Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data
subject: deep learning, SARS, Cheminformatics, machine learning, Data mining, random forest
description: Abstract Background In recent years, research in artificial neural networks has resurged, now under the deep-learning umbrella, and grown extremely popular. Recently reported success of DL techniques in crowd-sourced QSAR and predictive toxicology competitions has showcased these methods as powerful tools in drug-discovery and toxicology research. The aim of this work was dual, first large number of hyper-parameter configurations were explored to investigate how they affect the performance of DNNs and could act as starting points when tuning DNNs and second their performance was compared to popular methods widely employed in the field of cheminformatics namely Naïve Bayes, k-nearest neighbor, random forest and support vector machines. Moreover, robustness of machine learning methods to different levels of artificially introduced noise was assessed. The open-source Caffe deep-learning framework and modern NVidia GPU units were utilized to carry out this study, allowing large number of DNN configurations to be explored. Results We show that feed-forward deep neural networks are capable of achieving strong classification performance and outperform shallow methods across diverse activity classes when optimized. Hyper-parameters that were found to play critical role are the activation function, dropout regularization, number hidden layers and number of neurons. When compared to the rest methods, tuned DNNs were found to statistically outperform, with p value
creator: Alexios Koutsoukas, Keith J. Monaghan, Xiaoli LI, Jun Huan
source: Journal of Cheminformatics
publisher: BMC
date: 2017
language: EN
identifier: DOI: 10.1186/s13321-017-0226-y
coverage: Chemistry, Information technology

Deep-water shrimp fisheries in Latin America: a review Pesquerías de camarones de aguas profundas en América Latina: una revisión
subject: América Central, Brasil, Brazil, Caridea, Central America, Chile, Colombia, México, Penaeoidea, Peru, estadísticas de pesca, fishery statistics, management, manejo, sustainability, sustentabilidad
description: Commercial fisheries are expanding their activities into deeper water. The life history features of these deep-water resources make them more vulnerable to exploitation than most shallow-water resources. Moreover, the apparent lack of solid information about the ecology of most deep-water species represents a major limitation for the development and implementation of management strategies. This scenario has caused great concern regarding the sustainability of these resources and the possible environmental impacts on the deep-sea ecosystem. In Latin America, commercial fisheries are going deep as well, and considering the above-mentioned concerns, we felt the need to compile the available information about the deep-water shrimp resources and the current status of their fisheries in Latin America. Focusing on Mexico, Central America, Peru, Chile and Brazil, this review describes the exploited species, and, whenever available, the fishing fleet, fishery statistics, and management strategies. A total of 17 species (10 spp. of Penaeoidea; 7 spp. of Caridea) are of commercial interest in Latin America, but deep-water shrimps are currently fished only in Costa Rica, Colombia and Chile. An implemented management plan exists in Chile and Colombia, while Brazil approved fishery regulations for the aristeid fishery, which were never implemented. Considering the lack of information about the biology of the deep-water shrimps, which hinders the development of adequate management strategies, we see the urgent need to improve the communication and collaboration between the different stakeholders in Latin American. We suggest the establishment of a searchable and constantly updated database, which may serve as a valuable source of information for researcher and decision makers. Finally, we propose the development of regional research plans aimed towards supporting measurements for a sustainable use of deep-water shrimps in Latin America.La pesca comercial está expandiendo sus activ…
creator: Ingo S Wehrtmann, Patricio M Arana, Edward Barriga, Adolfo Gracia, Paulo Ricardo Pezzuto
source: Latin American Journal of Aquatic Research
publisher: Escuela de Ciencias del Mar, Facultad de Recursos Naturales, Pontificia Universidad Católica de Valparaíso
date: 2012
relation: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-560X2012000300002
coverage: Biology (General), Oceanography, Aquaculture. Fisheries. Angling

Deeper understanding about the genetic structure of dengue virus using SVM
description: Dengue fever, mainly found in the tropical and subtropical regions, is carried by mosquitoes. With the help of greenhouse effect, places considered to be a Dengue safe-zone are becoming more and more dangerous. Dengue fever shows similar aspects to MERS, which caused heavy casualties in South Korea; Dengue virus does not have clear treatments nor vaccines like MERS. Development of Dengue vaccine is actively investigated lately. However, it is not easy to succeed; the fact that Dengue’s 4 serotypes have different properties and that repeated infections worsen the symptoms. This research aims to analyze the 4 serotypes (DENV1, DENV2, DENV3, DENV4) using SVM and ANN algorithms to investigate the constraints in the development of Dengue’s vaccines and treatments.
creator: Choi Subin, Choi Hyunjin, Yoon Taeseon
source: MATEC Web of Conferences
publisher: EDP Sciences
date: 2016
language: EN, FR
identifier: DOI: 10.1051/matecconf/20166901008
coverage: Engineering (General). Civil engineering (General)

DeepSOCIAL: Social Distancing Monitoring and Infection Risk Assessment in COVID-19 Pandemic
subject: covid-19, social distancing, deep convolutional neural networks, distance estimation, crowd monitoring, human detection and tracking
description: Social distancing is a recommended solution by the World Health Organisation (WHO) to minimise the spread of COVID-19 in public places. The majority of governments and national health authorities have set the 2-m physical distancing as a mandatory safety measure in shopping centres, schools and other covered areas. In this research, we develop a hybrid Computer Vision and YOLOv4-based Deep Neural Network (DNN) model for automated people detection in the crowd in indoor and outdoor environments using common CCTV security cameras. The proposed DNN model in combination with an adapted inverse perspective mapping (IPM) technique and SORT tracking algorithm leads to a robust people detection and social distancing monitoring. The model has been trained against two most comprehensive datasets by the time of the research—the Microsoft Common Objects in Context (MS COCO) and Google Open Image datasets. The system has been evaluated against the Oxford Town Centre dataset (including 150,000 instances of people detection) with superior performance compared to three state-of-the-art methods. The evaluation has been conducted in challenging conditions, including occlusion, partial visibility, and under lighting variations with the mean average precision of 99.8% and the real-time speed of 24.1 fps. We also provide an online infection risk assessment scheme by statistical analysis of the spatio-temporal data from people’s moving trajectories and the rate of social distancing violations. We identify high-risk zones with the highest possibility of virus spread and infection. This may help authorities to redesign the layout of a public place or to take precaution actions to mitigate high-risk zones. The developed model is a generic and accurate people detection and tracking solution that can be applied in many other fields such as autonomous vehicles, human action recognition, anomaly detection, sports, crowd analysis, or any other research areas where the human detection is in the c…
creator: Mahdi Rezaei, Mohsen Azarmi
source: Epidemiology and Health
publisher: Korean Society of Epidemiology
date: 2020
coverage: Biology (General), Chemistry, Engineering (General). Civil engineering (General), Technology, Physics

DeepSuperSage analysis of the Vicia faba transcriptome in response to Ascochyta fabae infection
subject: SuperSAGE, ascochyta, faba bean
description: Understanding the host response to Ascochyta fabae in faba bean (Vicia faba L.), is crucial to elucidate the biology of host resistance. In an attempt to unravel the faba bean – A. fabae interaction, we performed genome-wide transcriptome profiling by deepSuperSAGE that quantified the early transcriptional changes elicited by the fungus in the resistant 29H faba bean genotype. The total number of 26 bp tags obtained was 1,313,009, of which 51,484 were unique sequences (UniTags) and 161 of them corresponded to fungal sequences. Sequences with a full match of the 26 bp revealed 2,222 tags with a significant P-value that were expressed differentialy between inoculated and control leaves. After gene ontology (GO) annotation, 2,143 of these matched to databases sequences (approximately 1/3 into each GO domain). At a 2.7-fold change threshold, 1,197 sequences were significantly differentially expressed in infected as compared to control leaves. Of these, nearly half were up- and the other downregulated. The most enriched GO terms corresponded to tags related with photosynthesis metabolism or structural components. Ten of them can be associated with plant defense, due to their association with responses to the jasmonic acid pathway, pectin esterase activity or gene silencing. Validation of the SuperSAGE data by qPCR of ten differentially expressed UniTags confirmed a rapid increase or decrease in mRNA 8 to 12 hours after inoculation in most of the up-regulated tags and, less consistently, in the downregulated ones. This study represents the most comprehensive analysis of the Ascochyta-response transcriptome of faba bean available to date. The applicability of these tags will increase as more faba bean genomic and cDNA sequences become available.
creator: Eva MADRID, Carmen PALOMINO, Anne PLÖTNER, Ralf HORRES, Björn ROTTER, Peter WINTER, Nicolas KREZDORN, Ana TORRES
source: Phytopathologia Mediterranea
publisher: Firenze University Press
date: 2013
relation: https://oajournals.fupress.net/index.php/pm/article/view/5686
coverage: Botany

Deficits in the Statistical and Probabilistic Literacy of Citizens: Effects in a World in Crisis
subject: crisis, professional development, pedagogical content knowledge, Statistical literacy, mathematics teachers, probabilistic literacy
description: The emergency caused by coronavirus disease 2019 (COVID-19) has revealed significant deficiencies in citizens’ statistical and probabilistic knowledge and in people’s understanding of mathematical and, particularly, stochastic models, which may lead to wrong personal or institutional choices, with critical consequences for the entire population. Mathematics teachers play an essential role in ensuring citizens’ statistical and probabilistic literacy. This study aimed at analyzing the pedagogical content knowledge that teachers utilized to teach statistics and probability through considering contextualized situations. In order to accomplish this purpose, fourteen secondary mathematics teachers participated in a formative and evaluative activity that was designed using the transformational professional competence model. During each evaluative phase, a group discussion was conducted. Participants were asked to reflect on their actions when promoting statistical and probabilistic literacy by considering a range of topics (data science, didactic resources, and methodological approaches) that were addressed during the training phase. A mixed, quantitative–qualitative methodological design was used for the data collection and analysis, which involved open-ended, multiple-choice, or scale-type questions that were moderated by the Metaplan® approach and the Mentimeter® software. The main ideas that emerged from the results indicated the need to reinforce the use of real data, technological resources to handle the visualization of information, the elaboration of different types of graphs besides the classical ones, and the formulation of hypotheses. The initial diagnosis will continue within a research and practice community made up of teachers and researchers. Therefore, a working proposal based on examples and models contextualized within the COVID-19 crisis is presented in order to enhance secondary mathematics teachers’ pedagogical content knowledge.
creator: Laura Muñiz-Rodríguez, Luis J. Rodríguez-Muñiz, Ángel Alsina
source: Epidemiology and Health
publisher: Korean Society of Epidemiology
date: 2020
coverage: Mathematics

Definición de “Agricultura Familiar” como categoría socioeconómica
subject: El desarrollo rural. Definición teórica. Agricultura
description: El objeto del presente artículo es definir consistentemente y con claridad qué características son propias definen a la “Agricultura familiar”. De esta forma se realizó una recopilación de las definiciones y metodologías comúnmente más aceptadas y utilizadas a nivel de los países, así como a nivel regional e internacional para definir y caracterizar a la agricultura familiar, tomando en cuenta su diversidad. Además o estudio intenta hacer definiciones sobre la AF como categoría socioeconómica de análisis y como las dichas definiciones se sustenten en criterios y luego en parámetros e indicadores, que puedan hacer comparables situaciones muy diferentes. El desafío ahora es reconocer la heterogenidad de la AF y comenzar a hablar de “matrices de políticas públicas” que permitan atender la complejidad de la finca familiar, la necesidad de asociar las mismas para asegurar el autoconsumo familiar y competir, así como la necesidad de asegurar los parámetros de la SAN. Finalmente, encarar una análisis de la AF como categoría socio / económica no es atemporal ni a – geográfica, está fuertemente vinculada a cada contexto y cada contexto tiene que ver con estos factores: (a) los derivados de la situación geográfica y agroecológica y distancia relativa a los mercados; (b) los derivados de los procesos económicos; (c) los derivados de la historia, la cultura, la relación con la tierra y el territorio. El Concepto de AF es una construcción multidimensional. Dentro de ella los criterios fundamentales son: (i) organización del trabajo familiar en la finca y contratación eventual de mano de obra asalariada; (ii) administración de la finca o empresa familiar, o sea quién toma las decisiones productivas y/o técnicas y/o comerciales; (c) situación relativa de autonomía o dependencia respecto de los distintos mercados (insumos, factores, productos).
creator: Álvaro Ramos
source: Redes
publisher: Universidade de Santa Cruz do Sul
date: 2016
relation: https://online.unisc.br/seer/index.php/redes/article/view/8243
coverage: Social Sciences, Social sciences (General), Human ecology. Anthropogeography

Definición de estrategias para la educación ambiental en el nivel básico de Tumaco, Nariño, Colombia
subject: Educación Ambiental, Estrategias, planes nacionales de desarrollo
description: El trabajo centra la atención en la Educación Ambiental desde tres perspectivas, las definiciones, las estrategias globales que se desarrollan en varios países del área Iberoamericana y el estado de la problemática ambiental en Tumaco Nariño. Se utilizan métodos empíricos de obtención de la información apoyados en la escala Likenrt; los resultados de entrevistas a docentes y estudiantes se comparan con los obtenidos del análisis de las estrategias actuales en la Educación Ambiental para el Departamento de Tumaco, para reafirmar la necesidad de elaborar estrategias contextualizadas desde la institución educativa tal y como se evidencia en experiencias que derivan desde el trabajo desde la Universidad Metropolitana del Ecuador. Por ello, el objetivo es mostrar el estado de la temática y puntualizar hacia donde deben estar dirigidos los cambios en las estrategias de Educación Ambiental. Como conclusiones se comparte la necesidad de contextualizar las estrategias de Educación Ambiental con un enfoque integrador de las acciones priorizando la participación de todos los actores socio ambientales, para lograr una conciencia ambiental y efectos positivos en la mitigación del cambio climático.
creator: Raúl Rodríguez Muñoz, Aleyda Emilce Guerrero Caicedo
source: Revista Metropolitana de Ciencias Aplicadas
publisher: Universidad Metropolitana de Ecuador
date: 2019
relation: http://remca.umet.edu.ec/index.php/REMCA/article/download/176/235
coverage: Social Sciences, Social sciences (General)

Definición de las Brechas en el Uso de las Tic’s para la Innovación Productiva en Pymes del Sector Pecuario Chileno
subject: Análisis descriptivo, Análisis multivariante, Chile, Productividad, Pymes, TIC’s, brechas digitales, innovación, producción pecuaria, sector lechero
description: El presente artículo tiene por objetivo general definir las brechas que dificultan el acceso y el uso adecuado de las TIC’s en las Pymes dedicadas a la producción pecuaria en Chile. Con el fin de concretar dicho objetivo se realizó una encuesta a una muestra compuesta por 151 directivos de Pymes lecheras ubicadas en la Región de los Ríos y la Región de los Lagos en Chile (provincias de Valdivia, Osorno y Llanquihue). Los datos obtenidos fueron tratados mediante análisis estadístico descriptivo y multivariante. A partir del estudio realizado se obtuvieron los siguientes resultados: a) la falta de capacitación fue la principal brecha registrada para el acceso a las TIC’s en las empresas analizadas, b) el deficiente acceso a software específico es otra de las brechas más relevantes y c) la mitad de los directivos encuestados presentaban una actitud desfavorable a la actualización constante de las TIC’s en sus empresas. Finalmente, se recomienda una política pública que tenga por objetivo además del acceso a equipamiento básico y específico, la capacitación profesional en los distintos niveles jerárquicos de las Pymes.
creator: Marcos Mora, Juan Lerdon, Luis Torralbo, Juan Salazar, Sofía Boza, Rodrigo Vásquez
source: Journal of Technology Management & Innovation
publisher: Universidad Alberto Hurtado
date: 2012
relation: http://www.jotmi.org/index.php/GT/article/view/835
coverage: Technology, Technology (General)

Definiciones de acceso a recursos genéticos en la legislación colombiana y sus efectos en la investigacion científica
subject: biologia molecular, biotecnología, genética
description: La aplicación de las definiciones sobre Acceso a Recursos Genéticos (ARG) contenidas en diversas normas legislativas nacionales o comunitarias, pueden afectar la investigación científica (no-comercial y comercial). Se definen dos momentos, entre 1996 y 2013 con la implementación de la decisión 391 de 1996, resultado de la aplicación del Convenio sobre la Biodiversidad Biológica (CDB) de 1992, y a partir de 2013 con decretos que establecen excepciones al ARG y resoluciones del Ministerio de Ambiente y Desarrollo Sostenible que especifican las actividades de ARG. La visión es la de un biotecnólogo, que se concentrará en los elementos técnico-científicos de las normas. En la primera fase no se plantearon excepciones: cualquier investigación que utilizara recursos genéticos y usara herramientas convencionales o moleculares, precisaba de contrato de ARG. Los científicos ignoraron la norma, que trajo como consecuencia la ilegalidad para sus actividades, pero no tuvo efectos prácticos para la mayoría, exceptuando a la Universidad Nacional de Colombia que recibió una sanción administrativa. En la segunda fase se excluyó la investigación científica no comercial en cuatro áreas (ecología, biogeografía, sistemática y evolución), y se limitaron las actividades de ARG a herramientas moleculares. Se espera que estas precisiones resuelvan la ilegalidad de una amplia gama de actividades de la investigación científica, pero se mantiene el peso de los procesos sobre la investigación científica con fines comerciales.
creator: Alejandro Chaparro Giraldo
source: Acta Biológica Colombiana
publisher: Universidad Nacional de Colombia
date: 2016
relation: https://revistas.unal.edu.co/index.php/actabiol/article/view/50695
coverage: Biology (General)