In this paper, we propose a procedure based on Bounded Dynamic Programming (BDP) to solve the Mix... more In this paper, we propose a procedure based on Bounded Dynamic Programming (BDP) to solve the Mixed-Model Sequencing Problem with Workload Minimisation (MMSP-W), with serial workstations and unrestricted (or free) interruption of the operations. We performed a computational experiment with 225 instances from the literature. The results of our proposal are compared with those obtained through the CPLEX solver.
The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit ... more The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit a strong antibody response in almost all HIV-1 infected individuals. This disulfide-bonded loop region is conserved in most retroviruses suggesting the existence of an essential function in virus life cycle. In this study, we displayed the peptides comprising 12 amino acids of the immunodominant loop of gp41 on the surface of M13 phage as N-terminal fusions to the minor coat protein pIII and major coat protein pVIII of the phage and demonstrated that cysteine loop containing peptide expressed on phage recognized 62 out of 63 (98.4%) HIV-1 positive samples but not control negative sera while phage bearing linear peptides detected 4-30% of HIV-1-positive sera. The main advantage of phage-based ELISA or other antibody detection-based diagnostic tests of HIV-infection to be used for massive screening in developing countries is the reproducible, simple, rapid and low-cost production of recombinant antigens.
To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patient... more To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patients with confirmed neurocysticercosis, we used a phage peptide library that displayed random dodecapeptides as a fusion to the minor coat protein (pIII) of phage M13. To increase the specificity of selection, plates coated with anti-human Fc antibody were used in five rounds of biopanning. The DNA inserts of 30 selected clones were determined and the deduced amino acid sequences were analyzed. Sequence similarities between affinity-selected clones and three known T. solium and T. crassiceps proteins were encountered. Two phage clones have been shown to react in enzyme-linked immunosorbent assay with CSF samples from other patients with neurocysticercosis, and no reaction was observed with CSF samples from patients with other neurological disorders used as negative controls. Our results suggest that affinity selection of peptides from phage libraries using CSF samples from patients is an attractive tool for the development of novel reagents for a simple and sensitive immunodiagnostic test and for understanding the molecular mechanisms participating in the pathogenesis of neurocysticercosis.
DNA immunization or inoculation is a recent vaccination method that induces both humoral and cell... more DNA immunization or inoculation is a recent vaccination method that induces both humoral and cellular immune responses in a range of hosts. Independent of the route or site of vaccination, the transfer of antigen-presenting cells (APC) or antigens into lymphoid organs is necessary. The aim of this investigation was to test whether intraspleen (i.s.) DNA inoculation is capable of inducing a protective immune response. We immunized mice by a single i.s. injection of a DNA construct expressing the immunoglobulin (Ig) heavy-chain variable domain (VH) in which the complementarity-determining regions (CDR) had been replaced by a Taenia crassiceps T-cell epitope. In these mice, immune responses and protective effects elicited by the vaccine were measured. We have shown here for the first time that i.s. DNA inoculation can induce protective cellular immune responses and activate CD8(+) T cells. Also, Ig V(H) appeared to be the minimal delivery unit of "antigenized" Ig capable of inducing T-cell activation in a lymphoid organ. The strategy of introducing T-cell epitopes into the molecular context of the V(H) domain in combination with i.s. DNA immunization could have important implications and applications for human immunotherapy.
The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit ... more The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit a strong antibody response in almost all HIV-1 infected individuals. This disulfide-bonded loop region is conserved in most retroviruses suggesting the existence of an essential function in virus life cycle. In this study, we displayed the peptides comprising 12 amino acids of the immunodominant loop of gp41 on the surface of M13 phage as N-terminal fusions to the minor coat protein pIII and major coat protein pVIII of the phage and demonstrated that cysteine loop containing peptide expressed on phage recognized 62 out of 63 (98.4%) HIV-1 positive samples but not control negative sera while phage bearing linear peptides detected 4-30% of HIV-1-positive sera. The main advantage of phage-based ELISA or other antibody detection-based diagnostic tests of HIV-infection to be used for massive screening in developing countries is the reproducible, simple, rapid and low-cost production of recombinant antigens.
To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patient... more To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patients with confirmed neurocysticercosis, we used a phage peptide library that displayed random dodecapeptides as a fusion to the minor coat protein (pIII) of phage M13. To increase the specificity of selection, plates coated with anti-human Fc antibody were used in five rounds of biopanning. The DNA inserts of 30 selected clones were determined and the deduced amino acid sequences were analyzed. Sequence similarities between affinity-selected clones and three known T. solium and T. crassiceps proteins were encountered. Two phage clones have been shown to react in enzyme-linked immunosorbent assay with CSF samples from other patients with neurocysticercosis, and no reaction was observed with CSF samples from patients with other neurological disorders used as negative controls. Our results suggest that affinity selection of peptides from phage libraries using CSF samples from patients is an attractive tool for the development of novel reagents for a simple and sensitive immunodiagnostic test and for understanding the molecular mechanisms participating in the pathogenesis of neurocysticercosis.
DNA immunization or inoculation is a recent vaccination method that induces both humoral and cell... more DNA immunization or inoculation is a recent vaccination method that induces both humoral and cellular immune responses in a range of hosts. Independent of the route or site of vaccination, the transfer of antigen-presenting cells (APC) or antigens into lymphoid organs is necessary. The aim of this investigation was to test whether intraspleen (i.s.) DNA inoculation is capable of inducing a protective immune response. We immunized mice by a single i.s. injection of a DNA construct expressing the immunoglobulin (Ig) heavy-chain variable domain (VH) in which the complementarity-determining regions (CDR) had been replaced by a Taenia crassiceps T-cell epitope. In these mice, immune responses and protective effects elicited by the vaccine were measured. We have shown here for the first time that i.s. DNA inoculation can induce protective cellular immune responses and activate CD8(+) T cells. Also, Ig V(H) appeared to be the minimal delivery unit of "antigenized" Ig capable of inducing T-cell activation in a lymphoid organ. The strategy of introducing T-cell epitopes into the molecular context of the V(H) domain in combination with i.s. DNA immunization could have important implications and applications for human immunotherapy.
We present some results attained with two variants of the bounded dynamic programming algorithm t... more We present some results attained with two variants of the bounded dynamic programming algorithm to solve the Fm|block|Cmax problem using as experimental data the well-known Taillard instances. We have improved the best-known solutions for four of the Taillard's instances.
Engineering Applications of Artificial Intelligence
We present some results attained with two variants of Bounded Dynamic Programming algorithm to so... more We present some results attained with two variants of Bounded Dynamic Programming algorithm to solve the Fm9block9C max problem using as an experimental data the well-known Taillard instances. We have improved the best known solutions for 17 of Taillard's instances, including the 10 instances from set 12.
In this manuscript, we present a formulation for the MMSP-W (Mixed model sequencing problem with ... more In this manuscript, we present a formulation for the MMSP-W (Mixed model sequencing problem with workload minimisation) for production lines with serial workstations. We demonstrate the validity of the basic models in the presence of a control system on the production line that allows the stopping of operations with no restrictions. We propose an extension of the basic models that allows conditioned interruption of operations to facilitate line management. We then propose a procedure to solve the proposed problem through BDP (Bounded Dynamic Programming), and demonstrate its validity through a computational experiment with reference instances and a case study linked to the Nissan powertrain plant in Barcelona.
In this paper a Grammar Guided Genetic Programming-based method for the learning of rule-based cl... more In this paper a Grammar Guided Genetic Programming-based method for the learning of rule-based classification systems is proposed. The method learns disjunctive normal form rules generated by means of a context-free grammar. The individual constitutes a rule based decision list that represents the full classifier. To overcome the problem of computational time of this system, it parallelizes the evaluation phase reducing significantly the computation time. Moreover, different operator genetics are designed to maintain the diversity of the population and get a compact set of rules. The results obtained have been validated by the use of non-parametric statistical tests, showing a good performance in terms of accuracy and interpretability.
The efficiency of evolutionary algorithms has become a studied problem since it is one of the maj... more The efficiency of evolutionary algorithms has become a studied problem since it is one of the major weaknesses in these algorithms. Specifically, when these algorithms are employed for the classification task, the computational time required by them grows excessively as the problem complexity increases. This paper proposes an efficient scalable and massively parallel evaluation model using the NVIDIA CUDA GPU programming model to speed up the fitness calculation phase and greatly reduce the computational time. Experimental results show that our model significantly reduces the computational time compared to the sequential approach, reaching a speedup of up to 820×. Moreover, the model is able to scale to multiple GPU devices and can be easily extended to any evolutionary algorithm.
WEKA has recently become a very referenced DM tool. In spite of all the functionality it provides... more WEKA has recently become a very referenced DM tool. In spite of all the functionality it provides, it does not include any framework for the development of evolutionary algorithms. An evolutionary computation framework is JCLEC, which has been successfully employed for developing several EAs. The combination of both may lead in a mutual benefit. Thus, this paper proposes an intermediate layer to connect WEKA with JCLEC. It also presents a study case which samples the process of including a JCLEC’s EA into WEKA.
Genetic Programming is very efficient in problem solving compared to other proposals but its perf... more Genetic Programming is very efficient in problem solving compared to other proposals but its performance is very slow when the size of the data increases. This paper proposes a model for multi-threaded Genetic Programming classification evaluation using a NVIDIA CUDA GPUs programming model to parallelize the evaluation phase and reduce computational time. Three different well-known Genetic Programming classification algorithms are evaluated using the parallel evaluation model proposed. Experimental results using UCI Machine Learning data sets compare the performance of the three classification algorithms in single and multithreaded Java, C and CUDA GPU code. Results show that our proposal is much more efficient.
In this paper, we propose a procedure based on Bounded Dynamic Programming (BDP) to solve the Mix... more In this paper, we propose a procedure based on Bounded Dynamic Programming (BDP) to solve the Mixed-Model Sequencing Problem with Workload Minimisation (MMSP-W), with serial workstations and unrestricted (or free) interruption of the operations. We performed a computational experiment with 225 instances from the literature. The results of our proposal are compared with those obtained through the CPLEX solver.
The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit ... more The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit a strong antibody response in almost all HIV-1 infected individuals. This disulfide-bonded loop region is conserved in most retroviruses suggesting the existence of an essential function in virus life cycle. In this study, we displayed the peptides comprising 12 amino acids of the immunodominant loop of gp41 on the surface of M13 phage as N-terminal fusions to the minor coat protein pIII and major coat protein pVIII of the phage and demonstrated that cysteine loop containing peptide expressed on phage recognized 62 out of 63 (98.4%) HIV-1 positive samples but not control negative sera while phage bearing linear peptides detected 4-30% of HIV-1-positive sera. The main advantage of phage-based ELISA or other antibody detection-based diagnostic tests of HIV-infection to be used for massive screening in developing countries is the reproducible, simple, rapid and low-cost production of recombinant antigens.
To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patient... more To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patients with confirmed neurocysticercosis, we used a phage peptide library that displayed random dodecapeptides as a fusion to the minor coat protein (pIII) of phage M13. To increase the specificity of selection, plates coated with anti-human Fc antibody were used in five rounds of biopanning. The DNA inserts of 30 selected clones were determined and the deduced amino acid sequences were analyzed. Sequence similarities between affinity-selected clones and three known T. solium and T. crassiceps proteins were encountered. Two phage clones have been shown to react in enzyme-linked immunosorbent assay with CSF samples from other patients with neurocysticercosis, and no reaction was observed with CSF samples from patients with other neurological disorders used as negative controls. Our results suggest that affinity selection of peptides from phage libraries using CSF samples from patients is an attractive tool for the development of novel reagents for a simple and sensitive immunodiagnostic test and for understanding the molecular mechanisms participating in the pathogenesis of neurocysticercosis.
DNA immunization or inoculation is a recent vaccination method that induces both humoral and cell... more DNA immunization or inoculation is a recent vaccination method that induces both humoral and cellular immune responses in a range of hosts. Independent of the route or site of vaccination, the transfer of antigen-presenting cells (APC) or antigens into lymphoid organs is necessary. The aim of this investigation was to test whether intraspleen (i.s.) DNA inoculation is capable of inducing a protective immune response. We immunized mice by a single i.s. injection of a DNA construct expressing the immunoglobulin (Ig) heavy-chain variable domain (VH) in which the complementarity-determining regions (CDR) had been replaced by a Taenia crassiceps T-cell epitope. In these mice, immune responses and protective effects elicited by the vaccine were measured. We have shown here for the first time that i.s. DNA inoculation can induce protective cellular immune responses and activate CD8(+) T cells. Also, Ig V(H) appeared to be the minimal delivery unit of "antigenized" Ig capable of inducing T-cell activation in a lymphoid organ. The strategy of introducing T-cell epitopes into the molecular context of the V(H) domain in combination with i.s. DNA immunization could have important implications and applications for human immunotherapy.
The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit ... more The HIV-1 envelope glycoprotein gp41 contains Cys(X) 5 Cys motif, which has been shown to elicit a strong antibody response in almost all HIV-1 infected individuals. This disulfide-bonded loop region is conserved in most retroviruses suggesting the existence of an essential function in virus life cycle. In this study, we displayed the peptides comprising 12 amino acids of the immunodominant loop of gp41 on the surface of M13 phage as N-terminal fusions to the minor coat protein pIII and major coat protein pVIII of the phage and demonstrated that cysteine loop containing peptide expressed on phage recognized 62 out of 63 (98.4%) HIV-1 positive samples but not control negative sera while phage bearing linear peptides detected 4-30% of HIV-1-positive sera. The main advantage of phage-based ELISA or other antibody detection-based diagnostic tests of HIV-infection to be used for massive screening in developing countries is the reproducible, simple, rapid and low-cost production of recombinant antigens.
To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patient... more To identify epitopes for antibodies present in cerebrospinal fluid (CSF) samples from two patients with confirmed neurocysticercosis, we used a phage peptide library that displayed random dodecapeptides as a fusion to the minor coat protein (pIII) of phage M13. To increase the specificity of selection, plates coated with anti-human Fc antibody were used in five rounds of biopanning. The DNA inserts of 30 selected clones were determined and the deduced amino acid sequences were analyzed. Sequence similarities between affinity-selected clones and three known T. solium and T. crassiceps proteins were encountered. Two phage clones have been shown to react in enzyme-linked immunosorbent assay with CSF samples from other patients with neurocysticercosis, and no reaction was observed with CSF samples from patients with other neurological disorders used as negative controls. Our results suggest that affinity selection of peptides from phage libraries using CSF samples from patients is an attractive tool for the development of novel reagents for a simple and sensitive immunodiagnostic test and for understanding the molecular mechanisms participating in the pathogenesis of neurocysticercosis.
DNA immunization or inoculation is a recent vaccination method that induces both humoral and cell... more DNA immunization or inoculation is a recent vaccination method that induces both humoral and cellular immune responses in a range of hosts. Independent of the route or site of vaccination, the transfer of antigen-presenting cells (APC) or antigens into lymphoid organs is necessary. The aim of this investigation was to test whether intraspleen (i.s.) DNA inoculation is capable of inducing a protective immune response. We immunized mice by a single i.s. injection of a DNA construct expressing the immunoglobulin (Ig) heavy-chain variable domain (VH) in which the complementarity-determining regions (CDR) had been replaced by a Taenia crassiceps T-cell epitope. In these mice, immune responses and protective effects elicited by the vaccine were measured. We have shown here for the first time that i.s. DNA inoculation can induce protective cellular immune responses and activate CD8(+) T cells. Also, Ig V(H) appeared to be the minimal delivery unit of "antigenized" Ig capable of inducing T-cell activation in a lymphoid organ. The strategy of introducing T-cell epitopes into the molecular context of the V(H) domain in combination with i.s. DNA immunization could have important implications and applications for human immunotherapy.
We present some results attained with two variants of the bounded dynamic programming algorithm t... more We present some results attained with two variants of the bounded dynamic programming algorithm to solve the Fm|block|Cmax problem using as experimental data the well-known Taillard instances. We have improved the best-known solutions for four of the Taillard's instances.
Engineering Applications of Artificial Intelligence
We present some results attained with two variants of Bounded Dynamic Programming algorithm to so... more We present some results attained with two variants of Bounded Dynamic Programming algorithm to solve the Fm9block9C max problem using as an experimental data the well-known Taillard instances. We have improved the best known solutions for 17 of Taillard's instances, including the 10 instances from set 12.
In this manuscript, we present a formulation for the MMSP-W (Mixed model sequencing problem with ... more In this manuscript, we present a formulation for the MMSP-W (Mixed model sequencing problem with workload minimisation) for production lines with serial workstations. We demonstrate the validity of the basic models in the presence of a control system on the production line that allows the stopping of operations with no restrictions. We propose an extension of the basic models that allows conditioned interruption of operations to facilitate line management. We then propose a procedure to solve the proposed problem through BDP (Bounded Dynamic Programming), and demonstrate its validity through a computational experiment with reference instances and a case study linked to the Nissan powertrain plant in Barcelona.
In this paper a Grammar Guided Genetic Programming-based method for the learning of rule-based cl... more In this paper a Grammar Guided Genetic Programming-based method for the learning of rule-based classification systems is proposed. The method learns disjunctive normal form rules generated by means of a context-free grammar. The individual constitutes a rule based decision list that represents the full classifier. To overcome the problem of computational time of this system, it parallelizes the evaluation phase reducing significantly the computation time. Moreover, different operator genetics are designed to maintain the diversity of the population and get a compact set of rules. The results obtained have been validated by the use of non-parametric statistical tests, showing a good performance in terms of accuracy and interpretability.
The efficiency of evolutionary algorithms has become a studied problem since it is one of the maj... more The efficiency of evolutionary algorithms has become a studied problem since it is one of the major weaknesses in these algorithms. Specifically, when these algorithms are employed for the classification task, the computational time required by them grows excessively as the problem complexity increases. This paper proposes an efficient scalable and massively parallel evaluation model using the NVIDIA CUDA GPU programming model to speed up the fitness calculation phase and greatly reduce the computational time. Experimental results show that our model significantly reduces the computational time compared to the sequential approach, reaching a speedup of up to 820×. Moreover, the model is able to scale to multiple GPU devices and can be easily extended to any evolutionary algorithm.
WEKA has recently become a very referenced DM tool. In spite of all the functionality it provides... more WEKA has recently become a very referenced DM tool. In spite of all the functionality it provides, it does not include any framework for the development of evolutionary algorithms. An evolutionary computation framework is JCLEC, which has been successfully employed for developing several EAs. The combination of both may lead in a mutual benefit. Thus, this paper proposes an intermediate layer to connect WEKA with JCLEC. It also presents a study case which samples the process of including a JCLEC’s EA into WEKA.
Genetic Programming is very efficient in problem solving compared to other proposals but its perf... more Genetic Programming is very efficient in problem solving compared to other proposals but its performance is very slow when the size of the data increases. This paper proposes a model for multi-threaded Genetic Programming classification evaluation using a NVIDIA CUDA GPUs programming model to parallelize the evaluation phase and reduce computational time. Three different well-known Genetic Programming classification algorithms are evaluated using the parallel evaluation model proposed. Experimental results using UCI Machine Learning data sets compare the performance of the three classification algorithms in single and multithreaded Java, C and CUDA GPU code. Results show that our proposal is much more efficient.
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Papers by Alberto Cano