@Note: A workbench for Biomedical Text Mining

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists’ needs is crucial to solve real-world problems and promote further research.We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation.@Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.     

Continuing Medical Education Program in Echocardiography

Article Title: Study of Left Ventricular Rotation and Torsion in the Acute Phase of ST-Elevation Myocardial Infarction by Speckle Tracking Echocardiography (Echocardiography 2010;27:44)     

Stem cell and lung cancer development: blaming the Wnt,Hh and Notch signalling pathway

Primary lung cancer may arise from the central (bronchial) or peripheral (bronchiolo-alveolar) compartments. However the origins of the different histological types of primary lung cancer are not well understood. Stem cells are believed to be crucial players in tumour development and there is much interest in identifying those compartments that harbour stem cells involved in lung cancer. Although the role of stem cells in carcinogenesis is not well characterised, emerging evidence is providing new insights into this process. Numerous studies have indicated that lung cancer is not a result of a sudden transforming event but a multistep process in which a sequence of molecular changes result in genetic and morphological aberrations. The exact sequence of molecular events involved in lung carcinogenesis is not yet well understood, therefore deeper knowledge of the aberrant stem cell fate signalling pathway could be crucial in the development of new drugs against the advanced setting.     

Derivation of the Uncontrolled Donation after Circulatory Determination of Death Protocol for New York City

Evidence from Europe suggests establishing out‐of‐hospital, uncontrolled donation after circulatory determination of death (UDCDD) protocols has potential to substantially increase organ availability. The study objective was to derive an out‐of‐hospital UDCDD protocol that would be acceptable to New York City (NYC) residents. Participatory action research and the SEED‐SCALE process for social change guided protocol development in NYC from July 2007 to September 2010. A coalition of government officials, subject experts and communities necessary to achieve support was formed. Authorized NY State and NYC government officials and their legal representatives collaboratively investigated how the program could be implemented under current law and regulations. Community stakeholders (secular and religious organizations) were engaged in town hall style meetings. Ethnographic data (meeting minutes, field notes, quantitative surveys) were collected and posted in a collaborative internet environment. Data were analyzed using an iterative coding scheme to discern themes, theoretical constructs and a summary narrative to guide protocol development. A clinically appropriate, ethically sound UDCDD protocol for out‐of‐hospital settings has been derived. This program is likely to be accepted by NYC residents since the protocol was derived through partnership with government officials, subject experts and community participants.     

Effect of Freezing Rate and Dendritic Ice Formation on Concentration Profiles of Proteins Frozen in Cylindrical Vessels

The process of freezing protein solutions can perturb the conformation of the protein and potentially lead to aggregate formation during long-term storage in the frozen state. Radial macroscopic freeze concentration and temperature profiles for bovine serum albumin (BSA) solutions in small cylindrical stainless steel vessels were determined for various freezing rates. The measured concentrations of both BSA and immunoglobulin G2, as well as trehalose in sampled ice sections, increased by up to twofold to threefold toward the bottom and radial center for slow freezing rates produced in stagnant air freezers. The concentration and temperature profiles result in density gradients that transport solutes by convective flow. For faster external cooling by either forced convection of air or a liquid coolant, the increased freezing rate raised the ice front velocity resulting in enhanced dendritic ice growth. The ice trapped the solutes more effectively before they were removed from the ice front by diffusion and convection, resulting in more uniform solute concentration profiles. The dynamic temperature profiles from multiple radial thermocouples were consistent with the independently measured freeze concentration profiles. The ability to control the protein concentration profile in the frozen state offers the potential to improve stability of protein in long-term frozen storage.