ADBD  Anàlisi de Dades Complexes per a les Decisions Empresarials
http://hdl.handle.net/2117/79665
20190521T05:32:48Z

Transfer function and time series outlier analysis: modelling Soil salinity in loamy sand soil by including the influences of irrigation management and soil temperature
http://hdl.handle.net/2117/130637
Transfer function and time series outlier analysis: modelling Soil salinity in loamy sand soil by including the influences of irrigation management and soil temperature
Aljoumani, Basem; Sánchez Espigares, Josep Anton; Cañameras Riba, Núria; Wessdek, Gerd; Josa March, Ramon
In variable interval irrigation, simply including soil salinity data in the soil salinity model is not valid for making predictions, because changes in irrigation frequency must also be taken into account. This study on variable interval irrigation used capacitance soil sensors simultaneously to obtain hourly measurements of bulk electrical conductivity (sb), soil temperature (t) and soil water content (¿). Observations of sb were converted so that the electrical conductivity of the pore water (sp) could be estimated as an indicator of soil salinity. Values of ¿, t and sp were used to test a mathematical model for studying how sp crosscorrelates with t and ¿ to predict soil salinity at a given depth. These predictions were based on measurements of sp, t, and ¿ at a shallow depth. As a result, prediction at shallow depth was successful after integrating intervention analysis and outlier detection into the seasonal autoregressive integrated moving average (ARIMA) model. We then used the (multipleinput/oneoutput) transfer function models to logically predict soil salinity at the depths of interest. The model could also correctly determine the effect of the irrigation event on soil salinity
20190320T07:49:21Z
Aljoumani, Basem
Sánchez Espigares, Josep Anton
Cañameras Riba, Núria
Wessdek, Gerd
Josa March, Ramon
In variable interval irrigation, simply including soil salinity data in the soil salinity model is not valid for making predictions, because changes in irrigation frequency must also be taken into account. This study on variable interval irrigation used capacitance soil sensors simultaneously to obtain hourly measurements of bulk electrical conductivity (sb), soil temperature (t) and soil water content (¿). Observations of sb were converted so that the electrical conductivity of the pore water (sp) could be estimated as an indicator of soil salinity. Values of ¿, t and sp were used to test a mathematical model for studying how sp crosscorrelates with t and ¿ to predict soil salinity at a given depth. These predictions were based on measurements of sp, t, and ¿ at a shallow depth. As a result, prediction at shallow depth was successful after integrating intervention analysis and outlier detection into the seasonal autoregressive integrated moving average (ARIMA) model. We then used the (multipleinput/oneoutput) transfer function models to logically predict soil salinity at the depths of interest. The model could also correctly determine the effect of the irrigation event on soil salinity

Which runs to skip in twolevel factorial designs when not all can be performed
http://hdl.handle.net/2117/130379
Which runs to skip in twolevel factorial designs when not all can be performed
Xampeny Solani, Rafael; Grima Cintas, Pedro; TortMartorell Llabrés, Xavier
When a twolevel factorial design allows estimating contrasts that can be considered negligible from scratch, it is possible to omit some runs and later estimate their values by equating to zero the expressions of some of that contrasts. This article presents the combinations of runs to be omitted in 8 and 16 runs twolevel factorial designs so that the responses can be estimated in such a way as to produce the least possible impact on the desired properties of the estimated contrasts: low and equal variance and the smallest possible correlation among them.
20190313T12:22:31Z
Xampeny Solani, Rafael
Grima Cintas, Pedro
TortMartorell Llabrés, Xavier
When a twolevel factorial design allows estimating contrasts that can be considered negligible from scratch, it is possible to omit some runs and later estimate their values by equating to zero the expressions of some of that contrasts. This article presents the combinations of runs to be omitted in 8 and 16 runs twolevel factorial designs so that the responses can be estimated in such a way as to produce the least possible impact on the desired properties of the estimated contrasts: low and equal variance and the smallest possible correlation among them.

Selecting significant effects in factorial designs: Lenth's method versus using negligible interactions
http://hdl.handle.net/2117/130367
Selecting significant effects in factorial designs: Lenth's method versus using negligible interactions
Xampeny Solani, Rafael; Grima Cintas, Pedro; TortMartorell Llabrés, Xavier
Among the many analytical techniques that have been published to analyze the significance of the effects in the absence of replications, two have emerged as the most widely used in text books as well as statistical software packages: The Lenth's method and the estimation of the variance of the effects from the values of those considered negligible. This article shows that neither is better than the other in all cases, and by analyzing the results obtained in a wide variety of situations it provides guidelines on when it is preferable to use one or the other technique
20190313T11:43:26Z
Xampeny Solani, Rafael
Grima Cintas, Pedro
TortMartorell Llabrés, Xavier
Among the many analytical techniques that have been published to analyze the significance of the effects in the absence of replications, two have emerged as the most widely used in text books as well as statistical software packages: The Lenth's method and the estimation of the variance of the effects from the values of those considered negligible. This article shows that neither is better than the other in all cases, and by analyzing the results obtained in a wide variety of situations it provides guidelines on when it is preferable to use one or the other technique

Brassica aphid (Hemiptera: Aphididae) populations are conditioned by climatic variables and parasitism level: a study case of Triângulo Mineiro, Brazil
http://hdl.handle.net/2117/130097
Brassica aphid (Hemiptera: Aphididae) populations are conditioned by climatic variables and parasitism level: a study case of Triângulo Mineiro, Brazil
Sampaio, M. V.; Korndörfer, A. P.; Pujade Villar, Juli; Hubaide, J.E.A.; Ferreira, S. E.; Arantes, S. O.; Bortoletto, D. M.; Guimarães, C. M.; Sánchez Espigares, Josep Anton; Caballero López, Berta
Cosmopolitan pests such as Brevicoryne brassicae, Lipaphis pseudobrassicae, and Myzus persicae (Aphididae) cause significant damage to Brassicaceae crops. Assessment of the important biotic and abiotic factors that regulate these pests is an essential step in the development of effective Integrated Pest Management programs for these aphids. This study evaluated the influence of leaf position, precipitation, temperature, and parasitism on populations of L. pseudobrassicae, M. persicae, and B. brassicae in collard greens fields in the Triângulo Mineiro region (Minas Gerais state), Brazil. Similar numbers of B. brassicae were found on all parts of the collard green plants, whereas M. persicae and L. pseudobrassicae were found in greatest numbers on the middle and lower parts of the plant. While temperature and precipitation were positively related to aphid population size, their effects were not accumulative, as indicated by a negative interaction term. Although Diaeretiella rapae was the main parasitoid of these aphids, hyperparasitism was dominant; the main hyperparasitoid species recovered from plant samples was Alloxysta fuscicornis. Parasitoids seem to have similar distributions on plants as their hosts. These results may help predict aphid outbreaks and gives clues for specific intraplant locations when searching for and monitoring aphid populations.
20190306T12:08:41Z
Sampaio, M. V.
Korndörfer, A. P.
Pujade Villar, Juli
Hubaide, J.E.A.
Ferreira, S. E.
Arantes, S. O.
Bortoletto, D. M.
Guimarães, C. M.
Sánchez Espigares, Josep Anton
Caballero López, Berta
Cosmopolitan pests such as Brevicoryne brassicae, Lipaphis pseudobrassicae, and Myzus persicae (Aphididae) cause significant damage to Brassicaceae crops. Assessment of the important biotic and abiotic factors that regulate these pests is an essential step in the development of effective Integrated Pest Management programs for these aphids. This study evaluated the influence of leaf position, precipitation, temperature, and parasitism on populations of L. pseudobrassicae, M. persicae, and B. brassicae in collard greens fields in the Triângulo Mineiro region (Minas Gerais state), Brazil. Similar numbers of B. brassicae were found on all parts of the collard green plants, whereas M. persicae and L. pseudobrassicae were found in greatest numbers on the middle and lower parts of the plant. While temperature and precipitation were positively related to aphid population size, their effects were not accumulative, as indicated by a negative interaction term. Although Diaeretiella rapae was the main parasitoid of these aphids, hyperparasitism was dominant; the main hyperparasitoid species recovered from plant samples was Alloxysta fuscicornis. Parasitoids seem to have similar distributions on plants as their hosts. These results may help predict aphid outbreaks and gives clues for specific intraplant locations when searching for and monitoring aphid populations.

Validation and implementation of a diagnostic algorithm for DNA Detection of Bordetella pertussis, B. parapertussis, and Bholmesii in a Pediatric Referral Hospital in Barcelona, Spain
http://hdl.handle.net/2117/129052
Validation and implementation of a diagnostic algorithm for DNA Detection of Bordetella pertussis, B. parapertussis, and Bholmesii in a Pediatric Referral Hospital in Barcelona, Spain
Valero Rello, Anna; Henares Bonilla, Desirée; Acosta Argueta, Lesly María; Jané Checa, Mireia; Godoy Garcia, Pere; Muñoz Almagro, Carmen
This study aimed to validate a comprehensive diagnostic protocolbased on realtime PCR for the rapid detection and identification ofBordetella pertussis,Bordetella parapertussis, andBordetella holmesii, as well as its implementationin the diagnostic routine of a reference children’s hospital. The new algorithm included a triplex quantitative PCR (qPCR) targeting IS481gene (inB. pertussis,B. holmesii, and someBordetella bronchisepticastrains), pIS1001(B. parapertussisspecific)andrnaseP as the human internal control. Two confirmatory singleplex tests forB.pertussis(ptxAPr) andB. holmesii(hIS1001) were performed if IS481was positive. Analytical validation included determination of linear range, linearity, efficiency, precision, sensitivity, and a reference panel with clinical samples. Once validated, the newalgorithm was prospectively implemented in children with clinical suspicion ofwhooping cough presenting to Hospital Sant Joan de Deu (Barcelona, Spain) over12 months. Lower limits of detection obtained were 4.4, 13.9, and 27.3 genomicequivalents/ml of sample for IS481(onB. pertussis), pIS1001and hIS1001, and 777.9forptxAPr. qPCR efficiencies ranged from 86.0% to 96.9%. Intra and interassay variabilities were 3% and 5%, respectively. Among 566 samples analyzed,B. pertussis,B. holmesii, andB. parapertussiswere detected in 11.1%, 0.9% (only in females 4 years old), and 0.2% of samples, respectively. The new algorithm proved to be auseful microbiological diagnostic tool for whooping cough, demonstrating a low rateof other nonpertussis Bordetellaspecies in our surveilled area
20190213T12:56:16Z
Valero Rello, Anna
Henares Bonilla, Desirée
Acosta Argueta, Lesly María
Jané Checa, Mireia
Godoy Garcia, Pere
Muñoz Almagro, Carmen
This study aimed to validate a comprehensive diagnostic protocolbased on realtime PCR for the rapid detection and identification ofBordetella pertussis,Bordetella parapertussis, andBordetella holmesii, as well as its implementationin the diagnostic routine of a reference children’s hospital. The new algorithm included a triplex quantitative PCR (qPCR) targeting IS481gene (inB. pertussis,B. holmesii, and someBordetella bronchisepticastrains), pIS1001(B. parapertussisspecific)andrnaseP as the human internal control. Two confirmatory singleplex tests forB.pertussis(ptxAPr) andB. holmesii(hIS1001) were performed if IS481was positive. Analytical validation included determination of linear range, linearity, efficiency, precision, sensitivity, and a reference panel with clinical samples. Once validated, the newalgorithm was prospectively implemented in children with clinical suspicion ofwhooping cough presenting to Hospital Sant Joan de Deu (Barcelona, Spain) over12 months. Lower limits of detection obtained were 4.4, 13.9, and 27.3 genomicequivalents/ml of sample for IS481(onB. pertussis), pIS1001and hIS1001, and 777.9forptxAPr. qPCR efficiencies ranged from 86.0% to 96.9%. Intra and interassay variabilities were 3% and 5%, respectively. Among 566 samples analyzed,B. pertussis,B. holmesii, andB. parapertussiswere detected in 11.1%, 0.9% (only in females 4 years old), and 0.2% of samples, respectively. The new algorithm proved to be auseful microbiological diagnostic tool for whooping cough, demonstrating a low rateof other nonpertussis Bordetellaspecies in our surveilled area

Estimating pore water electrical conductivity of sandy soil from time domain reflectometry records using a timevarying dynamic linear model
http://hdl.handle.net/2117/127845
Estimating pore water electrical conductivity of sandy soil from time domain reflectometry records using a timevarying dynamic linear model
Aljoumani, Basem; Sánchez Espigares, Josep Anton; Wessolek, Gerd
Despite the importance of computing soil pore water electrical conductivity (sp) from soil bulk electrical conductivity (sb) in ecological and hydrological applications, a good method of doing so remains elusive. The Hilhorst concept offers a theoretical model describing a linear relationship between sb, and relative dielectric permittivity (eb) in moist soil. The reciprocal of pore water electrical conductivity (1/sp) appears as a slope of the Hilhorst model and the ordinary least squares (OLS) of this linear relationship yields a single estimate ( 1/spˆ ) of the regression parameter vector (sp) for the entire data. This study was carried out on a sandy soil under laboratory conditions. We used a timevarying dynamic linear model (DLM) and the Kalman filter (Kf) to estimate the evolution of sp over time. A time series of the relative dielectric permittivity (eb) and sb of the soil were measured using time domain reflectometry (TDR) at different depths in a soil column to transform the deterministic Hilhorst model into a stochastic model and evaluate the linear relationship between eb and sb in order to capture deterministic changes to (1/sp). Applying the Hilhorst model, strong positive autocorrelations between the residuals could be found. By using and modifying them to DLM, the observed and modeled data of eb obtain a much better match and the estimated evolution of sp converged to its true value. Moreover, the offset of this linear relation varies for each soil depth
20190130T07:34:00Z
Aljoumani, Basem
Sánchez Espigares, Josep Anton
Wessolek, Gerd
Despite the importance of computing soil pore water electrical conductivity (sp) from soil bulk electrical conductivity (sb) in ecological and hydrological applications, a good method of doing so remains elusive. The Hilhorst concept offers a theoretical model describing a linear relationship between sb, and relative dielectric permittivity (eb) in moist soil. The reciprocal of pore water electrical conductivity (1/sp) appears as a slope of the Hilhorst model and the ordinary least squares (OLS) of this linear relationship yields a single estimate ( 1/spˆ ) of the regression parameter vector (sp) for the entire data. This study was carried out on a sandy soil under laboratory conditions. We used a timevarying dynamic linear model (DLM) and the Kalman filter (Kf) to estimate the evolution of sp over time. A time series of the relative dielectric permittivity (eb) and sb of the soil were measured using time domain reflectometry (TDR) at different depths in a soil column to transform the deterministic Hilhorst model into a stochastic model and evaluate the linear relationship between eb and sb in order to capture deterministic changes to (1/sp). Applying the Hilhorst model, strong positive autocorrelations between the residuals could be found. By using and modifying them to DLM, the observed and modeled data of eb obtain a much better match and the estimated evolution of sp converged to its true value. Moreover, the offset of this linear relation varies for each soil depth

Saving runs in fractional factorial designs
http://hdl.handle.net/2117/127443
Saving runs in fractional factorial designs
Grima Cintas, Pedro; Rodero de Lamo, Lourdes; TortMartorell Llabrés, Xavier
When it is known a priori that some contrasts are negligible in a factorial design, their expressions can be used to deduce the missing results. In this article we propose a method for using this procedure when, as in the case of fractional designs, it is not known which contrasts will be null. The method is based on first establishing an interval of possible values corresponding to each of the missing results, then identifying which contrasts are always null independently of the value of said results.
20190123T12:02:32Z
Grima Cintas, Pedro
Rodero de Lamo, Lourdes
TortMartorell Llabrés, Xavier
When it is known a priori that some contrasts are negligible in a factorial design, their expressions can be used to deduce the missing results. In this article we propose a method for using this procedure when, as in the case of fractional designs, it is not known which contrasts will be null. The method is based on first establishing an interval of possible values corresponding to each of the missing results, then identifying which contrasts are always null independently of the value of said results.

Consequences of using estimated response values from negligible interactions in factorial designs
http://hdl.handle.net/2117/127438
Consequences of using estimated response values from negligible interactions in factorial designs
Xampeny Solani, Rafael; Grima Cintas, Pedro; TortMartorell Llabrés, Xavier
This article analyzes the increase in the probability of committing type I and type II errors in assessing the significance of the effects when some properly selected runs have not been carried out and their responses have been estimated from the interactions considered null from scratch. This is done by simulating the responses from known models that represent a wide variety of practical situations that the experimenter will encounter; the responses considered to be missing are then estimated and the significance of the effects is assessed. Through comparison with the parameters of the model, the errors are then identified. To assess the significance of the effects when there are missing values, the BoxMeyer method has been used. The conclusions are that 1 missing value in 8 run designs and up to 3 missing values in 16 run designs experiments can be estimated without hardly any notable increase in the probability of error when assessing the significance of the effects.
20190123T11:44:04Z
Xampeny Solani, Rafael
Grima Cintas, Pedro
TortMartorell Llabrés, Xavier
This article analyzes the increase in the probability of committing type I and type II errors in assessing the significance of the effects when some properly selected runs have not been carried out and their responses have been estimated from the interactions considered null from scratch. This is done by simulating the responses from known models that represent a wide variety of practical situations that the experimenter will encounter; the responses considered to be missing are then estimated and the significance of the effects is assessed. Through comparison with the parameters of the model, the errors are then identified. To assess the significance of the effects when there are missing values, the BoxMeyer method has been used. The conclusions are that 1 missing value in 8 run designs and up to 3 missing values in 16 run designs experiments can be estimated without hardly any notable increase in the probability of error when assessing the significance of the effects.

Selecting significant effects in factorial designs: Lenth’s method versus the BoxMeyer approach
http://hdl.handle.net/2117/126950
Selecting significant effects in factorial designs: Lenth’s method versus the BoxMeyer approach
Xampeny Solani, Rafael; Grima Cintas, Pedro; Tort Martorell, X.
The Lenth method is conceptually simple and probably the most common approach to analyzing the significance of the effects in factorial designs. Here, we compare it with a Bayesian approach proposed by Box and Meyer and which does not appear in the usual software packages. The comparison is made by simulating the results of 4, 8 and 16 run designs in a set of scenarios that mirror practical situations and analyzing the results provided by both methods. Although the results depend on the number of runs and the scenario considered, the use of the Box and Meyer method generally produces better results. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
20190116T11:58:53Z
Xampeny Solani, Rafael
Grima Cintas, Pedro
Tort Martorell, X.
The Lenth method is conceptually simple and probably the most common approach to analyzing the significance of the effects in factorial designs. Here, we compare it with a Bayesian approach proposed by Box and Meyer and which does not appear in the usual software packages. The comparison is made by simulating the results of 4, 8 and 16 run designs in a set of scenarios that mirror practical situations and analyzing the results provided by both methods. Although the results depend on the number of runs and the scenario considered, the use of the Box and Meyer method generally produces better results. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.

A dynamic model of the proteins that form the initial ironsulfur cluster biogenesis machinery in yeast mitochondria
http://hdl.handle.net/2117/126682
A dynamic model of the proteins that form the initial ironsulfur cluster biogenesis machinery in yeast mitochondria
Amela Abellán, Isaac; Delicado Useros, Pedro Francisco; Gómez, Antonio; Querol Murillo, Enrique; Cedano, J
The assembly of ironsulfur clusters (ISCs) in eukaryotes involves the protein Frataxin. Deficits in this protein have been associated with iron inside the mitochondria and impair ISC biogenesis as it is postulated to act as the iron donor for ISCs assembly in this organelle. A pronounced lack of Frataxin causes Friedreich’s Ataxia, which is a human neurodegenerative and hereditary disease mainly affecting the equilibrium, coordination, muscles and heart. Moreover, it is the most common autosomal recessive ataxia. High similarities between the human and yeast molecular mechanisms that involve Frataxin have been suggested making yeast a good model to study that process. In yeast, the protein complex that forms the central assembly platform for the initial step of ISC biogenesis is composed by yeast frataxin homolog, Nfs1–Isd11 and Isu. In general, it is commonly accepted that protein function involves interaction with other protein partners, but in this case not enough is known about the structure of the protein complex and, therefore, how it exactly functions. The objective of this work is to model the protein complex in order to gain insight into structural details that end up with its biological function. To achieve this goal several bioinformatics tools, modeling techniques and protein docking programs have been used. As a result, the structure of the protein complex and the dynamic behavior of its components, along with that of the iron and sulfur atoms required for the ISC assembly, have been modeled. This hypothesis will help to better understand the function and molecular properties of Frataxin as well as those of its ISC assembly protein partners.
The final publication is available at link.springer.com
20190114T12:00:31Z
Amela Abellán, Isaac
Delicado Useros, Pedro Francisco
Gómez, Antonio
Querol Murillo, Enrique
Cedano, J
The assembly of ironsulfur clusters (ISCs) in eukaryotes involves the protein Frataxin. Deficits in this protein have been associated with iron inside the mitochondria and impair ISC biogenesis as it is postulated to act as the iron donor for ISCs assembly in this organelle. A pronounced lack of Frataxin causes Friedreich’s Ataxia, which is a human neurodegenerative and hereditary disease mainly affecting the equilibrium, coordination, muscles and heart. Moreover, it is the most common autosomal recessive ataxia. High similarities between the human and yeast molecular mechanisms that involve Frataxin have been suggested making yeast a good model to study that process. In yeast, the protein complex that forms the central assembly platform for the initial step of ISC biogenesis is composed by yeast frataxin homolog, Nfs1–Isd11 and Isu. In general, it is commonly accepted that protein function involves interaction with other protein partners, but in this case not enough is known about the structure of the protein complex and, therefore, how it exactly functions. The objective of this work is to model the protein complex in order to gain insight into structural details that end up with its biological function. To achieve this goal several bioinformatics tools, modeling techniques and protein docking programs have been used. As a result, the structure of the protein complex and the dynamic behavior of its components, along with that of the iron and sulfur atoms required for the ISC assembly, have been modeled. This hypothesis will help to better understand the function and molecular properties of Frataxin as well as those of its ISC assembly protein partners.