Using an incomplete block design to allocate lines to environments improves sparse genome-based prediction in plant breeding

Osval Antonio Montesinos-Lopez ABELARDO MONTESINOS LOPEZ RICARDO ACOSTA DIAZ Rajeev Varshney Jose Crossa ALISON BENTLEY (2022, [Artículo])

Genomic selection (GS) is a predictive methodology that trains statistical machine-learning models with a reference population that is used to perform genome-enabled predictions of new lines. In plant breeding, it has the potential to increase the speed and reduce the cost of selection. However, to optimize resources, sparse testing methods have been proposed. A common approach is to guarantee a proportion of nonoverlapping and overlapping lines allocated randomly in locations, that is, lines appearing in some locations but not in all. In this study we propose using incomplete block designs (IBD), principally, for the allocation of lines to locations in such a way that not all lines are observed in all locations. We compare this allocation with a random allocation of lines to locations guaranteeing that the lines are allocated to

the same number of locations as under the IBD design. We implemented this benchmarking on several crop data sets under the Bayesian genomic best linear unbiased predictor (GBLUP) model, finding that allocation under the principle of IBD outperformed random allocation by between 1.4% and 26.5% across locations, traits, and data sets in terms of mean square error. Although a wide range of performance improvements were observed, our results provide evidence that using IBD for the allocation of lines to locations can help improve predictive performance compared with random allocation. This has the potential to be applied to large-scale plant breeding programs.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA Bayes Theorem Genome Inflammatory Bowel Diseases Models, Genetic Plant Breeding

The potential of UAV and very high-resolution satellite imagery for yellow and stem rust detection and phenotyping in Ethiopia

Gerald Blasch David Hodson Francelino Rodrigues (2023, [Artículo])

Very high (spatial and temporal) resolution satellite (VHRS) and high-resolution unmanned aerial vehicle (UAV) imagery provides the opportunity to develop new crop disease detection methods at early growth stages with utility for early warning systems. The capability of multispectral UAV, SkySat and Pleiades imagery as a high throughput phenotyping (HTP) and rapid disease detection tool for wheat rusts is assessed. In a randomized trial with and without fungicide control, six bread wheat varieties with differing rust resistance were monitored using UAV and VHRS. In total, 18 spectral features served as predictors for stem and yellow rust disease progression and associated yield loss. Several spectral features demonstrated strong predictive power for the detection of combined wheat rust diseases and the estimation of varieties’ response to disease stress and grain yield. Visible spectral (VIS) bands (Green, Red) were more useful at booting, shifting to VIS–NIR (near-infrared) vegetation indices (e.g., NDVI, RVI) at heading. The top-performing spectral features for disease progression and grain yield were the Red band and UAV-derived RVI and NDVI. Our findings provide valuable insight into the upscaling capability of multispectral sensors for disease detection, demonstrating the possibility of upscaling disease detection from plot to regional scales at early growth stages.

Very High Resolution Imagery Disease Detection Methods Early Growth Stages CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA UNMANNED AERIAL VEHICLES STEM RUST PHENOTYPING HIGH-THROUGHPUT PHENOTYPING WHEAT

Debaryomyces hansenii: una nueva levadura probiótica

Debaryomyces hansenii: A new probiotic yeast

MIRIAM GORETTY ANGULO VILLAVICENCIO MARTHA CANDELARIA REYES BECERRIL Carlos Eliud Angulo Valadez (2022, [Artículo])

"Los probióticos son bichos diminutos cuyo consumo genera efectos benéficos en la salud. De hecho, la palabra probiótico significa 'pro-vida'. Algunas levaduras, como la utilizada para hacer pan o cerveza, pueden ser probióticos para animales y humanos. Desde hace algunos años, los estudios con la levadura Debaryomyces hansenii han demostrado que ésta es un probiótico. Se ha demostrado que, administrada por vía oral, esta levadura tiene efectos estimulantes del sistema de defensa y beneficios para la función digestiva de animales terrestres y acuáticos. Por lo anterior, se describen los hallazgos que revelan que D. hansenii es un probiótico para animales y posiblemente para humanos."

"Probiotics are tiny bugs that when consumed have beneficial effects on health. In fact, the word probiotic means pro-life. Some yeasts, such as that used to make bread or beer, can be probiotics for animals and humans. For some years, studies with the yeast Debaryomyces hansenii indicate that it is a probiotic.

This yeast administered orally has been shown to have stimulating effects on the defense system and beneficial effects on the digestive function of terrestrial and aquatic animals. Therefore, we will try to describe the findings of D. hansenii that indicate that it is a probiotic for animals and possibly also for humans."

probióticos, bienestar, microbios, enfermedad, supervivencia probiotics, wellbeing, microbes, disease, survival BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA MICROBIOLOGÍA MICOLOGÍA (LEVADURAS) MICOLOGÍA (LEVADURAS)

OPTIMIZING THE TRANSFER OF ENERGY IN A HEAT EXCHANGER MINIMIZING THE CORROSION PROBLEMS IN PIPES IN A HYDROELECTRIC POWER STATION USING DATA MINING AND SUPPORT VECTOR MACHINE

VICTOR MANUEL ZEZATTI FLORES GUSTAVO URQUIZA BELTRAN MIGUEL ANGEL BASURTO PENSADO LAURA LILIA CASTRO GOMEZ (2019, [Artículo])

This research is based on the operation tube heat exchangers, their use and problematic on hydroelectric power plants. It is based on the design heat exchanger tubes for industrial use, which took the parameters of operation, design, working fluids (air and water) and conditions to assemble a monitoring equipment at appropriate scale for the laboratory, with the necessary measurement instruments to analyze the behavior of heat energy transfer by means of thermocouples, the velocity of the air with a hot wire anemometer and the flow of water with a turbine flow meter, in pipes of different materials: copper, steel 1018 and stainless steel 316L, all in ideal conditions, and with this to found a comparative parameter with pipes of the same materials but under conditions of deterioration with the presence of forced oxidation and with the data mining and support vector machine can be minimized the corrosion problems in pipes.

INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS Data Mining, Support Vector Machine, Pattern Recognition and Decision Support System, heat exchangers.

Implementation of a Nickel-Electroless Coating in Heat Exchanger Pipes Considering the Problem of the Environmental Conditions ofthe Cooling Water Without Recirculation to Increase the Effectiveness Under Uncertainty

VICTOR MANUEL ZEZATTI FLORES GUSTAVO URQUIZA BELTRAN MIGUEL ANGEL BASURTO PENSADO LAURA LILIA CASTRO GOMEZ JUAN CARLOS GARCIA CASTREJON (2022, [Artículo])

This research is based on the operation tube heat exchangers, their use and problematic on hydroelectric power plants. It is based on the design heat exchanger tubes for industrial use, which took the parameters of operation, design, working fluids (air and water) and conditions to assemble a monitoring equipment at appropriate scale for the laboratory, with the necessary measurement instruments to analyze the behavior of heat energy transfer by means of thermocouples, the velocity of the air with a hot wire anemometer and the flow of water with a turbine flow meter, in pipes of different materials: copper, steel 1018 and stainless steel 316L, all in ideal conditions, and with this to found a comparative parameter with pipes of the same materials but under conditions of deterioration with the presence of forced oxidation and with the data mining and support vector machine can be minimized the corrosion problems in pipes.

INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS Data mining, Support Vector Machine, Pattern Recognition and Decision Support System, Heat exchangers

Nanopartículas híbridas cargadas con un compuesto bioactivo y su efecto en biomarcadores neuroinflamatorios como potencial tratamiento de la enfermedad de Alzheimer

Hybrid nanoparticles loaded with a bioactive compound and their effect on neuroinflammatory biomarkers as a potential treatment for Alzheimer’s disease

Alondra Vargas Barona (2024, [Tesis de maestría])

La enfermedad de Alzheimer (EA) es una enfermedad neurodegenerativa progresiva caracterizada por el deterioro cognitivo asociado a la acumulación de la proteína beta amiloide (Aβ). La Aβ activa a las células gliales del cerebro, generando un aumento en la secreción de citocinas pro-inflamatorias que conducen a la neuroinflamación y muerte neuronal. Actualmente no existen tratamientos efectivos que curen o detengan su progresión, por ello, la EA se considera como una prioridad de salud mundial. Las principales limitaciones son la baja biodisponibilidad del fármaco y la impermeabilidad de la barrera hematoencefálica (BHE). Afortunadamente, la nanomedicina ha surgido como un campo prometedor para el desarrollo de nuevos sistemas para la entrega controlada y dirigida de fármacos hacia el cerebro. Por ello, en este trabajo se sintetizaron nanopartículas híbridas de polímeros y lípidos (NPsHPL) conjugadas con transferrina (Tf) para facilitar el cruce de la BHE, y cargadas con N-acetilcisteína (NAC) por su efecto anti-inflamatorio, y se llevó a cabo su caracterización fisicoquímica. Posteriormente se implementó un modelo in vitro con astrocitos humanos derivados de células pluripotentes inducidas (iPSC) provenientes de un paciente diagnosticado con la EA, las cuales se llevaron a un estado reactivo por la estimulación con lipopolisacárido (LPS). El cultivo de células fue tratado con las NPsHPL conjugadas con Tf y cargadas con NAC (NPsHPL-Tf-NAC) a 0.25 mg/mL y NAC libre a 5 mM. Los resultados mostraron que las NPsHPL-Tf-NAC modularon favorablemente la expresión de genes pro-inflamatorios, como la interleucina-1β (IL-1β), la proteína precursora de amiloide (APP) y la proteína ácida fibrilar glial (GFAP). Además, redujo la secreción de las citocinas pro-inflamatorias interleucina 6 (IL-6), IL-1β e interferóngamma (INF-γ), ambos casos respecto al grupo de células que no recibieron algún tratamiento. Por otra parte, la NAC libre sólo tuvo este efecto en la expresión de IL-1β y la secreción de las citocinas IL-6 e INF-γ. Estos resultados posicionan a las NPsHPL-Tf-NAC como un potencial tratamiento para la EA.

Alzheimer’s disease (AD) is a progressive neurodegenerative disease characterized by cognitive impairment associated with the accumulation of beta-amyloid protein (Aβ). Aβ activates glial cells in the brain, increasing the secretion of pro-inflammatory cytokines that lead to neuroinflammation and neuronal death. Currently, there are no effective treatments that cure or stop its progression, therefore AD is considered a global health priority. The main limitations are the low drug bioavailability and impermeability of the blood-brain barrier (BBB). Fortunately, nanomedicine has emerged as a promising field for the development of new nanosystems for the controlled and targeted delivery of drugs to the brain. Therefore, in this work, lipid–polymer hybrid nanoparticles (LPHNPs) conjugated with transferrin (Tf) to facilitate crossing the BBB, and loaded with N-acetylcysteine (NAC) for its anti-inflammatory effect were synthesized, and their physicochemical characterization was carried out. Subsequently, an in vitro model with human astrocytes derived from induced pluripotent stem cells (iPSC) from an AD diagnosed patient was implemented, which were brought to a reactive state by stimulation with lipopolysaccharide (LPS). The cell culture was treated with Tf-conjugated LPHNPs loaded with NAC (LPHNPs-Tf-NAC) at 0.25 mg/mL and free NAC at 5 mM. The results showed that LPHNPs-Tf-NAC favorably modulated the expression of pro-inflammatory genes, such as interleukin-1β (IL-1β), amyloid precursor protein (APP) and glial fibrillary acidic protein (GFAP). In addition, they reduced the secretion of the pro-inflammatory cytokines interleukin 6 (IL-6), IL-1β and interferon-gamma (INF-γ), both cases compared to the group of cells that did not receive any treatment. On the other hand, free NAC only had this effect on the expression of IL-1β and the secretion of the cytokines IL-6 and INF-γ. These results position LPHNPs-Tf-NAC as a potential treatment for AD.

nanopartículas híbridas; enfermedad de Alzheimer; neuroinflamación; astrocitos; iPSC; nanomedicina hybrid nanoparticles, Alzheimer’s disease, neuroinflammation; astrocytes; iPSC; nanomedicine BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA OTRAS ESPECIALIDADES DE LA BIOLOGÍA OTRAS OTRAS

Modelado y acoplamiento de la conductividad eléctrica e hidráulica a partir de tomografía de rocas

Modeling and coupling of electrical and hydraulic conductivity from rock tomography

Miguel Ángel Martínez Rodríguez (2022, [Tesis de maestría])

En este trabajo se emplearon técnicas de modelado numérico para simular el flujo de corriente eléctrica y de fluido a través de medios porosos con el fin de determinar el factor de resistividad y la permeabilidad, así como la distribución de los campos de densidad de corriente eléctrica y velocidad de flujo. Para el modelado de flujo eléctrico se desarrolló un algoritmo basado en diferencias finitas, mientras que para el modelado hidráulico se empleó una librería reportada en la literatura, basada en el método de redes de Boltzmann. En ambos esquemas de modelado se establecieron condiciones en la frontera poro-grano para modelar los procesos físicos exclusivamente en el espacio poroso. Los valores estimados de factor de resistividad y de permeabilidad, así como la porosidad, se emplearon para estudiar las correlaciones entre estas propiedades a través de relaciones petrofísicas. Para esto, se propuso una expresión que relaciona la permeabilidad y la porosidad y, empleando una relación existente entre el factor de resistividad y la porosidad, se propuso también una relación directa entre la permeabilidad y el factor de resistividad. Las relaciones propuestas fueron aplicadas a los valores numéricos obtenidos para paquetes de esferas generados numéricamente y se encontró que se ajustan mejor a los datos en comparación con las relaciones más comúnmente utilizadas, especialmente para porosidades altas. Se mostró también que estas relaciones petrofísicas toman la forma de las relaciones más comunes conocidas cuando se trata con porosidades bajas. Valores obtenidos de imágenes digitales de un paquete de esferas sintético y una muestra de dolomita mostraron que las expresiones para porosidades bajas son suficientes para ajustar datos de medios porosos con porosidades menores a un valor entre 0.3 y 0.4. Finalmente, se analizaron el factor de resistividad, la permeabilidad, las relaciones petrofísicas, y las distribuciones espaciales y estadísticas de los campos vectoriales de flujo se analizaron para comparar los fenómenos de transporte eléctrico e hidráulico, encontrando que algunos factores, como la porosidad efectiva, son importantes en ambos fenómenos de flujo; mientras que otros, como la adherencia del fluido a las paredes del poro, son particularmente relevantes para el flujo hidráulico.

In this work, numerical modeling techniques were used to simulate the flow of electric current and fluid through porous media in order to determine the resistivity factor and permeability, as well as the distribution of electric current density and flow velocity fields. For electric flow modeling, an algorithm based on finite differences was developed, while for hydraulic modeling, a library reported in the literature, based on lattice Boltzmann method, was used. In both modeling schemes, pore-grain boundary conditions were established to model the physical processes exclusively in the pore space. The estimated values of resistivity factor and permeability, as well as porosity, were used to study the correlations between these properties through petrophysical relationships. An expression relating permeability and porosity was proposed and, using an existing relationship between the resistivity factor and the porosity, a direct relation between permeability and resistivity factor was also proposed. The proposed relations were applied to data obtained for numerically generated sphere packs and were found to fit the data better than the most commonly used relationships, especially for high porosities. It was also shown that these petrophysical relationships take the form of the most common relationships known when dealing with low porosities. Modeling data on digital images of a synthetic sphere pack and a dolomite sample showed that the expressions for low porosities are sufficient to fit data from porous media with porosities lower than 0.3 to 0.4. Finally, resistivity factors, permeabilities, petrophysical relationships, and spatial and statistical distributions of flow vector fields were analyzed to compare electrical and hydraulic transport phenomena, finding that some factors, such as the effective porosity, are important in both flow phenomena; whereas some other, such as the pore-wall adherence, are particularly relevant to hidraulic flux.

Física de rocas, modelado numérico, relaciones petrofísicas, fenómenos de transporte, factor de resistividad, permeabilidad, porosidad, tomografía de rocas, campos vectoriales, distribución estadística Rock physics, numerical modelling, petrophysical relations, transport phenomena, resistivity factor, permeability, porosity, rock tomography, vector fields, statistical distribution CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA CIENCIAS DE LA TIERRA Y DEL ESPACIO GEOFÍSICA GEOFÍSICA DE LA MASA SÓLIDA TERRESTRE GEOFÍSICA DE LA MASA SÓLIDA TERRESTRE

Suppression of breast tumor growth and metastasis by an engineered transcription factor

Adriana Beltran Lopez (2011, [Artículo])

Maspin is a tumor and metastasis suppressor playing an essential role as gatekeeper of tumor progression. It is highly expressed in epithelial cells but is silenced in the onset of metastatic disease by epigenetic mechanisms. Reprogramming of Maspin epigenetic silencing offers a therapeutic potential to lock metastatic progression. Herein we have investigated the ability of the Artificial Transcription Factor 126 (ATF-126) designed to upregulate the Maspin promoter to inhibit tumor progression in pre-established breast tumors in immunodeficient mice. ATF-126 was transduced in the aggressive, mesenchymal-like and triple negative breast cancer line, MDA-MB-231. Induction of ATF expression in vivo by Doxycycline resulted in 50% reduction in tumor growth and totally abolished tumor cell colonization. Genome-wide transcriptional profiles of ATF-induced cells revealed a gene signature that was found over-represented in estrogen receptor positive (ER+) "Normal-like" intrinsic subtype of breast cancer and in poorly aggressive, ER+ luminal A breast cancer cell lines. The comparison transcriptional profiles of ATF-126 and Maspin cDNA defined an overlapping 19-gene signature, comprising novel targets downstream the Maspin signaling cascade. Our data suggest that Maspin up-regulates downstream tumor and metastasis suppressor genes that are silenced in breast cancers, and are normally expressed in the neural system, including CARNS1, SLC8A2 and DACT3. In addition, ATF-126 and Maspin cDNA induction led to the re-activation of tumor suppressive miRNAs also expressed in neural cells, such as miR-1 and miR-34, and to the down-regulation of potential oncogenic miRNAs, such as miR-10b, miR-124, and miR-363. As expected from its over-representation in ER+ tumors, the ATF-126-gene signature predicted favorable prognosis for breast cancer patients. Our results describe for the first time an ATF able to reduce tumor growth and metastatic colonization by epigenetic reactivation of a dormant, normal-like, and more differentiated gene program. © 2011 Beltran et al.

artificial transcription factor 126, complementary DNA, doxycycline, estrogen receptor, maspin, microRNA, retrovirus vector, transcription factor, unclassified drug, estrogen receptor, serine proteinase inhibitor, SERPIN B5, SERPIN-B5, transcription BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)