A novel method for genomic-enabled prediction of cultivars in new environments.

Introduction: Genomic selection (GS) has gained global importance due to its potential to accelerate genetic progress and improve the efficiency of breeding programs. Objectives of the research: In this research we proposed a method to improve the prediction accuracy of tested lines in new (untested) environments. Method-1: The new method trained the model with a modified response variable (a difference of response variables) that decreases the lack of a non-stationary distribution between the training and testing and improved the prediction accuracy. Comparing new and conventional method: We compared the prediction accuracy of the conventional genomic best linear unbiased prediction (GBLUP) model (M1) including (or not) genotype × environment interaction (GE) (M1_GE; M1_NO_GE) versus the proposed method (M2) on several data sets. Results and discussion: The gain in prediction accuracy of M2, versus M1_GE, M1_NO_GE in terms of Pearson´s correlation was of at least 4.3%, while in terms of percentage of top-yielding lines captured when was selected the 10% (Best10) and 20% (Best20) of lines was at least of 19.5%, while in terms of Normalized Root Mean Squared Error (NRMSE) was of at least of 42.29%.

A Comparison of Three Machine Learning Methods for Multivariate Genomic Prediction Using the Sparse Kernels Method (SKM) Library.

Genomic selection (GS) changed the way plant breeders select genotypes. GS takes advantage of phenotypic and genotypic information to training a statistical machine learning model, which is used to predict phenotypic (or breeding) values of new lines for which only genotypic information is available. Therefore, many statistical machine learning methods have been proposed for this task. Multi-trait (MT) genomic prediction models take advantage of correlated traits to improve prediction accuracy. Therefore, some multivariate statistical machine learning methods are popular for GS. In this paper, we compare the prediction performance of three MT methods: the MT genomic best linear unbiased predictor (GBLUP), the MT partial least squares (PLS) and the multi-trait random forest (RF) methods. Benchmarking was performed with six real datasets. We found that the three investigated methods produce similar results, but under predictors with genotype (G) and environment (E), that is, E + G, the MT GBLUP achieved superior performance, whereas under predictors E + G + genotype × environment (GE) and G + GE, random forest achieved the best results. We also found that the best predictions were achieved under the predictors E + G and E + G + GE. Here, we also provide the R code for the implementation of these three statistical machine learning methods in the sparse kernel method (SKM) library, which offers not only options for single-trait prediction with various statistical machine learning methods but also some options for MT predictions that can help to capture improved complex patterns in datasets that are common in genomic selection.

Deep-learning power and perspectives for genomic selection.

Deep learning (DL) is revolutionizing the development of artificial intelligence systems. For example, before 2015, humans were better than artificial machines at classifying images and solving many problems of computer vision (related to object localization and detection using images), but nowadays, artificial machines have surpassed the ability of humans in this specific task. This is just one example of how the application of these models has surpassed human abilities and the performance of other machine-learning algorithms. For this reason, DL models have been adopted for genomic selection (GS). In this article we provide insight about the power of DL in solving complex prediction tasks and how combining GS and DL models can accelerate the revolution provoked by GS methodology in plant breeding. Furthermore, we will mention some trends of DL methods, emphasizing some areas of opportunity to really exploit the DL methodology in GS; however, we are aware that considerable research is required to be able not only to use the existing DL in conjunction with GS, but to adapt and develop DL methods that take the peculiarities of breeding inputs and GS into consideration.

Effect of an ecosystem-centered community participation programme on the incidence of dengue. A field randomized, controlled trial.

OBJECTIVES: The purpose of this study is to analyse the effect of a community participation programme based on the ecosystem model on the incidence of dengue in urban communities. METHODS: A randomized controlled field trial was conducted in the state of Colima, Mexico. The intervention consisted of a community participation programme focused on the ecosystem; simultaneously, the control groups were communities that only received the usual official prevention programs. The incidence of dengue was estimated in people of both groups due to the appearance of de novo IgM antibodies during the follow-up period. RESULTS: The incidence of dengue in the intervened group was 2.58%/month (n = 818) and in control group 2.26%/month (n = 994), with a risk ratio of 1.14 (95% CI 0.89-1.45) and a PAF of 0.06 (95% CI - 0.056 to 0.16). The A. aegypti larval density (Breteau Index) was reduced in the treated group. CONCLUSIONS: The implementation of a community participation programme in the cities of Colima, Mexico, showed a slightly counterproductive effect on the incidence of dengue. This happened even with a reduction in the A. aegypti index.

Cost-Effectiveness of the Strategies to Reduce the Incidence of Dengue in Colima, México.

Dengue fever is considered to be one of the most important arboviral diseases globally. Unsuccessful vector-control strategies might be due to the lack of sustainable community participation. The state of Colima, located in the Western region of Mexico, is a dengue-endemic area despite vector-control activities implemented, which may be due to an insufficient health economic analysis of these interventions. A randomized controlled community trial took place in five urban municipalities where 24 clusters were included. The study groups (n = 4) included an intervention to improve the community participation in vector control (A), ultra-low volume (ULV) spraying (B), both interventions (AB), and a control group. The main outcomes investigated were dengue cumulative incidence, disability-adjusted life years (DALYs), and the direct costs per intervention. The cumulative incidence of dengue was 17.4%, A; 14.3%, B; 14.4%, AB; and 30.2% in the control group. The highest efficiency and effectiveness were observed in group B (0.526 and 6.97, respectively) and intervention A was more likely to be cost-effective ($3952.84 per DALY avoided) followed by intervention B ($4472.09 per DALY avoided). Our findings suggest that efforts to improve community participation in vector control and ULV-spraying alone are cost-effective and may be useful to reduce the vector density and dengue incidence.

Violencia doméstica y riesgo de conducta suicida en universitarios adolescentes / Domestic violence and risk of suicidal behavior among university students

OBJETIVO: Estimar el grado de asociación entre violencia doméstica física, verbal y sexual con la conducta suicida en adolescentes universitarios. MATERIAL Y MÉTODOS: Estudio de casos y controles pareado en estudiantes universitarios de Colima. Los casos fueron 235 adolescentes que presentaron tanto ideación suicida como intento suicida; los controles fueron 470 individuos de la misma edad y sexo. RESULTADOS: El abuso sexual mostró el mayor grado de asociación con conducta suicida (RM= 27.4), seguido de violencia verbal (RM= 9.28), uso de drogas (RM= 8.6), violencia física (RM= 5.5) y tabaquismo (RM= 3.6). La regresión logística multivariada mostró que la violencia verbal se asoció con conducta suicida en forma independiente, mientras que violencia física, abuso sexual, tabaquismo y uso de drogas parecen depender de aquella. CONCLUSIONES: La violencia intrafamiliar, particularmente la verbal, está fuertemente asociada con la conducta suicida en adolescentes y debe ser considerada dentro de programas preventivos contra suicidio.

OBJECTIVE: To estimate the degree of association between domestic violence -physical, verbal or sexual- with suicidal behavior among university students. MATERIAL AND METHODS: A matched case-control study was done with students attending the University of Colima, Mexico. The cases were 235 teenagers who presented both suicidal ideation and suicide attempt; the controls were 470 individuals of the same age and sex. RESULTS: Sexual abuse showed the highest degree of association with suicidal behavior (OR= 27.4), followed by verbal violence (OR= 9.28), drug use (OR= 8.6), physical violence (OR= 5.5) and smoking (OR= 3.6). Multivariate logistic regression showed that verbal violence was associated with suicidal behavior independently of the other variables, while physical violence, sexual abuse, smoking and drug use seem to depend on verbal violence. CONCLUSIONS: Domestic violence, particularly verbal or sexual, is strongly associated with suicidal behavior in adolescents and should be considered in suicide prevention programs.

[Domestic violence and risk of suicidal behavior among university students]. / Violencia doméstica y riesgo de conducta suicida en universitarios adolescentes.

OBJECTIVE: To estimate the degree of association between domestic violence -physical, verbal or sexual- with suicidal behavior among university students. MATERIAL AND METHODS: A matched case-control study was done with students attending the University of Colima, Mexico. The cases were 235 teenagers who presented both suicidal ideation and suicide attempt; the controls were 470 individuals of the same age and sex. RESULTS: Sexual abuse showed the highest degree of association with suicidal behavior (OR= 27.4), followed by verbal violence (OR= 9.28), drug use (OR= 8.6), physical violence (OR= 5.5) and smoking (OR= 3.6). Multivariate logistic regression showed that verbal violence was associated with suicidal behavior independently of the other variables, while physical violence, sexual abuse, smoking and drug use seem to depend on verbal violence. CONCLUSIONS: Domestic violence, particularly verbal or sexual, is strongly associated with suicidal behavior in adolescents and should be considered in suicide prevention programs.

Modelos matemáticos para enfermedades infecciosas / Mathematical models for infectious diseases

OBJETIVO: Describir la importancia de los modelos matemáticos en la comprensión de la dinámica de transmisión de las enfermedades infecciosas, así como en el diseño de medidas eficaces de control. MATERIAL Y MÉTODOS: Se revisaron las publicaciones internacionales sobre el tema a través de medios digitales; se identificaron alrededor de 60 artículos, aunque sólo se revisaron 27 de éstos por su estrecha relación con el tema. RESULTADOS: Este trabajo explica de manera sinóptica los antecedentes, importancia y clasificación de los modelos matemáticos en padecimientos infecciosos. De modo adicional se describen con detalle algunos modelos comunes de transmisión de enfermedades y otros de uso más reciente que se utilizan en la modelación de trastornos infecciosos. CONCLUSIONES: El empleo de modelos matemáticos ha crecido en grado significativo en los últimos años y son de gran ayuda para idear medidas eficaces de control y erradicación de las enfermedades infecciosas.

OBJECTIVE: To describe the importance of mathematical models in the understanding of infectious disease transmission dynamics, as well as in the design of effective strategies for control. MATERIAL AND METHODS: International literature was reviewed on the subject through digital means. Around 60 papers about the subject were identified; nevertheless, this study is based on only 27 of these, due to the fact that they were directly related to the subject. RESULTS:This work presents a brief explanation of the antecedents, importance and classification of mathematical models for infectious diseases. In addition, a detailed description of some classical models is discussed as well as other more recent models used in the modeling of infectious disease. CONCLUSIONS: The use of mathematical models for infectious diseases has grown significantly in the last few years and has proven to be of great help in designing efficient strategies for control and eradication of infectious diseases.

[Mathematical models for infectious diseases]. / Modelos matemáticos para enfermedades infecciosas.

OBJECTIVE: To describe the importance of mathematical models in the understanding of infectious disease transmission dynamics, as well as in the design of effective strategies for control. MATERIAL AND METHODS: International literature was reviewed on the subject through digital means. Around 60 papers about the subject were identified; nevertheless, this study is based on only 27 of these, due to the fact that they were directly related to the subject. RESULTS: This work presents a brief explanation of the antecedents, importance and classification of mathematical models for infectious diseases. In addition, a detailed description of some classical models is discussed as well as other more recent models used in the modeling of infectious disease. CONCLUSIONS: The use of mathematical models for infectious diseases has grown significantly in the last few years and has proven to be of great help in designing efficient strategies for control and eradication of infectious diseases.

[Interepidemic transmission of dengue in the city of Colima, Mexico]. / Transmisión interepidémica del dengue en la ciudad de Colima, México.

OBJECTIVE: To determine the occurrence of interepidemic dengue in a community infested with Aedes aegypti and to analyze its epidemiologic characteristics. MATERIAL AND METHODS: A longitudinal probabilistic study was carried out in Colima City between 2001 and 2002. The sample population consisted of 245 subjects. The following were recorded for each subject: sex, age, socio-economic level and dengue fever symptoms, testing for serum IgG and IgM antidengue, using quick immunochromatography as well as ELISA tests, in a seven-month follow-up period. RESULTS: Twelve individuals showed recent dengue infection (incidence: 1.77%; 95%: confidence interval 0.9-3.1%). Of these, eight had recent clinical symptoms (chi 2 = 19.6; p < 0.0001, odss ratio 19.6). Poisson regression analysis showed no evidence of correlation between recent infection and sex, age, or socioeconomic level. CONCLUSIONS: Communities infested with A. aegypti, like Colima, may continually exhibit dengue infection with no apparent epidemic. Such infections are seemingly not associated with age, sex, or socioeconomic level, but with clinical symptoms. This situation could be considered an early indicator of interepidemic transmission.

Transmisión interepidémica del dengue en la ciudad de Colima, México / Interepidemic transmission of dengue in Colima City, Mexico

OBJETIVO: Determinar la presencia de dengue interepidémico en una comunidad infestada por Aedes aegypti, y analizar sus características epidemiológicas. MATERIAL Y MÉTODOS: Entre 2001 y 2002 se realizó un estudio probabilístico longitudinal en 245 habitantes de la ciudad de Colima, México. En cada caso se registraron: edad, sexo, nivel socioeconómico, cuadro clínico sugestivo de dengue, y se buscó la presencia de IgG e IgM antidengue por inmunocromatografía rápida y por ELISA, en un seguimiento de siete meses. Los datos se analizaron mediante tablas de contingencia y regresión de Poisson univariada. RESULTADOS: Doce individuos resultaron con infección reciente (incidencia de 1.77 por ciento; IC 95 por ciento: 0.9-3.1 por ciento), ocho de ellos refirieron cuadro clínico reciente (ji2=19.6; p=0.0001, RM: 19.6). La regresión de Poisson no reveló correlación de la infección reciente con edad, sexo, ni con nivel socioeconómico. CONCLUSIONES: En comunidades infestadas por A aegypti, como Colima, pueden ocurrir infecciones continuas por dengue sin epidemia aparente. Dichas infecciones no parecen asociarse con la edad, el sexo, ni con el nivel socioeconómico, pero sí con el cuadro clínico, el cual podría considerarse como indicador precoz de posible transmisión interepidémica

Presence of triatominae (Hemiptera, Reduviidae) and risk of transmission of Chagas disease in Colima, México.

With the purpose of evaluating the risk of transmission of the Chagas disease in the State of Colima, México, an entomological survey was performed to obtain triatominae and the rate of infection by Trypanosoma cruzi determined by examination of its dejections. Two hundred eighteen houses located in 16 villages were sampled. In each house the intradomestic and peridomestic habitats were examined by the man-hour-house method, sensor boxes and mouse-baited traps. Also, 12 silvatic places were explored around the same areas using the same techniques as the ones sampled. In total, 456 specimens were captured, of which 139 correspond to Triatoma phyllosoma pallidipennis; 80 to T.p. longipennis; one specimen of T. dimidiata and 236 nymphs of Triatoma sp. Two hundred ninety seven insects were captured in the intradomestic habitat, 132 in the peridomestic and 26 in the silvatic. The index of positive houses was 27%, located in the central area of the state. The rate of natural infection with T. cruzi showed 25.6%. This results confirmed the presence of two important vectors of the Chagas disease in Colima. Its preference for the domestic habitat and its high levels of natural infection with T. cruzi suggested the existence of a significant risk for its transmission in this area of the country.

Presence of Triatominae (Hemiptera, Reduviidae) and risk of transmission of Chagas disease in Colima, México

With the purpose of evaluating the risk of transmission of the Chagas disease in the State of Colima, México, an entomological survey was performed to obtain triatominae and the rate of infection by Trypanosoma cruzi determined by examination of its dejections. Two hundred eighteen houses located in 16 villages were sampled. In each house the intradomestic and peridomestic habitats were examined by the man-hour-house method, sensor boxes and mouse-baited traps. Also, 12 silvatic places were explored around the same areas using the same techniques as the ones sampled. In total, 456 specimens were captured, of which 139 correspond to Triatoma phyllosoma pallidipennis; 80 to T. p. longipennis; one specimen of T. dimidiata and 236 nymphs of Triatoma sp. Two hundred ninety seven insects were captured in the intradomestic habitat, 132 in the peridomestic and 26 in the silvatic. The index of positive houses was 27 percent, located in the central area of the state. The rate of natural infection with T. cruzi showed 25.6 percent. This results confirmed the presence of two important vectors of the Chagas disease in Colima. Its preference for the domestic habitat and its high levels of natural infection with T. cruzi suggested the existence of a significant risk for its transmission in this area of the country