and compared with an ensemble of global climate models (GCMs) and an ensemble of atmosphere-only regional climate models (RCMs) in order to assess the role of the horizontal resolution. The coupled system reproduces the larger scale pattern of the CCUS and its latitudinal and seasonal variability over the coastal band, improving the GCMs outputs. Moreover, it shows a performance comparable to the ensemble of RCMs in representing the coastal wind stress and near-surface air temperature fields, showing the impact of the higher resolution and coupling for CCUS climate modelling. The model is able of properly reproducing mesoscale structures, being able to simulate the upwelling filaments events off Cape Ghir, which are not well represented in most of GCMs. Our results stress the ability of the regionally coupled model to reproduce the larger scale as well as mesoscale processes over the CCUS, opening the possibility to evaluate the climate change signal there with increased confidence.Open Access funding enabled and organized by Projekt DEAL. Ruben Vazquez was supported through a doctoral grant at the University of Ferrara and University of Cadiz. Dmitry Sein was supported in the framework of the state assignment of the Ministry of Science and Higher Education of Russia (No. 0128-2021-0014). This work used resources of the Deutsches Klimarechenzentrum (DKRZ) granted by its Scientific Steering Committee (WLA) under project ID ba0987

Secondary phytohaemagglutinin (PHA) swelling response is a good indicator of T-cell-mediated immunity in free-living birds

El phytohaemagglutinin (PHA) se prueba para medir la inmunidad adquirida y es uno de los métodos más utilizados; actualmente, está siendo debatido a raíz de los nuevos conocimientos sobre la compleja fisiología del proceso. Como respuesta secundaria reiterada a los mayores desafíos vinculados a los aumentos de los niveles de linfocitos T circulantes sería indicativo de una respuesta inmune mediada por células, se realizó por primera vez un experimento bajo condiciones naturales con repetidas PHA desafíos en libre-viviendo los pájaros adultos y polluelos para arrojar luz sobre este tema. Hemos encontrado significativamente más fuerte respuesta a PHA inyección secundaria independiente del sexo o la edad, mientras que el control de la condición corporal, la segunda respuesta es en promedio 90% más grande que el primero. Igualmente, los recuentos de linfocitos fueron significativamente superiores en el segundo reto de PHA, mientras que no se encontraron diferencias significativas entre las aves no tratadas. Las correlaciones positivas significativas entre la PHA respuesta y ambos recuentos de linfocitos y los niveles de proteínas plasmáticas (principalmente albúmina, globulina (precursor) fueron recuperados, mientras que no hubo diferencias significativas en los niveles de proteínas plasmáticas recuperados entre los retos. Nuestros resultados son consistentes con las aves cautivas, apoyando la validez del PHA de la hinchazón de la piel como prueba precisa de haber adquirido células T como la inmunidad en aves.The validity of using the phytohaemagglutinin (PHA) test to measure acquired immunity, one of the most widely used methods, is currently being debated due to new knowledge on the complex physiology of the process. As a greater secondary response to repeated challenges linked to increases of circulating lymphocyte levels would be indicative of a T-cell-mediated immune response, we performed for the first time an experiment under natural conditions with repeated PHA challenges in free-living adult birds and chicks to shed light on this topic. We found significantly stronger secondary response to PHA injection independent of sex or age, while controlling for body condition, the second response being on average 90% larger than the first. Likewise, lymphocyte counts were significantly higher in the second PHA challenge, whereas no significant differences were found among untreated birds. Significant positive correlations between the PHA response and both lymphocyte counts and plasma protein levels (mainly albumin, globulin (precursor) were recovered, whereas no significant differences were recovered in plasma protein levels between challenges. Our results are consistent with those from captive birds, supporting the validity of the PHA skin-swelling test as an accurate gauge of acquired T-cell-mediated immunity in birds.Trabajo patrocinado por: Fondo Mejicano para Conservación de la Naturaleza. Proyecto PIE 2012 A-P-C-IGSI-12-12 Gobierno de Extremadura. CONACYT (I010/176/2012) y becas PO10014 y RE12002 Gobierno de Extremadura. Dirección General de Vida Silvestre. SGPA/ DGVS/08559/11peerReviewe

Efecto de diferentes niveles de forraje de madrecacao (gliricidia sepium jacq) y melaza sobre la produccion de leche en ganado encastado

El presente estudio se realizó en la Hacienda "El Jícaro, ubicada en el Caserío El Jícaro, jurisdicción de San Matías, Departamento de La Libertad, durante los meses de junio a septiembre de 1991, a 13°53' latitud norte y 89°91' longitud oeste. A una altura de 450 msnm, precipitación anual promedio de 1701 mm, temperatura media anual de 23,8°C, humedad relativa de 76%. El objetivo fue determinar el efecto de diferentes niveles de forraje de madrecacao en la dieta de vacas lecheras encastadas. Se utilizaron 12 vacas, (mitad Pardo Suiza por mitad Brahmán), con dos meses de lactancia como máximo, bajo un diseño de doble cambio con períodos de adaptación de 14 días y 14 días de fase experimental. Se ofrecieron 4 raciones suplementarias: T0 = 6 kg de concentrado comercial; T1 = 4 kg de concentrado comercial más una mezcla de 1,5 kg de madrecacao y 1 kg de melaza; T2 =2 kg de concentrado comercial y una mezcla de 3 kg de madrecacao más 1,5 kg de melaza; T3 = 4,5 kg de madrecacao más 2 kg de melaza. En los cuatro tratamientos la ración base fue pasto Estrella (Cynodon plectostachyus) bajo pastoreo durante el día y Napier picado (Pennisetum purpureum) por la noche, suministrándole el madrecacao más melaza y el concentrado durante el ordeño. Los parámetros utilizados para, la determinación del objetivo antes mencionado fueron: a) producción láctea; las medias diarias de producción por vaca por día fueron: 6,83, 6,85, 5,47 y 6,20 kg para los tratamientos T0, T1, T2 y T3 respectivamente, con un coeficiente de variación de 7,08%; b) proteína láctea (Pt.L) con los siguientes resultados: 3,20, 3,19, 3,25 y 2,89% para T0, T1, T2 y T3; y un coeficiente de variación de 12,36%; c) grasa láctea: para este parámetro se tiene 3,85, 3,80, 4,08 y 3,69% para T0, T1, T2 y T3; y un coeficiente de variación de 5,19%; d) consumo voluntario en el cual se pudo determinar un 24% de rechazo para T3; e) cambios de peso, los cuales no pueden ser concluyentes debido al corto período transcurrido entre la toma de los datos. El análisis económico indica que el uso de madrecacao con melaza como suplemento resultó en un menor costo adicional comparado con el uso de concentrado. La suplementación según tratamiento tuvo un costo diario por animal de ₵9,44; ₵7,08; ₵4,55 y ₵2,01 para T0, T1, T2 y T3. Según los resultados anteriores se concluye que la suplementación con madrecacao a vacas de ordeño con el potencial genético utilizado en el ensayo, mantiene la producción de le che igual a la que se obtiene con el concentrado; pero a un menor costo

Evaluación de metodologías para la aplicación de sistemas de protección contra la corrosión en el interior de tanques de lastre en embarcaciones marinas

In this paper, different methodologies of surface preparation for applyinga paint system used in ballast tanks of marine vessels are studied andtheir influences in the performance of the paint system are evaluated.Typical rusts found on boat surfaces were characterized, field tests wereconducted with different surface preparations in hard-to-reach areas,controlling the contamination degree by soluble salts and comparingdifferent methods (Bresle method, Sleeve test, Saltsmart test and ionchromatography) and different roughness profiles (sand blasting, powergrinding and sandpaper, scraping and picketing) in order to determinethe more efficient combination of methods for the surface preparation inhard-to-reach areas. Different properties of a paint system were evaluateduring laboratory and field exposure tests. The final exposure time was 7months. It was found that the methods of surface preparation by picketingand power grinding + sandpaper have the higher salt contents (> 10 μg/cm2), exceeding the maximum permitted limit of 5.0 μg/cm2Este artículo presenta los resultados de la evaluación del desempeño ymetodologías de preparación superficial para la aplicación de un sistemade pinturas utilizado en tanques de lastre de embarcaciones marinas.Se caracterizaron las herrumbres típicas encontradas en superficies deembarcaciones, se realizaron pruebas de campo haciendo diferentespreparaciones de superficies en áreas de difícil acceso que permitierancontrolar el grado de contaminación por sales solubles, comparandodiferentes métodos (Método Bresle, Sleeve test, Saltsmart, cromatografíaiónica) y varios perfiles de anclaje (sand blasting, grata y lija, escariadory piqueteo) con el fin de determinar la combinación de los métodos máseficientes en la práctica para la preparación de zonas de difícil acceso. Seevaluaron las propiedades de un sistema de pinturas en laboratorio y encampo durante 7 meses de exposición. Se encontró que los métodos depreparación de superficie por piqueteo y grata + lija son los que presentanel mayor contenido de sales (> de 10 μg/cm2), superando el límitemáximo permitido de 5.0 μg/cm2. A partir del método de preparacióncon escariador están por debajo de los 10 μg/cm2

Coral Reef Resilience Index for Novel Ecosystems: A Spatial Planning Tool for Managers and Decision Makers - A Case Study from Puerto Rico

Timely information is critical for coral reef managers and decision-makers to implement sustainable management measures. A Coral Reef Resilience Index (CRRI) was developed with a GIS-coupled decision-making tool applicable for Caribbean coral reef ecosystems. The CRRI is based on a five-point scale parameterized from the quantitative characterization of benthic assemblages. Separate subindices such as the Coral Index, the Threatened Species Index, and the Algal Index also provide specific information regarding targeted benthic components. This case study was based on assessments conducted in 2014 on 11 reef sites located across 3 geographic zones and 3 depth zones along the southwestern shelf of the island of Puerto Rico, Caribbean Sea. There was a significant spatial and bathymetric gradient (p < 0.05) in the distribution of CRRI values indicating higher degradation of inshore reefs. Mean global CRRI ranged from 2.78 to 3.17 across the shelf, ranking them as “fair.” The Coral Index ranged from 2.60 to 3.76, ranking reefs from “poor” to “good,” showing a general cross-shelf trend of improving conditions with increasing distance from pollution sources. Turbidity and ammonia were significantly correlated to CRRI scores. Multiple recommendations are provided based on coral reef conditions according to observed CRRI rankings