Departament d'Estadística i Investigació Operativa
http://hdl.handle.net/2117/3941
2017-12-07T09:55:01ZIdentification of interleukin-27 (IL-27)/IL-27 receptor subunit alpha as a critical immune axis for in vivo hiv control
http://hdl.handle.net/2117/111542
Identification of interleukin-27 (IL-27)/IL-27 receptor subunit alpha as a critical immune axis for in vivo hiv control
Ruiz-Riol, M.; Berdnik, D.; Llano, A.; Mothe, Beatriz; Gálvez, C.; Pérez Alvarez, Susana; Oriol Tordera, B.; Olvera Van der Stoep, Alex; Silva Arrieta, S.; Meulbroek, M.; Salvat Pujol, Francesc; Coll, J.; Martínez Picado, Javier; Ganoza, Carmela; Sánchez, J.; Gómez Melis, Guadalupe; Coray, Wyss; Brander, Christian
Intact and broad immune cell effector functions and specific individual cytokines have been linked to HIV disease outcome, but their relative contribution to HIV control remains unclear. We asked whether the proteome of secreted cytokines and signaling factors in peripheral blood can be used to discover specific pathways critical for host viral control. A custom glass-based microarray, able to measure >600 plasma proteins involved in cell-to-cell communication, was used to measure plasma protein profiles in 96 HIV-infected, treatment-naive individuals with high (> 50,000) or low (<10,000 HIV RNA copies/ml) viral loads. Univariate and regression model analysis demonstrate that plasma levels of soluble interleukin-27 (IL-27) are significantly elevated in individuals with high plasma viremia (P < 0.0001) and are positively correlated with proviral HIV-DNA copy numbers in peripheral blood mononuclear cells (PBMC) (Rho = 0.4011; P = 0.0027). Moreover, soluble IL-27 plasma levels are negatively associated with the breadth and magnitude of the total virus-specific T-cell responses and directly with plasma levels of molecules involved in Wnt/beta-catenin signaling. In addition to IL-27, gene expression levels of the specific IL-27 receptor (IL27RA) in PBMC correlated directly with both plasma viral load (Rho = 0.3531; P = 0.0218) and the proviral copy number in the peripheral blood as an indirect measure of partial viral reservoir (Rho = 0.4580; P = 0.0030). These results were validated in unrelated cohorts of early infected subjects as well as subjects before and after initiation of antiretroviral treatment, and they identify IL-27 and its specific receptor as a critical immune axis for the antiviral immune response and as robust correlates of viral load and proviral reservoir size in PBMC.
IMPORTANCE The detailed knowledge of immune mechanisms that contribute to HIV control is a prerequisite for the design of effective treatment strategies to achieve HIV cure. Cells communicate with each other by secreting signaling proteins, and the blood is a key conduit for transporting such factors. Investigating the communication factors promoting effective immune responses and having potentially antiviral functions against HIV using a novel focused omics approach (
2017-12-04T14:41:37ZRuiz-Riol, M.Berdnik, D.Llano, A.Mothe, BeatrizGálvez, C.Pérez Alvarez, SusanaOriol Tordera, B.Olvera Van der Stoep, AlexSilva Arrieta, S.Meulbroek, M.Salvat Pujol, FrancescColl, J.Martínez Picado, JavierGanoza, CarmelaSánchez, J.Gómez Melis, GuadalupeCoray, WyssBrander, ChristianIntact and broad immune cell effector functions and specific individual cytokines have been linked to HIV disease outcome, but their relative contribution to HIV control remains unclear. We asked whether the proteome of secreted cytokines and signaling factors in peripheral blood can be used to discover specific pathways critical for host viral control. A custom glass-based microarray, able to measure >600 plasma proteins involved in cell-to-cell communication, was used to measure plasma protein profiles in 96 HIV-infected, treatment-naive individuals with high (> 50,000) or low (<10,000 HIV RNA copies/ml) viral loads. Univariate and regression model analysis demonstrate that plasma levels of soluble interleukin-27 (IL-27) are significantly elevated in individuals with high plasma viremia (P < 0.0001) and are positively correlated with proviral HIV-DNA copy numbers in peripheral blood mononuclear cells (PBMC) (Rho = 0.4011; P = 0.0027). Moreover, soluble IL-27 plasma levels are negatively associated with the breadth and magnitude of the total virus-specific T-cell responses and directly with plasma levels of molecules involved in Wnt/beta-catenin signaling. In addition to IL-27, gene expression levels of the specific IL-27 receptor (IL27RA) in PBMC correlated directly with both plasma viral load (Rho = 0.3531; P = 0.0218) and the proviral copy number in the peripheral blood as an indirect measure of partial viral reservoir (Rho = 0.4580; P = 0.0030). These results were validated in unrelated cohorts of early infected subjects as well as subjects before and after initiation of antiretroviral treatment, and they identify IL-27 and its specific receptor as a critical immune axis for the antiviral immune response and as robust correlates of viral load and proviral reservoir size in PBMC.
IMPORTANCE The detailed knowledge of immune mechanisms that contribute to HIV control is a prerequisite for the design of effective treatment strategies to achieve HIV cure. Cells communicate with each other by secreting signaling proteins, and the blood is a key conduit for transporting such factors. Investigating the communication factors promoting effective immune responses and having potentially antiviral functions against HIV using a novel focused omics approach (Heuristic solucions to the facility location problem with general Bernoulli demands
http://hdl.handle.net/2117/111476
Heuristic solucions to the facility location problem with general Bernoulli demands
Albareda Sambola, Maria; Fernández Aréizaga, Elena; Saldanha da Gama, Francisco
In this paper, a heuristic procedure is proposed for the facility location problem with general Bernoulli demands. This is a discrete facility location problem with stochastic demands that can be formulated as a two-stage stochastic program with recourse. In particular, facility locations and customer assignments must be decided here and now, i.e., before knowing the customers who will actually require to be served. In a second stage, service decisions are made according to the actual requests. The heuristic proposed consists of a greedy randomized adaptive search procedure followed by a path relinking. The heterogeneous Bernoulli demands make prohibitive the computational effort for evaluating feasible solutions. Thus the expected cost of a feasible solution is simulated when necessary. The results of extensive computational tests performed for evaluating the quality of the heuristic are reported, showing that high-quality feasible solutions can be obtained for the problem in fairly small computational times.
2017-12-01T15:29:15ZAlbareda Sambola, MariaFernández Aréizaga, ElenaSaldanha da Gama, FranciscoIn this paper, a heuristic procedure is proposed for the facility location problem with general Bernoulli demands. This is a discrete facility location problem with stochastic demands that can be formulated as a two-stage stochastic program with recourse. In particular, facility locations and customer assignments must be decided here and now, i.e., before knowing the customers who will actually require to be served. In a second stage, service decisions are made according to the actual requests. The heuristic proposed consists of a greedy randomized adaptive search procedure followed by a path relinking. The heterogeneous Bernoulli demands make prohibitive the computational effort for evaluating feasible solutions. Thus the expected cost of a feasible solution is simulated when necessary. The results of extensive computational tests performed for evaluating the quality of the heuristic are reported, showing that high-quality feasible solutions can be obtained for the problem in fairly small computational times.Fundamentos teóricos del análisis de correspondencias
http://hdl.handle.net/2117/111105
Fundamentos teóricos del análisis de correspondencias
Martí Recober, Manuel; Aluja Banet, Tomàs; Bécue Bertaut, Mónica María
2017-11-23T09:03:26ZMartí Recober, ManuelAluja Banet, TomàsBécue Bertaut, Mónica MaríaAnálisis de correspondencias múltiples sobre un grafo
http://hdl.handle.net/2117/111092
Análisis de correspondencias múltiples sobre un grafo
Aluja Banet, Tomàs; Martí Recober, Manuel
En anàlisi de dades sovint hom analitza matrius de dades formades per variables nominals, correlacionades amb unes altres anomenades variables
2017-11-22T18:23:20ZAluja Banet, TomàsMartí Recober, ManuelEn anàlisi de dades sovint hom analitza matrius de dades formades per variables nominals, correlacionades amb unes altres anomenades variablesOn the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers
http://hdl.handle.net/2117/111053
On the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers
Graffelman, Jan; Weir, B.S.
Standard statistical tests for equality of allele frequencies in males and females and tests for Hardy-Weinberg equilibrium are tightly linked by their assumptions. Tests for equality of allele frequencies assume Hardy-Weinberg equilibrium, whereas the usual chi-square or exact test for Hardy-Weinberg equilibrium assume equality of allele frequencies in the sexes. In this paper, we propose ways to break this interdependence in assumptions of the two tests by proposing an omnibus exact test that can test both hypotheses jointly, as well as a likelihood ratio approach that permits these phenomena to be tested both jointly and separately. The tests are illustrated with data from the 1000 Genomes project.
2017-11-22T10:07:59ZGraffelman, JanWeir, B.S.Standard statistical tests for equality of allele frequencies in males and females and tests for Hardy-Weinberg equilibrium are tightly linked by their assumptions. Tests for equality of allele frequencies assume Hardy-Weinberg equilibrium, whereas the usual chi-square or exact test for Hardy-Weinberg equilibrium assume equality of allele frequencies in the sexes. In this paper, we propose ways to break this interdependence in assumptions of the two tests by proposing an omnibus exact test that can test both hypotheses jointly, as well as a likelihood ratio approach that permits these phenomena to be tested both jointly and separately. The tests are illustrated with data from the 1000 Genomes project.Interventions to improve adherence to reporting guidelines in health research: a scoping review protocol
http://hdl.handle.net/2117/111049
Interventions to improve adherence to reporting guidelines in health research: a scoping review protocol
Blanco de Tena Davila, David; Kirkham, Jamie; Altman, D.G.; Moher, David; Boutron, Isabelle; Cobo Valeri, Erik
There is evidence that the use of some reporting guidelines, such as the Consolidated Standards for Reporting Trials, is associated with improved completeness of reporting in health research. However, the current levels of adherence to reporting guidelines are suboptimal. Over the last few years, several actions aiming to improve compliance with reporting guidelines have been taken and proposed. We will conduct a scoping review of interventions to improve adherence to reporting guidelines in health research that have been evaluated or suggested, in order to inform future interventions.
2017-11-22T09:27:02ZBlanco de Tena Davila, DavidKirkham, JamieAltman, D.G.Moher, DavidBoutron, IsabelleCobo Valeri, ErikThere is evidence that the use of some reporting guidelines, such as the Consolidated Standards for Reporting Trials, is associated with improved completeness of reporting in health research. However, the current levels of adherence to reporting guidelines are suboptimal. Over the last few years, several actions aiming to improve compliance with reporting guidelines have been taken and proposed. We will conduct a scoping review of interventions to improve adherence to reporting guidelines in health research that have been evaluated or suggested, in order to inform future interventions.The use of a binary composite endpoint and sample size requirement: influence of endpoints overlap
http://hdl.handle.net/2117/110928
The use of a binary composite endpoint and sample size requirement: influence of endpoints overlap
Ramon Marsal, Josep; Ferreira González, Ignacio; Bertrán, Sandra; Ribera, Aida; Permanyer-Miralda, Gaietà; Garcia Dorado, Antonio David; Gómez Melis, Guadalupe
Although composite endpoints (CE) are common in clinical trials, the impact of the relationship between the components of a binary CE on the sample size requirement (SSR) has not been addressed. We performed a computational study considering 2 treatments and a CE with 2 components: the relevant endpoint (RE) and the additional endpoint (AE). We assessed the strength of the components’ interrelation by the degree of relative overlap between them, which was stratified into 5 groups. Within each stratum, SSR was computed for multiple scenarios by varying the events proportion and the effect of the therapy. A lower SSR using CE was defined as the best scenario for using the CE. In 25 of 66 scenarios the degree of relative overlap determined the benefit of using CE instead of the RE. Adding an AE with greater effect than the RE leads to lower SSR using the CE regardless of the AE proportion and the relative overlap. The influence of overlapping decreases when the effect on RE increases. Adding an AE with lower effect than the RE constitutes the most uncertain situation. In summary, the interrelationship between CE components, assessed by the relative overlap, can help to define the SSR in specific situations and it should be considered for SSR computation.
2017-11-20T15:21:50ZRamon Marsal, JosepFerreira González, IgnacioBertrán, SandraRibera, AidaPermanyer-Miralda, GaietàGarcia Dorado, Antonio DavidGómez Melis, GuadalupeAlthough composite endpoints (CE) are common in clinical trials, the impact of the relationship between the components of a binary CE on the sample size requirement (SSR) has not been addressed. We performed a computational study considering 2 treatments and a CE with 2 components: the relevant endpoint (RE) and the additional endpoint (AE). We assessed the strength of the components’ interrelation by the degree of relative overlap between them, which was stratified into 5 groups. Within each stratum, SSR was computed for multiple scenarios by varying the events proportion and the effect of the therapy. A lower SSR using CE was defined as the best scenario for using the CE. In 25 of 66 scenarios the degree of relative overlap determined the benefit of using CE instead of the RE. Adding an AE with greater effect than the RE leads to lower SSR using the CE regardless of the AE proportion and the relative overlap. The influence of overlapping decreases when the effect on RE increases. Adding an AE with lower effect than the RE constitutes the most uncertain situation. In summary, the interrelationship between CE components, assessed by the relative overlap, can help to define the SSR in specific situations and it should be considered for SSR computation.Comparison of production strategies and degree of postponement when incorporating additive manufacturing to product supply chains
http://hdl.handle.net/2117/110899
Comparison of production strategies and degree of postponement when incorporating additive manufacturing to product supply chains
Minguella Canela, Joaquim; Muguruza Blanco, Asier; Ramón Lumbierres, Daniel Jacobo; Heredia, F.-Javier (Francisco Javier); Gimeno Feu, Robert; Guo, Ping; Hamilton, Mary; Shastry, Kiron; Webb, Sunny
The best-selling products manufactured nowadays are made in long series along rigid product value chains. Product repetition and continuous/stable manufacturing is seen as a chance for achieving economies of scale. Nevertheless, these speculative strategies fail to meet special customer demands, thus reducing the effective market share of a product in a range.
Additive Manufacturing technologies open promising product customization opportunities; however, to achieve it, it is necessary to delay the production operations in order to incorporate the customer’s inputs in the product materialization.
The study offered in the present paper compares different possible production strategies for a product (via conventional technologies and Additive Manufacturing) and assesses the degree of postponement that it would be recommended in order to meet a certain demand distribution. The problem solving is calculated by a program containing a stochastic mathematical model which incorporates extensive information on costs and lead times for the required manufacturing operations.
2017-11-20T08:13:49ZMinguella Canela, JoaquimMuguruza Blanco, AsierRamón Lumbierres, Daniel JacoboHeredia, F.-Javier (Francisco Javier)Gimeno Feu, RobertGuo, PingHamilton, MaryShastry, KironWebb, SunnyThe best-selling products manufactured nowadays are made in long series along rigid product value chains. Product repetition and continuous/stable manufacturing is seen as a chance for achieving economies of scale. Nevertheless, these speculative strategies fail to meet special customer demands, thus reducing the effective market share of a product in a range.
Additive Manufacturing technologies open promising product customization opportunities; however, to achieve it, it is necessary to delay the production operations in order to incorporate the customer’s inputs in the product materialization.
The study offered in the present paper compares different possible production strategies for a product (via conventional technologies and Additive Manufacturing) and assesses the degree of postponement that it would be recommended in order to meet a certain demand distribution. The problem solving is calculated by a program containing a stochastic mathematical model which incorporates extensive information on costs and lead times for the required manufacturing operations.Local and partial correspondence analysis application to the analysis of electoral data
http://hdl.handle.net/2117/110727
Local and partial correspondence analysis application to the analysis of electoral data
Aluja Banet, Tomàs
In data analysis we must often analyze data sets whose observations are related by a graph structure. This is the case for electoral data, where the electoral units correspond to a definite geographical areas. In this case can be interesting to analyze the same phenomenon fixing some a priori relation.
First part we are going to present the rationale of these methods. The local analysis aims to eleiminate the effect of geographical position of individuals, represented by a contiguity graph, in an exploratory factorial analysis of spatial data. It will be proved interesting to analyze the electoral results keeping the socio-economic position constant, by means of a similarity graph. This is called partial analysis beacuse is based on the same idea of instrumental variables of Rao and partial correlation analysis.
In the second part of the article, this methodology is applied to the data matrix formed by 1059 electoral units, called sections, giving the electoral results in the last autonomous election of 1984 in Barcelona. Moreover, it will be interesting to define regions of units with homogeneous electoral behaviour, obtained by an algorithm of clustering with contiguity constraint.
2017-11-16T09:07:20ZAluja Banet, TomàsIn data analysis we must often analyze data sets whose observations are related by a graph structure. This is the case for electoral data, where the electoral units correspond to a definite geographical areas. In this case can be interesting to analyze the same phenomenon fixing some a priori relation.
First part we are going to present the rationale of these methods. The local analysis aims to eleiminate the effect of geographical position of individuals, represented by a contiguity graph, in an exploratory factorial analysis of spatial data. It will be proved interesting to analyze the electoral results keeping the socio-economic position constant, by means of a similarity graph. This is called partial analysis beacuse is based on the same idea of instrumental variables of Rao and partial correlation analysis.
In the second part of the article, this methodology is applied to the data matrix formed by 1059 electoral units, called sections, giving the electoral results in the last autonomous election of 1984 in Barcelona. Moreover, it will be interesting to define regions of units with homogeneous electoral behaviour, obtained by an algorithm of clustering with contiguity constraint.Complementary remarks and improvements to a lagrangean heuristic for capacitated plant location problems
http://hdl.handle.net/2117/110692
Complementary remarks and improvements to a lagrangean heuristic for capacitated plant location problems
Barceló Bugeda, Jaime; Casanovas Garcia, Josep
In a former paper, [1], a heuristic using multipliers from a langrean relaxation was proposed for getting feasible solutions to a class of pure integer capacited plant location problems. The heuristic consisted of three steps, the last one being a plant interchange step. Further computational experience has shown that the proposed interchange procedure could fail. In this paper we investigate the computational behaviour of the heuristic without interchange procedure, and we give the result of our computational experience.
2017-11-15T15:24:05ZBarceló Bugeda, JaimeCasanovas Garcia, JosepIn a former paper, [1], a heuristic using multipliers from a langrean relaxation was proposed for getting feasible solutions to a class of pure integer capacited plant location problems. The heuristic consisted of three steps, the last one being a plant interchange step. Further computational experience has shown that the proposed interchange procedure could fail. In this paper we investigate the computational behaviour of the heuristic without interchange procedure, and we give the result of our computational experience.