Biomedical events extraction using the hidden vector state model

Objective: Biomedical events extraction concerns about events describing changes on the state of bio-molecules from literature. Comparing to the protein-protein interactions (PPIs) extraction task which often only involves the extraction of binary relations between two proteins, biomedical events extraction is much harder since it needs to deal with complex events consisting of embedded or hierarchical relations among proteins, events, and their textual triggers. In this paper, we propose an information extraction system based on the hidden vector state (HVS) model, called HVS-BioEvent, for biomedical events extraction, and investigate its capability in extracting complex events. Methods and material: HVS has been previously employed for extracting PPIs. In HVS-BioEvent, we propose an automated way to generate abstract annotations for HVS training and further propose novel machine learning approaches for event trigger words identification, and for biomedical events extraction from the HVS parse results. Results: Our proposed system achieves an F-score of 49.57% on the corpus used in the BioNLP'09 shared task, which is only 2.38% lower than the best performing system by UTurku in the BioNLP'09 shared task. Nevertheless, HVS-BioEvent outperforms UTurku's system on complex events extraction with 36.57% vs. 30.52% being achieved for extracting regulation events, and 40.61% vs. 38.99% for negative regulation events. Conclusions: The results suggest that the HVS model with the hierarchical hidden state structure is indeed more suitable for complex event extraction since it could naturally model embedded structural context in sentences.

Intracellular redox state modulates the T cell surface proteome – relevance to ageing

During ageing an altered redox balance has been observed in both intracellular and extracellular compartments, primarily due to glutathione depletion and metabolic stress. Maintaining redox homeostasis is important for controlling proliferation and apoptosis in response to specific stimuli for a variety of cells. For T cells, the ability to generate specific response to antigen is dependent on the oxidation state of cell surface and cytoplasmic protein-thiols. Here we describe the effects of depleting intracellular glutathione concentration for T cell exofacial expression of thioredoxin 1 and IL-2 production, and have determined the distribution of Trx1 with ageing. Using buthionine sulfoximine to deplete intracellular glutathione in Jurkat T cells we show using Western blotting that cell surface thioredoxin-1 is lowered and that the response to the lectin phytohaemagglutinin measured by ELISA as IL-2 production is also decreased. Using flow cytometry we show that the distribution of Trx1 on primary CD4+ T cells is age-dependent, with lower surface Trx1 expression and greater variability of surface expression observed with age. Together these data suggest that a relationship exists between the intracellular redox compartment and exofacial surface. Redox imbalance may be important for impaired T cell function during ageing.

Smallpox vaccination, the establishment of vaccination boards, and state formation in Venezuela and Cuba in the nineteenth century

The Balmis expedition, sent to America by the Spanish monarch Charles IV in 1803, was a watershed in the history of Medicine as it made smallpox vaccination available for the first time, effectively prevented the disease from spreading, and saved thousands of lives. Immunization required complex administrative measures and political decisions including the creation of Vaccination Boards, all of which involved different sectors of Spanish American society. This dissertation argues that at the beginning of the nineteenth century the Spanish American colonial state had reached some level of maturity and cohesion that made it capable of executing this complex project in public health. The significance of this mobilization and the every-day experience in implementing this new public health measure is the center of this work. It is situated geographically in Venezuela and Cuba, entities which took different evolutionary paths in the nineteenth century. The organization and functioning of Vaccination Boards in these two areas are used to illustrate the state formation process, and sharp political differences in this critical period.

Forging professional public health nursing in a southern state: Florida's public health nurses, 1889-1934

From 1889 to 1934, Florida's nurses belonging to a new group of professional women ushered in a pioneering phase of public health nursing in Florida. During this era, the nurses' ability to confront health and professional issues varied a great deal but in quiet and forceful ways they tackled cultural and environmental problems to assist people who were ill or help prevent people from becoming ill. This dissertation places the development of professional public health nursing in its social context by uncovering the relationships public health nurses formed with clubwomen, the medical profession, city leaders, midwives, and others. In 1888, there were few graduate nurses in the state, no state board of health and no organized nursing service to respond to Jacksonville's great yellow fever epidemic. By 1934, national and state leaders of public health nursing had built up the profession to become an essential part of the State Board of Health's service to the community. Between these milestones, in the era of white supremacy and Jim Crow, public health nurses combined their professional training with a pioneer spirit of innovation and risk-taking. In the predominately rural state, the public health nurses' resolve to overcome environmental hazards and cultural obstacles stands out as they attempted to reach those who were unserved or underserved by modern medicine.

Relational conceptions of paternalism : a way to rebut nanny-state accusations and evaluate public health interventions

This work is funded by NHMRC grant 1023197. Stacy Carter is funded by an NHMRC Career Development Fellowship 1032963.

Reframing the Debate Around State Responses to Infertility : Considering the Harms of Subfertility and Involuntary Childlessness

Peer reviewed

Treatment for Complicated Grief : State of the Science and Ways Forward

Peer reviewed

State-space modelling of geolocation data reveals sex differences in the use of management areas by breeding northern fulmars

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd and Marine Scotland for fieldwork and equipment support. Handling and tagging of fulmars was conducted under licences from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship and LQ was supported by a NERC Studentship. Thanks also to the many colleagues who assisted with fieldwork during the project, and to Helen Bailey and Arliss Winship for advice on implementing the state-space model.

State-space modelling of geolocation data reveals sex differences in the use of management areas by breeding northern fulmars

We thank Orkney Islands Council for access to Eynhallow and Talisman Energy (UK) Ltd and Marine Scotland for fieldwork and equipment support. Handling and tagging of fulmars was conducted under licences from the British Trust for Ornithology and the UK Home Office. EE was funded by a Marine Alliance for Science and Technology for Scotland/University of Aberdeen College of Life Sciences and Medicine studentship and LQ was supported by a NERC Studentship. Thanks also to the many colleagues who assisted with fieldwork during the project, and to Helen Bailey and Arliss Winship for advice on implementing the state-space model.

Laser-Driven Ion Accelerators: State of the Art and Applications

Laser-plasma based accelerators of protons and heavier ions are a source of potential interest for several applications, including in the biomedical area. While the potential future use in cancer hadrontherapy acts as a strong aspirational motivation for this research field, radiobiology employing laser-driven ion bursts is alreadyan active field of research. Here we give a summary of the state of the art in laser driven ion acceleration, of the main challenges currently faced by the research inthis field and of some of the current and future strategies for overcoming them.