A simple extension to the CMASA method for the prediction of catalytic residues in the presence of single point mutations

David Israel Flores Granados (2014, [Artículo])

The automatic identification of catalytic residues still remains an important challenge in structural bioinformatics. Sequence-based methods are good alternatives when the query shares a high percentage of identity with a well-annotated enzyme. However, when the homology is not apparent, which occurs with many structures from the structural genome initiative, structural information should be exploited. A local structural comparison is preferred to a global structural comparison when predicting functional residues. CMASA is a recently proposed method for predicting catalytic residues based on a local structure comparison. The method achieves high accuracy and a high value for the Matthews correlation coefficient. However, point substitutions or a lack of relevant data strongly affect the performance of the method. In the present study, we propose a simple extension to the CMASA method to overcome this difficulty. Extensive computational experiments are shown as proof of concept instances, as well as for a few real cases. The results show that the extension performs well when the catalytic site contains mutated residues or when some residues are missing. The proposed modification could correctly predict the catalytic residues of a mutant thymidylate synthase, 1EVF. It also successfully predicted the catalytic residues for 3HRC despite the lack of information for a relevant side chain atom in the PDB file. © 2014 Flores et al.

1UU9 protein, 3HRC protein, protein, thymidylate synthase, unclassified drug, protein kinase, thymidylate synthase, accuracy, algorithm, Article, CMASA, CMASA Substitution Matrix, Contact Matrix Average Deviation, controlled study, correlation coeffi CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA MATEMÁTICAS ANÁLISIS NUMÉRICO ANÁLISIS NUMÉRICO

La mirada de niños con NEE y maestros sobre la participación paterna en su aprendizaje: efectos de una intervención educativa

YANKO NORBERTO MEZQUITA HOYOS MARIA JOSE DE LILLE QUINTAL YOANY MARILY SOLIS KU (2016, [Artículo])

Esta investigación de corte cualitativo, tuvo como objetivo describir las percepciones que niños con NEE y sus maestros tienen sobre las estrategias de apoyo a su aprendizaje que tienen los padres antes y después de una intervención educativa. Para esto fue necesario, conocer desde la mirada de niños y profesores, las conductas de apoyo que brindan los padres en las actividades escolares a sus hijos y las situaciones que han facilitado o dificultado su involucramiento. Se trabajó con 6 docentes, que tienen en su grupo a uno o más alumnos con NEE y 8 alumnos con NEE de una escuela primaria pública, localizada al poniente de la ciudad de Mérida, Yucatán. En el diagnóstico se encontró que según los maestros, los padres de familia tienen un concepto impreciso de Necesidades Educativas Especiales, lo que repercute en sus expectativas académicas de sus hijos. Profesores y niños mencionaron que entre las principales barreras para el apoyo a sus hijos, se encuentran: su bajo nivel educativo y su comprensión de las tareas, la falta de paciencia, la carencia de información de cómo apoyarlos y la carencia de tiempo debido al trabajo. Se diseñó e implementó un taller para promover su participación, en el cual se consideraba tanto información teórica como experiencias personales de los participantes. Posterior a la implementación del taller los profesores consideraron que mejoró el conocimiento de los padres sobre NEE y coincidieron con los niños en que se mejoró la participación de los padres en el aprendizaje de sus hijos, implementando nuevas estrategias y mostrándose más colaborativos y tolerantes. Sin embargo los profesores destacaron la falta de participación de los padres en actividades escolares y comunitarias.

HUMANIDADES Y CIENCIAS DE LA CONDUCTA Necesidades educativas especiales Profesores Niños

Unanswered questions and unquestioned answers: the challenges of crop residue retention and weed control in Conservation Agriculture systems of southern Africa

Christian Thierfelder Blessing Mhlanga Hambulo Ngoma Paswel Marenya Md Abdul Matin Adane Tufa (2024, [Artículo])

Production and utilization of crop residues as mulch and effective weed management are two central elements in the successful implementation of Conservation Agriculture (CA) systems in southern Africa. Yet, the challenges of crop residue availability for mulch or the difficulties in managing weed proliferation in CA systems are bigger than a micro-level focus on weeds and crop residues themselves. The bottlenecks are symptoms of broader systemic complications that cannot be resolved without appreciating the interactions between the current scientific understanding of CA and its application in smallholder systems, private incentives, social norms, institutions, and government policy. In this paper, we elucidate a series of areas that represent some unquestioned answers about chemical weed control and unanswered questions about how to maintain groundcover demanding more research along the natural and social sciences continuum. In some communities, traditional rules that allow free-range grazing of livestock after harvesting present a barrier in surface crop residue management. On the other hand, many of the communities either burn, remove, or incorporate the residues into the soil thus hindering the near-permanent soil cover required in CA systems. The lack of soil cover also means that weed management through soil mulch is unachievable. Herbicides are often a successful stopgap solution to weed control, but they are costly, and most farmers do not use them as recommended, which reduces efficacy. Besides, the use of herbicides can cause environmental hazards and may affect human health. Here, we suggest further assessment of the manipulation of crop competition, the use of vigorously growing cover crops, exploration of allelopathy, and use of microorganisms in managing weeds and reducing seed production to deplete the soil weed seed bank. We also suggest in situ production of plant biomass, use of unpalatable species for mulch generation and change of grazing by-laws towards a holistic management of pastures to reduce the competition for crop residues. However, these depend on the socio-economic status dynamics at farmer and community level.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA INTEGRATED CROP-LIVESTOCK SYSTEMS CROP RESIDUES ZERO TILLAGE SOCIAL NORMS SUSTAINABLE INTENSIFICATION WEED CONTROL

El reto de la falta de acceso al servicio de agua potable en Sonora.

ALEJANDRO NAVARRO NAVARRO (2020, [Tesis de maestría])

Se estudió la Falta de Acceso al Agua Potable Entubada (FAAPE) en viviendas del estado se Sonora, México. El objetivo general fue identificar los principales lugares con esta problemática, así como los factores asociados a ésta. Desde las perspectivas de la seguridad hídrica, el derecho humano al agua y los Objetivos de Desarrollo Sostenible (ODS) de las Naciones Unidas se operacionalizó el concepto de FAAPE. A través de métodos cuantitativos de estadística descriptiva e inferencial, la construcción de un Sistema de Información Geográfica (SIG) y técnicas de análisis espacial se trabajó con datos oficiales de INEGI (2010, 2015) a nivel AGEB y vivienda, rurales o urbanos; también se realizaron visitas de campo y entrevistas semiestructuradas en dos casos de estudio. Los resultados del análisis de autocorrelación espacial a nivel AGEB mostraron que: 1) en el año 2010, los municipios con una mayor concentración de viviendas con FAAPE eran Nogales (11,054) y Huatabampo (2,459), en el ámbito urbano y rural, respectivamente; estos dos municipios se tomaron como estudio de caso para realizar trabajo de campo; y 2) se identifican a nivel estatal para 2010, 364 AGEB como agrupamientos con valores altos (hotspots) de viviendas con FAAPE. El modelo estadístico revelo que: 1) variables relacionadas con la precariedad de la vivienda (la ausencia de escrituras, tinaco, drenaje, pisos y electricidad) están altamente asociadas al no acceso de agua potable; y 2) por otro lado, altos niveles de escolaridad inhiben la falta de acceso al agua, al igual que altos niveles de ingreso. De las visitas de campo de los casos de estudio se destaca que: 1) El principal factor que afecta el acceso al agua potable en la ciudad de Nogales es la presencia de asentamientos irregulares; 2) El área rural del municipio de Huatabampo donde las pequeñas localidades se abastecen por medio de autogestión y la mayor parte del municipio sufre de escases y mala calidad del agua. Se concluye que en los casos de estudio se garantiza parcialmente la seguridad hídrica lo que se puede generalizar para todo el estado.

CIENCIAS SOCIALES Agua potable Derecho de aguas Servicio público Abastecimiento de agua Nogales Huatabampo

Transparencia y rendición de cuentas en la deuda pública municipal. Modelo de coherencia entre políticas y coordinación institucional para el estudio de casos: Hermosillo, Cajeme y Nogales, 2006-2016

LUIS ERNESTO FLORES FONTES (2019, [Tesis de doctorado])

CIENCIAS SOCIALES Deuda pública Finanzas municipales Finanzas públicas Hermosillo Cajeme Nogales Transparencia en el gobierno

Influence of residue type and method of placement on dynamics of decomposition and nitrogen release in maize-wheat-mungbean cropping on permanent raised beds: a litterbag study

ML JAT Rajeev Gupta (2022, [Artículo])

Decomposition Rate Nitrogen Release Placement Effect CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CROP RESIDUES DEGRADATION NITROGEN PLACEMENT

Modeling the growth, yield and N dynamics of wheat for decoding the tillage and nitrogen nexus in 8-years long-term conservation agriculture based maize-wheat system

C.M. Parihar Dipaka Ranjan Sena Prakash Chand Ghasal Shankar Lal Jat Yashpal Singh Saharawat Mahesh Gathala Upendra Singh Hari Sankar Nayak (2024, [Artículo])

Context: Agricultural field experiments are costly and time-consuming, and their site-specific nature limits their ability to capture spatial and temporal variability. This hinders the transfer of crop management information across different locations, impeding effective agricultural decision-making. Further, accurate estimates of the benefits and risks of alternative crop and nutrient management options are crucial for effective decision-making in agriculture. Objective: The objective of this study was to utilize the Crop Environment Resource Synthesis CERES-Wheat model to simulate crop growth, yield, and nitrogen dynamics in a long-term conservation agriculture (CA) based wheat system. The study aimed to calibrate the model using data from a field experiment conducted during the 2019-20-2020-21 growing seasons and evaluation it with independent data from the year 2021–22. Method: Crop simulation models, such as the Crop Environment Resource Synthesis CERES-Wheat (DSSAT v 4.8), may provide valuable insights into crop growth and nitrogen dynamics, enabling decision makers to understand and manage production risk more effectively. Therefore, the present study employed the CERES-Wheat (DSSAT v 4.8) model and calibrated it using field data, including plant phenological phases, leaf area index, aboveground biomass, and grain yield from the 2019-20-2020-21 growing seasons. An independent dataset from the year 2021–22 was used for model evaluation. The model was used to investigate the relationship between growing degree days (GDD), temperature, nitrate and ammonical concentration in soil, and nitrogen uptake by the crop. Additionally, the study explored the impact of contrasting tillage practices and fertilizer nitrogen management options on wheat yields. The experimental site is situated at ICAR-Indian Agricultural Research Institute (IARI), New Delhi, representing Indian Trans-Gangetic Plains Zone (28o 40’N latitude, 77o 11’E longitude and an altitude of 228 m above sea level). The treatments consist of four nitrogen management options, viz., N0 (zero nitrogen), N150 (150 kg N ha−1 through urea), GS (Green seeker based urea application) and USG (urea super granules @150 kg N ha−1) in two contrasting tillage systems, i.e., CA-based zero tillage (ZT) and conventional tillage (CT). Result: The outcomes exhibited favorable agreement between the model’s simulations and the observed data for crop phenology (With less than 2 days variation in 50% onset of flowering), grain and biomass yield (Root mean square error; RMSE 336 kg ha−1 and 649 kg ha−1, respectively), and leaf area index (LAI) (RMSE 0.28 & normalized RMSE; nRMSE 6.69%). The model effectively captured the nitrate-N (NO3−-N) dynamics in the soil profile, exhibiting a remarkable concordance with observed data, as evident from its low RMSE = 12.39 kg ha−1 and nRMSE = 13.69%. Moreover, as it successfully simulated the N balance in the production system, the nitrate leaching and ammonia volatilization pattern as described by the model are highly useful to understand these critical phenomena under both conventional tillage (CT) and CA-based Zero Tillage (ZT) treatments. Conclusion: The study concludes that the DSSAT-CERES-Wheat model has significant potential to assess the impacts of tillage and nitrogen management practices on crop growth, yield, and soil nitrogen dynamics in the western Indo-Gangetic Plains (IGP) region. By providing reliable forecasts within the growing season, this modeling approach can facilitate better planning and more efficient resource management. Future implications: The successful implementation of the DSSAT-CERES-Wheat model in this study highlights its applicability in assessing crop performance and soil dynamics. Future research should focus on expanding the model’s capabilities by reducing its sensitivity to initial soil nitrogen levels to refine its predictions further. Moreover, the model’s integration with decision support systems and real-time data can enhance its usefulness in aiding agricultural decision-making and supporting sustainable crop management practices.

Nitrogen Dynamics Mechanistic Crop Growth Models Crop Simulation CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA NITROGEN CONSERVATION AGRICULTURE WHEAT MAIZE CROP GROWTH RATE SIMULATION MODELS

Classification of Cucumber Leaves Based on Nitrogen Content Using the Hyperspectral Imaging Technique and Majority Voting.

Sajad Sabzi Razieh Pourdarbani Mohammad Hossein Rohban Alejandro Fuentes_Penna José Luis Hernández-Hernández Mario Hernández Hernández (2021, [Artículo])

Improper usage of nitrogen in cucumber cultivation causes nitrate accumulation in the fruit and results in food poisoning in humans; therefore, mandatory evaluation of food products becomes inevitable. Hyperspectral imaging has a very good ability to evaluate the quality of fruits and vegetables in a non-destructive manner. The goal of the present paper was to identify excess nitrogen in cucumber plants. To obtain a reliable result, the majority voting method was used, which takes into account the unanimity of five classifiers, namely, the hybrid artificial neural network¿imperialism competitive algorithm (ANN-ICA), the hybrid artificial neural network¿harmonic search (ANN-HS) algorithm, linear discrimination analysis (LDA), the radial basis function network (RBF), and the Knearest- neighborhood (KNN). The wavelengths of 723, 781, and 901 nm were determined as optimal wavelengths using the hybrid artificial neural network¿biogeography-based optimization (ANNBBO) algorithm, and the performance of classifiers was investigated using the optimal spectrum. The results of a t-test showed that there was no significant difference in the precision of the algorithm when using the optimal wavelengths and wavelengths of the whole range. The correct classification rate of the classifiers ANN-ICA, ANN-HS, LDA, RBF, and KNN were 96.14%, 96.11%, 95.73%, 64.03%, and 95.24%, respectively. The correct classification rate of majority voting (MV) was 95.55% for test data in 200 iterations, which indicates the system was successful in distinguishing nitrogen-rich leaves from leaves with a standard content of nitrogen.

artificial neural network cucumber hyperspectral imaging majority voting nitrogen INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS TECNOLOGÍA DE LOS ALIMENTOS

Mapping of SARS-CoV-2 spike protein evolution during the first and second waves of COVID-19 infections in India

Shailendra Sharma Avinash Kumar Apekshita Singh deepmala sehgal Shailendra Goel SoomNath Raina (2022, [Artículo])

Immune Evasion Mutation Analysis Novel Spike Mutations Reduced Neutralization SARS-CoV-2 CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA COVID-19 NEUTRALIZATION SPIKES

Análisis de la dinámica del monzón de Norteamérica usando modelos globales y regionales

SALVADOR CASTILLO LIÑAN (2021, [Tesis de maestría])

Maestro en Ciencias y Tecnología del Agua - Hidrometeorología) -- Instituto Mexicano de Tecnología del Agua. Coordinación de Desarrollo Profesional e Institucional. Subcoordinación de Posgrado.

El Monzón de Norteamérica (NAM) es un sistema atmosférico intraestacional causante de aproximadamente el 70% de las precipitaciones anuales en el noroeste de México y suroeste de Estados Unidos. Su estudio utilizando modelos numéricos es un reto debido a la compleja dinámica asociada a la abrupta orografía y al contraste térmico océano-continente que contribuyen a su desarrollo durante el verano. A pesar de que la gran mayoría de los modelos globales del experimento CMIP5 (Proyecto de Intercomparación de Modelos Acoplados), logran describir el periodo intraestacional de precipitaciones máximas sobre el dominio del NAM y reproducir su variabilidad espacial y temporal, se han identificado sesgos en las simulaciones con respecto a las observaciones y los datos de Reanálisis. Con el propósito de abordar estos sesgos, así como identificar y explicar el inicio-final del monzón, en este estudio se analiza el papel de los mecanismos entre la atmósfera, del continente y el océano, utilizando simulaciones numéricas regionales generadas con el modelo sueco RCA4 (Rossby Centre regional atmospheric model 4), el cual fue forzado con 10 modelos globales del CMIP5.

Monzón de Norteamérica Modelación numérica Precipitaciones INGENIERÍA Y TECNOLOGÍA