A New Method to Retrieve, Cluster And Annotate Clinical Literature Related To Electronic Health Records

The access to medical literature collections such as PubMed, MedScape or Cochrane has been increased notably in the last years by the web-based tools that provide instant access to the information. However, more sophisticated methodologies are needed to exploit efficiently all that information. The lack of advanced search methods in clinical domain produce that even using well-defined questions for a particular disease, clinicians receive too many results. Since no information analysis is applied afterwards, some relevant results which are not presented in the top of the resultant collection could be ignored by the expert causing an important loose of information. In this work we present a new method to improve scientific article search using patient information for query generation. Using federated search strategy, it is able to simultaneously search in different resources and present a unique relevant literature collection. And applying NLP techniques it presents semantically similar publications together, facilitating the identification of relevant information to clinicians. This method aims to be the foundation of a collaborative environment for sharing clinical knowledge related to patients and scientific publications

Ion Beam Experiments to Emulate Nuclear Fusion Environment on Structural Materials at CMAM

One of the major problems not only in nuclear fusion but in all the fields that have to face irradiation damage is to predict the microstructural evolution of all the features that are involved in the good response of the material. In the case of nuclear fusion, it is well known that structural materials that will be a fundamental piece in the future reactor must withstand severe neutron irradiation damage, high temperatures, and cyclic stresses which will result in a reduction of the lifetime of the component. For that reason, a big effort is being done for the scientific community in order to understand the complex mechanisms that lie in the relationship between irradiation damage, microstructure, temperature, stresses, etc. However, neutron irradiation brings inherently transmutation and nuclear activation, which makes extremely hard to study those samples. Therefore, the scientific community is using since long time ago ion beam facilities to emulate the neutron damage, without the worst inconvenience. In this chapter, the authors described briefly the facility located at Centro de MicroAnálisis de Materiales (CMAM), Madrid, and presented afterward some examples of experiments that Spanish Nuclear Fusion Laboratory at CIEMAT has been carrying out related to this matter

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems

Ionoluminescence induced by swift heavy ions in silica and quartz: A comparative analysis

Ionoluminescence (IL) of the two SiO 2 phases, amorphous silica and crystalline quartz, has been comparatively investigated in this work, in order to learn about the structural defects generated by means of ion irradiation and the role of crystalline order on the damage processes. Irradiations have been performed with Cl at 10 MeV and Br at 15 MeV, corresponding to the electronic stopping regime (i.e., where the electronic stopping power S e is dominant) and well above the amorphization threshold. The light-emission kinetics for the two main emission bands, located at 1.9 eV (652 nm) and 2.7 eV (459 nm), has been measured under the same ion irradiation conditions as a function of fluence for both, silica and quartz. The role of electronic stopping power has been also investigated and discussed within current views for electronic damage. Our experiments provide a rich phenomenological background that should help to elucidate the mechanisms responsible for light emission and defect creationThis work has been supported by Spanish Ministry MICINN through the project MAT-2008-06794-C03-03, JCI-2009-05681, and by Madrid Community through the project TECHNOFUSION (S2009/ENE-1679). OPR is grateful to CONACyT, Mexico, for extending a postdoctoral fellowshi

Relevance of infections on the outcomes of patients with myelodysplastic syndromes, chronic myelomonocytic leukemia, and acute myeloid leukemia treated with hypomethylating agents: a cohort study from the GESMD

Hypomethylating agent; Infection; Myelodysplastic syndromeAgente hipometilante; Infección; Síndrome mielodisplásicoAgent hipometilant; Infecció; Síndrome mielodisplàsticBackground: The consequences of infectious toxicity of hypomethylating agents (HMAs) on overall survival (OS) of patients diagnosed with high-risk myeloid neoplasms have not been thoroughly investigated. Objectives: We aimed to evaluate whether infectious events (IEs) negatively influenced the results of HMA treatment in a real-world setting. Design: Observational study. Methods: We obtained data from 412 non-selected consecutive patients from 23 Spanish hospitals who were diagnosed with high-risk myelodysplastic syndrome, chronic myelomonocytic leukemia, or acute myeloid leukemia and were treated with HMA. HMAs received after chemotherapy or stem cell transplant were excluded. All IEs were recorded. Outcomes included OS, modifications to the pre-planned treatment, incidence and characteristics of IEs, hospitalization, red blood cell transfusions, and factors associated with infection. Results: The rate of infection was 1.2 per patient/year. Next-cycle delay (p = 0.001) and hospitalizations (p = 0.001) were significantly influenced by IEs. Transfusion requirements during each cycle were significantly higher after infection compared with cycles without infection (coefficient = 1.55 [95% confidence interval (CI) = 1.26–1.84], p 20% (HR = 1.57 [95% CI = 1.19–2.01], p 9 g/dl (HR = 0.65 [95% CI = 0.51–0.82], p < 0.001) and higher platelet count (HR = 0.997 [95% CI = 0.996–0.998], p = 0.016) protected from it. Conclusion: HMA infectious toxicity worsens OS, hinders the adherence to antineoplastic treatment and results in significant morbidity. Preventive strategies are fundamental in vulnerable patients

Building sustainable capacity for health research in africa through cloud computing applications

Access to information and continuous education represent critical factors for physicians and researchers over the world. For African professionals, this situation is even more problematic due to the frequently difficult access to technological infrastructures and basic information. Both education and information technologies (e.g., including hardware, software or networking) are expensive and unaffordable for many African professionals. Thus, the use of e-learning and an open approach to information exchange and software use have been already proposed to improve medical informatics issues in Africa. In this context, the AFRICA BUILD project, supported by the European Commission, aims to develop a virtual platform to provide access to a wide range of biomedical informatics and learning resources to professionals and researchers in Africa. A consortium of four African and four European partners work together in this initiative. In this framework, we have developed a prototype of a cloud-computing infrastructure to demonstrate, as a proof of concept, the feasibility of this approach. We have conducted the experiment in two different locations in Africa: Burundi and Egypt. As shown in this paper, technologies such as cloud computing and the use of open source medical software for a large range of case present significant challenges and opportunities for developing countries, such as many in Africa

Patient-based Literature Retrieval and Integration: A Use Case for Diabetes and arterial Hypertension

Specialized search engines such as PubMed, MedScape or Cochrane have increased dramatically the visibility of biomedical scientific results. These web-based tools allow physicians to access scientific papers instantly. However, this decisive improvement had not a proportional impact in clinical practice due to the lack of advanced search methods. Even queries highly specified for a concrete pathology frequently retrieve too many information, with publications related to patients treated by the physician beyond the scope of the results examined. In this work we present a new method to improve scientific article search using patient information. Two pathologies have been used within the project to retrieve relevant literature to patient data and to be integrated with other sources. Promising results suggest the suitability of the approach, highlighting publications dealing with patient features and facilitating literature search to physicians

Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus

Lupinus mariae-josephi is a recently described endemic Lupinus species from a small area in Eastern Spain where it thrives in soils with active lime and high pH. The L. mariae-josephi root symbionts were shown to be very slow-growing bacteria with different phenotypic and symbiotic characteristics from those of Bradyrhizobium strains nodulating other Lupinus. Their phylogenetic status was examined by multilocus sequence analyses of four housekeeping genes (16S rRNA, glnII, recA, and atpD) and showed the existence of a distinct evolutionary lineage for L. mariae-josephi that also included Bradyrhizobium jicamae. Within this lineage, the tested isolates clustered in three different sub-groups that might correspond to novel sister Bradyrhizobium species. These core gene analyses consistently showed that all the endosymbiotic bacteria isolated from other Lupinus species of the Iberian Peninsula were related to strains of the B. canariense or B. japonicum lineages and were separate from the L. mariae-josephi isolates. Phylogenetic analysis based on nodC symbiotic gene sequences showed that L. mariae-josephi bacteria also constituted a new symbiotic lineage distant from those previously defined in the genus Bradyrhizobium. In contrast, the nodC genes of isolates from other Lupinus spp. from the Iberian Peninsula were again clearly related to the B. canariense and B. japonicum bv. genistearum lineages. Speciation of L. mariae-josephi bradyrhizobia may result from the colonization of a singular habitat by their unique legume host

Accessing and managing open medical resources in Africa over the Internet

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altruistic support of medical initiatives. We have carried out some experiments to demonstrate the feasibility of using this approach to disseminate open data and informatics resources in Africa. After the experiments we developed the AFRICA BUILD Portal, the first Social Network for African biomedical researchers. Through the AFRICA BUILD Portal users can access in a transparent way to several resources. Currently, over 600 researchers are using distributed and open resources through this platform committed to low connections

Independent and combined influence of healthy lifestyle factors on academic performance in adolescents: DADOS Study

BACKGROUND. Few studies have analyzed the combined effect of lifestyle factors on academic performance (AP) in adolescents. The aim of this study was to analyze the independent and combined effects of weight status, screen time, sleep quality, daily meal frequency, cardiorespiratory fitness and physical activity (PA) on AP in adolescents. METHODS. A total of 262 adolescents (13.9±0.3 years) from the DADOS study were included in the analysis. Weight status was assessed through body mass index (kg/m 2 ). Participants completed questionnaires to evaluate screen time, sleep quality and daily meal frequency. Cardiorespiratory fitness was assessed by the 20-m shuttle run test. PA was evaluated by a wrist-worn GENEActiv accelerometer. AP was assessed through the final academic grades and a validated questionnaire. RESULTS. Non-overweight status, low screen time, good sleep quality and proper meal frequency showed independent, positive influence on AP. Moreover, adolescents achieving at least 3 healthy lifestyles were more likely to be in the high-performance group for academic grades than those achieving ≤ 1 (math OR: 3.02-9.51, language OR: 3.51-6.76 and grade point average OR: 4.22-9.36). CONCLUSIONS. Although individual healthy lifestyles are independently and positively associated with AP, the cumulative effect of multiple healthy lifestyles have a stronger impact