Biblio-MetReS for user-friendly mining of genes and biological processes in scientific documents

One way to initiate the reconstruction of molecular circuits is by using automated text-mining techniques. Developing more efficient methods for such reconstruction is a topic of active research, and those methods are typically included by bioinfor- maticians in pipelines used to mine and curate large literature datasets. Nevertheless, experimental biologists have a limited number of available user-friendly tools that use text-mining for network reconstruction and require no programming skills to use. One of these tools is Biblio-MetReS. Originally, this tool permitted an on-the-fly analysis of documents contained in a number of web-based literature databases to identify co-occurrence of proteins/genes. This approach ensured results that were always up-to-date with the latest live version of the databases. However, this `up-to- dateness' came at the cost of large execution times. Here we report an evolution of the application Biblio-MetReS that permits constructing co-occurrence networks for genes, GO processes, Pathways, or any combination of the three types of entities and graphically represent those entities.We show that the performance of Biblio- MetReS in identifying gene co-occurrence is as least as good as that of other com- parable applications (STRING and iHOP). In addition, we also show that the iden- tification of GO processes is on par to that reported in the latest BioCreAtIvE chal- lenge. Finally, we also report the implementation of a new strategy that combines on-the-fly analysis of new documents with preprocessed information from docu- ments that were encountered in previous analyses. This combination simultaneously decreases program run time and maintains `up-to-dateness' of the results.RA was partially supported by the Ministerio de Ciencia e Innovación (MICINN, Spain through grant BFU2010-17704). FS was partially funded by the MICINN, with grants TIN2011-28689-C02-02. The authors are members of the research groups 2009SGR809 and 2009SGR145, funded by the “Generalitat de Catalunya”. AU is funded by a Generalitat de Catalunya (AGAUR) PhD fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Biblio-MetReS: A bibliometric network reconstruction application and server

<p>Abstract</p> <p>Background</p> <p>Reconstruction of genes and/or protein networks from automated analysis of the literature is one of the current targets of text mining in biomedical research. Some user-friendly tools already perform this analysis on precompiled databases of abstracts of scientific papers. Other tools allow <b>expert </b>users to elaborate and analyze the full content of a corpus of scientific documents. However, to our knowledge, no <b>user friendly </b>tool that simultaneously analyzes the latest set of scientific documents available on line and reconstructs the set of genes referenced in those documents is available.</p> <p>Results</p> <p>This article presents such a tool, Biblio-MetReS, and compares its functioning and results to those of other user-friendly applications (iHOP, STRING) that are widely used. Under similar conditions, Biblio-MetReS creates networks that are comparable to those of other user friendly tools. Furthermore, analysis of full text documents provides more complete reconstructions than those that result from using only the abstract of the document.</p> <p>Conclusions</p> <p>Literature-based automated network reconstruction is still far from providing complete reconstructions of molecular networks. However, its value as an auxiliary tool is high and it will increase as standards for reporting biological entities and relationships become more widely accepted and enforced. Biblio-MetReS is an application that can be downloaded from <url>http://metres.udl.cat/</url>. It provides an easy to use environment for researchers to reconstruct their networks of interest from an always up to date set of scientific documents.</p

Effectiveness of a Multi-Component Intervention for Overweight and Obese Children (Nereu Program): A Randomized Controlled Trial

Introduction: Treatment of childhood obesity is a complex challenge for primary health care professionals. Objectives: To evaluate the effectiveness of the Nereu Program in improving anthropometric parameters, physical activity and sedentary behaviours, and dietary intake. Methods: Randomized, controlled, multicentre clinical trial comparing Nereu Program and usual counselling group interventions in primary care settings. The 8-month study recruited 113 children aged 6 to 12 years with overweight/obesity. Before recruitment, eligible participants were randomly allocated to an intensive, family-based multi-component behavioural intervention (Nereu Program group) or usual advice from their paediatrician on healthy eating and physical activity. Anthropometric parameters, objectively measured sedentary and physical activity behaviours, and dietary intake were evaluated pre- and post-intervention. Results: At the end of the study period, both groups achieved a similar decrease in body mass index (BMIsd) compared to baseline. Nereu Program participants (n = 54) showed greater increases in moderate-intense physical activity (+6.27% vs. -0.61%, p<0.001) and daily fruit servings (+0.62 vs. +0.13, p<0.026), and decreased daily soft drinks consumption (-0.26 vs. -0.02, p<0.047), respectively, compared to the counselling group (n = 59). Conclusions: At the end of the 8-month intervention, participants in the Nereu Program group showed improvement in physical activity and dietary behaviours, compared to the counselling group

Evaluation of a family intervention programme for the treatment of overweight and obese children (Nereu Programme): a randomized clinical trial study protocol

Background: Obesity is mainly attributed to environmental factors. In developed countries, the time spent on physical activity tasks is decreasing, whereas sedentary behaviour patterns are increasing. The purpose of the intervention is to evaluate the effectiveness of an intensive family-based behavioural multicomponent intervention (Nereu programme) and compared it to counselling intervention such as a health centre intervention programme for the management of children"s obesity. Methods/Design: The study design is a randomized controlled multicenter clinical trial using two types of interventions: Nereu and Counselling. The Nereu programme is an 8-month intensive family-based multi-component behavioural intervention. This programme is based on a multidisciplinary intervention consisting of 4 components: physical activity sessions for children, family theoretical and practical sessions for parents, behaviour strategy sessions involving both, parents and children, and lastly, weekend extra activities for all. Counselling is offered to the family in the form of a monthly physical health and eating habits session. Participants will be recruited according the following criteria: 6 to 12 year-old-children, referred from their paediatricians due to overweight or obesity according the International Obesity Task Force criteria and with a sedentary profile (less than 2 hours per week of physical activity), they must live in or near the municipality of Lleida (Spain) and their healthcare paediatric unit must have previously accepted to cooperate with this study. The following variables will be evaluated: a) cardiovascular risk factors (anthropometric parameters, blood test and blood pressure), b) sedentary and physical activity behaviour and dietary intake, c) psychological aspects d) health related quality of life (HRQOL), e) cost-effectiveness of the intervention in relation to HRQOL. These variables will be then be evaluated 4 times longitudinally: at baseline, at the end of the intervention (8 months later), 6 and 12 months after the intervention. We have considered necessary to recruit 100 children and divide them in 2 groups of 50 to detect the differences between the groups. Discussion: This trial will provide new evidence for the long-term effects of childhood obesity management, as well as help to know the impact of the present intervention as a health intervention tool for healthcare centres. Trial registration: ClinicalTrials.gov, NCT01878994This research is partially funded by the Instituto de Salud Carlos III in Spain, from the Ministry of Economy and Competitiveness with the expedient number PI12/02220, the Diputació de Lleida, the Department of Health of the Generalitat de Catalunya and the City Council of Lleida “La Paeria - Ajuntament de Lleida”. This research was supported by the Institute of Physical Education of Catalonia (INEFC), University of Lleida, Spain, (VCP/3570/2010, de 29 d’octubre, DOGC NÚM. 5753 – 11.11.2010; VCP/28/2009, 14 of January, DOGC NÚM. 5302 – 22/01/1999)

Characterization of the CPAP-treated patient population in Catalonia

There are different phenotypes of obstructive sleep apnoea (OSA), many of which have not been characterised. Identification of these different phenotypes is important in defining prognosis and guiding the therapeutic strategy. The aim of this study was to characterise the entire population of continuous positive airway pressure (CPAP)-treated patients in Catalonia and identify specific patient profiles using cluster analysis. A total of 72,217 CPAP-treated patients who contacted the Catalan Health System (CatSalut) during the years 2012 and 2013 were included. Six clusters were identified, classified as “Neoplastic patients” (Cluster 1, 10.4%), “Metabolic syndrome patients” (Cluster 2, 27.7%), “Asthmatic patients” (Cluster 3, 5.8%), “Musculoskeletal and joint disorder patients” (Cluster 4, 10.3%), “Patients with few comorbidities” (Cluster 5, 35.6%) and “Oldest and cardiac disease patients” (Cluster 6, 10.2%). Healthcare facility use and mortality were highest in patients from Cluster 1 and 6. Conversely, patients in Clusters 2 and 4 had low morbidity, mortality and healthcare resource use. Our findings highlight the heterogeneity of CPAP-treated patients, and suggest that OSA is associated with a different prognosis in the clusters identified. These results suggest the need for a comprehensive and individualised approach to CPAP treatment of OSA.This study was supported by the Spanish Respiratory Society (SEPAR), Associació Lleidatana de Respiratori (ALLER) and ResMed, a company that provides diagnostic services and treatment for sleep apnoea

Repercusions de l'aplicació d'els ultrasons a l'activitat de la PPO i PRO en patata minimament processada

The food industry has as a priority the development of methods that allow obtaining food with safety, good appearance and at the same time preserve the organoleptic qualities. There are a large number of methods, among the new ones we find the application of high pressure and ultrasound. The objective of this work is to determine the effect of all the parameters of the sonication treatment (ultrasound, acid solutions, water and temperature) on the activity of the PPO and PRO. To determine the effect of water and temperature, a thermo water bath has been used where the cut potato has been submerged (5.10 and 20 minutes) at different temperatures (17 o C, 30 o C and 35 o C). To determine the effect of ultrasound and acid media, ultrasound treatment has been applied to the cut potato during different times (5,10 and 20 minutes) in different media, water, citric acid 1% and ascorbic acid 1%. The temperature and soluble solids in the medium and in the potato, sample have been evaluated for colour, and the activity of PPO and PRO. The enzymatic activity of the PPO has been quantified from the reaction with catechol and measuring the absorbance at λ = 410nm, and the PRO from the reaction with guaiacol in the presence of H 2 O 2 and subsequently measuring the absorbance at λ = 420nm, each One of them doing readings every 30 seconds for 10 minutes. The obtained results indicate that the immersion of the potato in water has an inhibiting effect on the activity of the PPO and the PRO, while the temperature has the opposite effect especially at higher temperature (35 o C) and longer exposure time (20 min). The application of ultrasound has an inhibition effect in the case of PPO activity, but it has a negative effect on the PRO. The application of ultrasound in different media generates an increase in temperature of about 14-16 o C at 20 minutes, reaching a maximum of 33 o C. The use of acid media in the treatment of sonication generates an increase in the inhibition of the activity of the PPO, however in the case of the PRO, conclusive results have not been obtained. In the case of treatments with acids, an increase in inhibition is observed with respect to the time of sonication, being greater than 20 minutes. The treatment of sonication with ascorbic acid 1% during 20 min, shows a greater inhibition of PPO. The study of colour shows a significant relationship between the PPO with luminosity, and the PRO with the Chroma of the potato. The best proposal for the inhibition of the darkening would be: The treatment of ultrasounds of 20 minutes in a medium of ascorbic acid at 1% that would be effective inhibiting the PPO while this treatment would not be effective for the PRO but does not contribute of the same in the darkening.La industria alimentaria tiene como prioridad el desarrollo de métodos que permitan la obtención de alimentos con seguridad, buen aspecto y que al mismo tiempo conserven las cualidades organolépticas. Hay un gran número de métodos, entre los nuevos encontramos el de aplicación de altas presiones y los ultrasonidos. El objetivo de este trabajo es determinar el efecto de todos los parámetros del tratamiento de sonicación (ultrasonidos, soluciones ácidas, agua y temperatura) sobre la actividad de la PPO y PRO. Para determinar el efecto del agua y la temperatura, se ha utilizado un baño de agua termoregulable donde se ha sumergido la patata cortada (5,10 y 20 minutos) en diferentes temperaturas (17 o C, 30 o C y 35 o C). Para determinar el efecto de los ultrasonidos y los medios ácidos, se ha aplicado tratamiento de ultrasonidos a la patata cortada durante diferentes tiempos (5,10 y 20 minutos) en diferentes medios, agua, ácido cítrico 1% y ácido ascórbico 1%. Se han evaluado la temperatura y los sólidos solubles en el medio y en la muestra de la patata el color, y la actividad de PPO y PRO. La actividad enzimática de la PPO se ha cuantificado a partir de la reacción con catecol y midiendo la absorbancia a λ = 410nm, y la PRO a partir de la reacción con guaiacol en presencia de H 2 O 2 y posteriormente midiendo la absorbancia a λ = 420nm, cada una de ellas realizando lecturas cada 30 segundos durante 10 minutos. Los resultados obtenidos indican que la inmersión de la patata en agua tiene un efecto inhibidor sobre la actividad de la PPO y la PRO, mientras que la temperatura tiene el efecto contrario especialmente a mayor temperatura (35 o C) y mayor tiempo de exposición (20 min). La aplicación ultrasonidos tiene un efecto inhibición en el caso de la actividad de la PPO teniendo el mayor efecto a los 10 minutos, en cambio tiene un efecto negativo en la PRO. La aplicación de los ultrasonidos en los diferentes medios genera un incremento de temperatura de unos 14-16 o C a los 20 minutos, llegando hasta un máximo de 33 o C. La utilización de medios ácidos en el tratamiento de sonicación genera un incremento de la inhibición de la actividad de la PPO, en cambio en el caso de la PRO no se han obtenido resultados concluyentes. En el caso de los tratamientos con ácidos observa un aumento de la inhibición respecto el tiempo de sonicación, siendo mayor a 20 minutos El tratamiento de sonicación con ácido ascórbico 1% durante 20 min, es el que muestra una mayor inhibición de la PPO. El estudio del color nos muestra una relación significativa entre la PPO con la luminosidad, y la PRO con el Chroma de la patata. La mejor propuesta para la inhibición del oscurecimiento sería: El tratamiento de ultrasonidos de 20 minutos en un medio de ácido ascórbico al 1% que sería efectivo inhibiendo la PPO mientras que este tratamiento no sería efectivo para la PRO, pero no contribuye de la igual en el oscurecimiento.La industria alimentaria té com a prioritat el desenvolupament de mètodes que permetin la obtenció d’aliments amb seguretat, bon aspecte i que al mateix temps conservin les qualitats organolèptiques. Hi ha un gran nombre de mètodes, entre els nous trobem el d’aplicació d’altes pressions i els ultrasons. L’objectiu d’aquest treball és determinar l’efecte de tots els paràmetres del tractament de sonicació( ultrasons, solucions acides, aigua i temperatura ) sobre l’activitat de la PPO i PRO. Per determinar l’efecte de l’aigua i la temperatura, s’ha utilitzat un bany d’aigua termoregulable on s’ha submergit la patata tallada (5,10 i 20 minuts) en diferents temperatures, (17 o C, 30 o C i 35 o C). Per determinar l’efecte dels ultrasons i els medis àcids, s’ha aplicat tractament d’ultrasons a la patata tallada durant diferents temps (5,10 i 20 minuts) en diferents medis, aigua, àcid cítric 1% i àcid ascòrbic 1%. S’han avaluat la temperatura i els sòlids solubles en el medi i en la mostra de la patata el color, i l’activitat de PPO i PRO. L’activitat enzimàtica de la PPO s’ha quantificat a partir de la reacció amb catecol i mesurant l’absorbància a λ=410nm, i la PRO a partir de la reacció amb guaiacol en presencia de H 2 O 2 i posteriorment mesurant l’absorbància a λ=420nm, cada una d’elles realitzant lectures cada 30 segons durant 10 minuts. Els resultats obtinguts indiquen que la immersió de la patata en aigua té un efecte inhibidor sobre l’activitat de la PPO i la PRO, mentre que la temperatura té l’efecte contrari especialment a major temperatura (35 o C) i major temps d’exposició (20 min). L’aplicació ultrasons té un efecte inhibició en el cas de l’activitat de la PPO, sent major als 10 minuts, en canvi té un efecte contrari en la PRO. L’aplicació dels ultrasons en els diferents medis genera un increment de temperatura d’uns 14-16 ºC als 20 minuts, arribant fins un màxim de 33 o C. La utilització de medis àcids en el tractament de sonicació genera un increment de la inhibició de l’activitat de la PPO, en canvi en el cas de la PRO no s’han obtingut resultats concloents. En el cas dels tractaments amb àcids s’observa un augment de la inhibició respecte el temps de sonicació, sent major a 20 minuts El tractament de sonicació amb àcid ascòrbic 1% durant 20 min, és el que mostra una major inhibició de la PPO. L’estudi del color ens mostra una relació significativa entre la PPO amb la lluminositat, i la PRO amb el Chroma de la patata. La millor proposta per la inhibició del enfosquiment seria: El tractament d’ultrasons de 20 minuts en un medi d’àcid ascòrbic al 1% que seria efectiu inhibint la PPO mentre que aquest tractament no seria efectiu per la PRO, però no contribueix de la mateixa manera en l’enfosquiment

Repercusions de l'aplicació d'els ultrasons a l'activitat de la PPO i PRO en patata minimament processada

The food industry has as a priority the development of methods that allow obtaining food with safety, good appearance and at the same time preserve the organoleptic qualities. There are a large number of methods, among the new ones we find the application of high pressure and ultrasound. The objective of this work is to determine the effect of all the parameters of the sonication treatment (ultrasound, acid solutions, water and temperature) on the activity of the PPO and PRO. To determine the effect of water and temperature, a thermo water bath has been used where the cut potato has been submerged (5.10 and 20 minutes) at different temperatures (17 o C, 30 o C and 35 o C). To determine the effect of ultrasound and acid media, ultrasound treatment has been applied to the cut potato during different times (5,10 and 20 minutes) in different media, water, citric acid 1% and ascorbic acid 1%. The temperature and soluble solids in the medium and in the potato, sample have been evaluated for colour, and the activity of PPO and PRO. The enzymatic activity of the PPO has been quantified from the reaction with catechol and measuring the absorbance at λ = 410nm, and the PRO from the reaction with guaiacol in the presence of H 2 O 2 and subsequently measuring the absorbance at λ = 420nm, each One of them doing readings every 30 seconds for 10 minutes. The obtained results indicate that the immersion of the potato in water has an inhibiting effect on the activity of the PPO and the PRO, while the temperature has the opposite effect especially at higher temperature (35 o C) and longer exposure time (20 min). The application of ultrasound has an inhibition effect in the case of PPO activity, but it has a negative effect on the PRO. The application of ultrasound in different media generates an increase in temperature of about 14-16 o C at 20 minutes, reaching a maximum of 33 o C. The use of acid media in the treatment of sonication generates an increase in the inhibition of the activity of the PPO, however in the case of the PRO, conclusive results have not been obtained. In the case of treatments with acids, an increase in inhibition is observed with respect to the time of sonication, being greater than 20 minutes. The treatment of sonication with ascorbic acid 1% during 20 min, shows a greater inhibition of PPO. The study of colour shows a significant relationship between the PPO with luminosity, and the PRO with the Chroma of the potato. The best proposal for the inhibition of the darkening would be: The treatment of ultrasounds of 20 minutes in a medium of ascorbic acid at 1% that would be effective inhibiting the PPO while this treatment would not be effective for the PRO but does not contribute of the same in the darkening.La industria alimentaria tiene como prioridad el desarrollo de métodos que permitan la obtención de alimentos con seguridad, buen aspecto y que al mismo tiempo conserven las cualidades organolépticas. Hay un gran número de métodos, entre los nuevos encontramos el de aplicación de altas presiones y los ultrasonidos. El objetivo de este trabajo es determinar el efecto de todos los parámetros del tratamiento de sonicación (ultrasonidos, soluciones ácidas, agua y temperatura) sobre la actividad de la PPO y PRO. Para determinar el efecto del agua y la temperatura, se ha utilizado un baño de agua termoregulable donde se ha sumergido la patata cortada (5,10 y 20 minutos) en diferentes temperaturas (17 o C, 30 o C y 35 o C). Para determinar el efecto de los ultrasonidos y los medios ácidos, se ha aplicado tratamiento de ultrasonidos a la patata cortada durante diferentes tiempos (5,10 y 20 minutos) en diferentes medios, agua, ácido cítrico 1% y ácido ascórbico 1%. Se han evaluado la temperatura y los sólidos solubles en el medio y en la muestra de la patata el color, y la actividad de PPO y PRO. La actividad enzimática de la PPO se ha cuantificado a partir de la reacción con catecol y midiendo la absorbancia a λ = 410nm, y la PRO a partir de la reacción con guaiacol en presencia de H 2 O 2 y posteriormente midiendo la absorbancia a λ = 420nm, cada una de ellas realizando lecturas cada 30 segundos durante 10 minutos. Los resultados obtenidos indican que la inmersión de la patata en agua tiene un efecto inhibidor sobre la actividad de la PPO y la PRO, mientras que la temperatura tiene el efecto contrario especialmente a mayor temperatura (35 o C) y mayor tiempo de exposición (20 min). La aplicación ultrasonidos tiene un efecto inhibición en el caso de la actividad de la PPO teniendo el mayor efecto a los 10 minutos, en cambio tiene un efecto negativo en la PRO. La aplicación de los ultrasonidos en los diferentes medios genera un incremento de temperatura de unos 14-16 o C a los 20 minutos, llegando hasta un máximo de 33 o C. La utilización de medios ácidos en el tratamiento de sonicación genera un incremento de la inhibición de la actividad de la PPO, en cambio en el caso de la PRO no se han obtenido resultados concluyentes. En el caso de los tratamientos con ácidos observa un aumento de la inhibición respecto el tiempo de sonicación, siendo mayor a 20 minutos El tratamiento de sonicación con ácido ascórbico 1% durante 20 min, es el que muestra una mayor inhibición de la PPO. El estudio del color nos muestra una relación significativa entre la PPO con la luminosidad, y la PRO con el Chroma de la patata. La mejor propuesta para la inhibición del oscurecimiento sería: El tratamiento de ultrasonidos de 20 minutos en un medio de ácido ascórbico al 1% que sería efectivo inhibiendo la PPO mientras que este tratamiento no sería efectivo para la PRO, pero no contribuye de la igual en el oscurecimiento.La industria alimentaria té com a prioritat el desenvolupament de mètodes que permetin la obtenció d’aliments amb seguretat, bon aspecte i que al mateix temps conservin les qualitats organolèptiques. Hi ha un gran nombre de mètodes, entre els nous trobem el d’aplicació d’altes pressions i els ultrasons. L’objectiu d’aquest treball és determinar l’efecte de tots els paràmetres del tractament de sonicació( ultrasons, solucions acides, aigua i temperatura ) sobre l’activitat de la PPO i PRO. Per determinar l’efecte de l’aigua i la temperatura, s’ha utilitzat un bany d’aigua termoregulable on s’ha submergit la patata tallada (5,10 i 20 minuts) en diferents temperatures, (17 o C, 30 o C i 35 o C). Per determinar l’efecte dels ultrasons i els medis àcids, s’ha aplicat tractament d’ultrasons a la patata tallada durant diferents temps (5,10 i 20 minuts) en diferents medis, aigua, àcid cítric 1% i àcid ascòrbic 1%. S’han avaluat la temperatura i els sòlids solubles en el medi i en la mostra de la patata el color, i l’activitat de PPO i PRO. L’activitat enzimàtica de la PPO s’ha quantificat a partir de la reacció amb catecol i mesurant l’absorbància a λ=410nm, i la PRO a partir de la reacció amb guaiacol en presencia de H 2 O 2 i posteriorment mesurant l’absorbància a λ=420nm, cada una d’elles realitzant lectures cada 30 segons durant 10 minuts. Els resultats obtinguts indiquen que la immersió de la patata en aigua té un efecte inhibidor sobre l’activitat de la PPO i la PRO, mentre que la temperatura té l’efecte contrari especialment a major temperatura (35 o C) i major temps d’exposició (20 min). L’aplicació ultrasons té un efecte inhibició en el cas de l’activitat de la PPO, sent major als 10 minuts, en canvi té un efecte contrari en la PRO. L’aplicació dels ultrasons en els diferents medis genera un increment de temperatura d’uns 14-16 ºC als 20 minuts, arribant fins un màxim de 33 o C. La utilització de medis àcids en el tractament de sonicació genera un increment de la inhibició de l’activitat de la PPO, en canvi en el cas de la PRO no s’han obtingut resultats concloents. En el cas dels tractaments amb àcids s’observa un augment de la inhibició respecte el temps de sonicació, sent major a 20 minuts El tractament de sonicació amb àcid ascòrbic 1% durant 20 min, és el que mostra una major inhibició de la PPO. L’estudi del color ens mostra una relació significativa entre la PPO amb la lluminositat, i la PRO amb el Chroma de la patata. La millor proposta per la inhibició del enfosquiment seria: El tractament d’ultrasons de 20 minuts en un medi d’àcid ascòrbic al 1% que seria efectiu inhibint la PPO mentre que aquest tractament no seria efectiu per la PRO, però no contribueix de la mateixa manera en l’enfosquiment