Desarrollo de un sistema para la integración de nomenclatura y campos textuales sobre genes y proteínas

Una de las áreas de más actividad investigadora en el análisis de texto biomédico es el reconocimiento de los nombres y abreviaturas utilizadas para referirse a dos entidades biológicas de gran relevancia: genes y proteínas. Muchos de los métodos propuestos se basan en vocabularios control construidos a partir de la información almacenada en distintas bases de datos utilizadas en bioinformática. Debido a la ambigüedad existente en la nomenclatura de genes y proteínas dentro del mundo de la bioinformática, el objetivo de este proyecto es el de diseñar y desarrollar un sistema que integre información normalizada sobre genes/proteínas, susceptible de ser utilizada para el reconocimiento automático de dicha nomenclatura en textos científicos. La normalización se realizará en base a los identificadores únicos (claves externas) de diversas bases de datos. Para ello se desarrollará una base de datos centralizada (datawarehouse), sobre la que se incorporarán los datos pertinentes de varias bases de datos públicas (ej. UniProt, NCBI Entrez, Gene Ontology), así como los mecanismos de actualización necesarios. Finalmente se proporcionará la funcionalidad para su acceso programático. Este sistema será consultado por las herramientas de análisis de texto biomédico desarrolladas en nuestro grupo de investigación. [ABSTRACT] Among the areas of principal activities’ investigation in biomedic text analysing field we find the recognition of names and abbreviations used to talk about two main entitys: genes and proteins. Many of the proposed methods are based in control vocabularies builded up from information stored in several databases used in bioinformatic. Designing and developing a system that integrates information about genes/proteins, susceptible of being used for the automatic recognise in science texts. This integration will be achieved by using the id numbers (foreign keys) from the main bioinformatics’ data bases (UniProt, NCBI Entrez) building up a datawarehouse that includes the principal features of this genes/proteins. This system will be used by the tools developed in the Department of Architecture and Automatic Engineering

Assessment of different spent mushroom substrates to bioremediate soils contaminated with petroleum hydrocarbons

Bioremediation techniques are being developed as substitutes for physical–chemical methodologies that are expensive and not sustainable. For example, using the agricultural waste spent mushroom substrate (SMS) which contains valuable microbiota for soil bioremediation. In this work, SMSs of four cultivated fungal species, Pleurotus eryngii, Lentinula edodes, Pleurotus ostreatus, and Agaricus bisporus were evaluated for the bioremediation of soils contaminated by petroleum hydrocarbons (TPHs). The bioremediation test was carried out by mixing the four different SMSs with the TPH-contaminated soil in comparison with an unamended soil control to assess its natural attenuation. To determine the most efficient bioremediation strategy, hydrolase, dehydrogenase, and ligninolytic activities, ergosterol content, and percentage of TPHs degradation (total and by chains) were determined at the end of the assay at 40 days. The application of SMS significantly improved the degradation of TPHs with respect to the control. The most effective spent mushroom substrate to degrade TPHs was A. bisporus, followed by L. edodes and P. ostreatus. Similar results were obtained for the removal of aliphatic and aromatic hydrocarbons. The results showed the effectiveness of SMS to remove aliphatic and aromatic hydrocarbons from C10 to C35. This work demonstrates an alternative to valorizing an abundant agricultural waste as SMS to bioremediate contaminated soil

Impact of primary healthcare providers' initial role security and therapeutic commitment on implementing brief interventions in managing risky alcohol consumption: a cluster randomised factorial trial

Brief interventions; Risky drinking; Primary healthcareIntervenciones breves; Bebedores de riesgo; Atención primariaIntervencions breus; Bevedors de risc; Atenció primàriaBackground: Brief interventions in primary healthcare are cost-effective in reducing drinking problems but poorly implemented in routine practice. Although evidence about implementing brief interventions is growing, knowledge is limited with regard to impact of initial role security and therapeutic commitment on brief intervention implementation. Methods: In a cluster randomised factorial trial, 120 primary healthcare units (PHCUs) were randomised to eight groups: care as usual, training and support, financial reimbursement, and the opportunity to refer patients to an internet-based brief intervention (e-BI); paired combinations of these three strategies, and all three strategies combined. To explore the impact of initial role security and therapeutic commitment on implementing brief interventions, we performed multilevel linear regression analyses adapted to the factorial design. Results: Data from 746 providers from 120 PHCUs were included in the analyses. Baseline role security and therapeutic commitment were found not to influence implementation of brief interventions. Furthermore, there were no significant interactions between these characteristics and allocated implementation groups. Conclusions: The extent to which providers changed their brief intervention delivery following experience of different implementation strategies was not determined by their initial attitudes towards alcohol problems. In future research, more attention is needed to unravel the causal relation between practitioners’ attitudes, their actual behaviour and care improvement strategies to enhance implementation science.The research leading to these results or outcomes has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 259268 – Optimizing delivery of healthcare intervention (ODHIN)

Professional's Attitudes Do Not Influence Screening and Brief Interventions Rates for Hazardous and Harmful Drinkers: Results from ODHIN Study

Detecció d'alcoholèmia; Intervenció breu; Actitud del personal sanitariDetección de alcoholemia; Intervención breve; Actitud del personal sanitarioAlcoholism detection; Brief intervention; Attitude of Health PersonnelAims: To determine the relation between existing levels of alcohol screening and brief interventionrates infive European jurisdictions and role security and therapeutic commitment by the participat-ing primary healthcare professionals. Methods: Health care professionals consisting of, 409 GPs, 282 nurses and 55 other staff including psy-chologists, social workers and nurse aids from 120 primary health care centres participated in a cross-sectional 4-week survey. The participants registered all screening and brief intervention activities aspart of their normal routine. The participants also completed the Shortened Alcohol and Alcohol Pro-blems Perception Questionnaire (SAAPPQ), which measure role security and therapeutic commitment. Results: The only significant but small relationship was found between role security and screeningrate in a multilevel logistic regression analysis adjusted for occupation of the provider, number ofeligible patients and the random effects of jurisdictions and primary health care units (PHCU). Nosignificant relationship was found between role security and brief intervention rate nor betweentherapeutic commitment and screening rate/brief intervention rate. The proportion of patientsscreened varied across jurisdictions between 2 and 10%. Conclusion: Thefindings show that the studied factors (role security and therapeutic commitment)are not of great importance for alcohol screening and BI rates. Given the fact that screening and briefintervention implementation rate has not changed much in the last decade in spite of increased pol-icy emphasis, training initiatives and more research being published, this raises a question aboutwhat else is needed to enhance implementation.Radboud university medical centre received co-funding from The NetherlandsOrganization for Health Research and Development (ZonMW, Prevention Pro-gramme), under Grant Agreement n° 200310017—ODHIN—Optimizing de-livery of healthcare interventions in the Netherlands, according to Art.II.17 ofthe FP7 EC Grant Agreement. Pomeranian Medical University in Szczecin re-ceived co-funding regarding presented research from the Polish sciencefinancialresources in the years 2012–2014 allocated to conduct the international co-funded project ODHIN

A randomised controlled non-inferiority trial of primary care-based facilitated access to an alcohol reduction website (EFAR Spain): the study protocol

Detecció d'alcoholèmia; Intervenció breu; Atenció electrònicaDetección de alcoholemia; Intervención breve; Atención electrónicaAlcoholism detection; Brief intervention; Electronic attentionIntroduction: Early identification (EI) and brief interventions (BIs) for risky drinkers are effective tools in primary care. Lack of time in daily practice has been identified as one of the main barriers to implementation of BI. There is growing evidence that facilitated access by primary healthcare professionals (PHCPs) to a web-based BI can be a time-saving alternative to standard face-to-face BIs, but there is as yet no evidence about the effectiveness of this approach relative to conventional BI. The main aim of this study is to test non-inferiority of facilitation to a web-based BI for risky drinkers delivered by PHCP against face-to-face BI. Method and analysis: A randomised controlled non-inferiority trial comparing both interventions will be performed in primary care health centres in Catalonia, Spain. Unselected adult patients attending participating centres will be given a leaflet inviting them to log on to a website to complete the Alcohol Use Disorders Identification Test (AUDIT-C) alcohol screening questionnaire. Participants with positive results will be requested online to complete a trial module including consent, baseline assessment and randomisation to either face-to-face BI by the practitioner or BI via the alcohol reduction website. Follow-up assessment of risky drinking will be undertaken online at 3 months and 1 year using the full AUDIT and D5-EQD5 scale. Proportions of risky drinkers in each group will be calculated and non-inferiority assessed against a specified margin of 10%. Assuming reduction of 30% of risky drinkers receiving standard intervention, 1000 patients will be required to give 90% power to reject the null hypothesis. Ethics and dissemination: The protocol was approved by the Ethics Commmittee of IDIAP Jordi Gol i Gurina P14/028. The findings of the trial will be disseminated through peer-reviewed journals, national and international conference presentations.This work has been funded by project PI042924 integrated in theNational R+D+I and funded by the Carlos III Health Institute-Deputy GeneralAssessment and the European Regional Development Fund (ERDF)

Oligomeric Formulas in Surgery: A Delphi and Consensus Study

Nutritional management of patients with intestinal failure often includes the use of oligomeric formulas. Implementing the use of oligomeric formulas in surgical patients with maldigestion or malabsorption could be a nutritional strategy to be included in clinical protocols. We aim to generate knowledge from a survey focused on the effectiveness of nutritional therapy with oligomeric formulas with Delphi methodology. Each statement that reached an agreement consensus among participants was defined as a median consensus score ≥7 and as an interquartile range ≤3. The use of oligomeric formulas in surgical patients, starting enteral nutrition in the post-operative phase in short bowel syndrome and in nonspecific diarrhea after surgical procedures, could improve nutritional therapy implementation. Stakeholders agreed that early jejunal enteral nutrition with oligomeric formula is more effective compared to intravenous fluid therapy and it is useful in patients undergoing upper gastro-intestinal tract major surgery when malabsorption or maldigestion is suspected. Finally, oligomeric formulas may be useful when a feeding tube is placed distally to the duodenum. This study shows a practical approach to the use of oligomeric formulas in surgical patients with intestinal disorders and malabsorption, and it helps clinicians in the decision-making process

Antibioticoterapia Intravenosa domiciliaria mediante bomba de perfusión continua de la sobreinfección respiratoria por Pseudomonas aeruginosa en el paciente con enfermedad pulmonar obstructiva crónica

La malaltia pulmonar obstructiva crónica (MPOC) té una prevalença elevada al nostra medi i un gran impacte econòmic. La sobreinfecció respiratoria en els pacients MPOC avançats, es bàsicament, per Pseudomonas. L'antibioticoteràpia domiciliaria endovenosa en aquest tipus de sobreinfecció es de gran importància. La forma d'administració de l'antibiòtic es mitjançant bombes d'infusió continues i bombes d'infusió intermitents. Es tracta d'un estudi comparatiu dels dos tipus de bombes d'infusió per l'erradicació de Pseudomonas aeruginosa en el pacient MPOC.La enfermedad pulmonar obstructiva crónica ( EPOC) en nuestro medio tiene una alta prevalencia e impacto socioeconómico. La sobreinfección respiratoria en los pacientes EPOC en estadios avanzados es causada ,básicamente, por Pseudomonas aeruginosa. La antibióticoterapia endovenosa domiciliaria en este tipo de sobreinfección es de gran importancia. La forma de administración del antibiótico es mediante bombas de perfusión continuas y bombas de infusión intermitente. Se trata de un estudio comparativo entre los dos tipos de bombas de infusión para la erradicación de Pseudomonas aeruginosa en el paciente EPOC

Trajectories of alcohol consumption during life and the risk of developing breast cancer

Background Whether there are lifetime points of greater sensitivity to the deleterious effects of alcohol intake on the breasts remains inconclusive. Objective To compare the influence of distinctive trajectories of alcohol consumption throughout a woman's life on development of breast cancer (BC). Methods 1278 confirmed invasive BC cases and matched (by age and residence) controls from the Epi-GEICAM study (Spain) were used. The novel group-based trajectory modelling was used to identify different alcohol consumption trajectories throughout women's lifetime. Results Four alcohol trajectories were identified. The first comprised women (45%) with low alcohol consumption (= 15 g/day), never having a low alcohol consumption. Comparing with the first trajectory, the fourth doubled BC risk (OR 2.19; 95% CI 1.27, 3.77), followed by the third (OR 1.44; 0.96, 2.16) and ultimately by the second trajectory (OR 1.17; 0.86, 1.58). The magnitude of BC risk was greater in postmenopausal women, especially in those with underweight or normal weight. When alcohol consumption was independently examined at each life stage, >= 15 g/day of alcohol consumption in adolescence was strongly associated with BC risk followed by consumption in adulthood. Conclusions The greater the alcohol consumption accumulated throughout life, the greater the risk of BC, especially in postmenopausal women. Alcohol consumption during adolescence may particularly influence BC risk.This study was funded by the Fundacion Cientifica Asociacion Espanola Contra el Cancer (AECC) (Scientific Foundation of the Spanish Association against Cancer 2006 & 2016) (Marina Pollan), Sociedad Espanola de Oncologia Medica (SEOM) (Spanish Society of Medical Oncology) (Miguel Martin), Scholarship 'Contrato de atraccion de talento' from Community of Madrid (Carolina Donat-Vargas), Fundacion Cerveza y Salud 2005 (Beer and Health Foundation 2005) (Miguel Martin) and Federacion de Asociaciones de Mujeres con Cancer de Mama (FECMA) (Spanish Federation of Associations of Women with Breast Cancer) (Miguel Martin, Marina Pollan)

Primary breast cancer and health related quality of life in Spanish women: The EpiGEICAM case-control study

This study evaluates the impact of breast cancer (BC) in health related quality of life (HRQL) and in psychological distress (PD) during the initial phases of the disease and looks for contributing factors. A multicentric case-control study, EpiGEICAM, was carried out. Incident BC cases and age- and residence- matched controls were included. Clinical, epidemiological, HRQL (SF-36) and PD information (GHQ-28) was collected. We used multivariable logistic regression models to estimate OR of low HRQL and of PD in cases compared to controls, and to identify factors associated with low HRQL and with PD. Among 896 BC cases and 890 control women, cases had poorer scores than both, the reference population and the control group, in all SF-36 scales. BC women with lower education, younger, active workers, never smokers, those with comorbidities, in stage IV and with surgical treatment had lower physical HRQL; factors associated with low mental HRQL were dissatisfaction with social support, being current smoker and having children. Cases had a fivefold increased odds of PD compared to controls. Managing comorbidities and trying to promote social support, especially in younger and less educated women, could improve well-being of BC patients