Biomedical text annotation and summarization

Advancements in the biomedical community are largely documented and published in text format in scientific forums such as conferences and journals. To address the scalability of utilizing the large volume of text-based information generated by continuing advances in the biomedical field, we propose a two-part text summarization system to reduce the volume of text which must be read by biomedical professionals. The contributions of the text summarization system are a) it utilizes biomedical concepts rather than terms to find the main points of a text, b) it uses two new concept-based algorithms to find important areas of a text for extracting sentences to form a summary, and c) it is supported by a new semantic annotation sub-system, which identifies biomedical concepts found in biomedical text documents. The semantic annotation subsystem uses a novel multiple-filter system architecture for online matching of concepts defined by a biomedical metathesaurus. The goal of semantic annotation is to show that online text-to-concept mapping can be performed without a significant loss of precision as compared to current offline systems. An evaluation shows the text summarization algorithms using concepts outperform existing summarization systems, and the semantic annotation system performs twenty times faster than a state-of-the-art system with no significant loss of precision

Evaluating the role of force feedback for biomanipulation tasks

Paper presented at the IEEE Virtual Reality, Haptics Symposium and Symposium on 3D User Interface, Alexandria, VA.Conventional cell manipulation techniques do not have the ability to provide force feedback to an operator. Poor control of cell injection force is one of the primary reasons for low success rates in cell injection and transgenesis in particular. Therefore, there exists a need to incorporate force feedback into a cell injection system. We have developed an automated cell injection system, which has the capability of measuring forces in the range of μN. We tested our system with 40 human subjects to evaluate the role of force feedback in cell injection task. Our experimental results indicate that the subjects were able to feel the cell injection force and confirmed our research hypothesis that the use of combined vision and force feedback leads to higher success rate in cell injection task compared to using vision feedback alone

Modern Breast Cancer Detection: A Technological Review

Breast cancer is a serious threat worldwide and is the number two killer of women in the United States. The key to successful management is screening and early detection. What follows is a description of the state of the art in screening and detection for breast cancer as well as a discussion of new and emerging technologies. This paper aims to serve as a starting point for those who are not acquainted with this growing field

Approaches to text mining for clinical medical records

The 21st Annual ACM Symposium on Applied Computing 2006, Technical tracks on Computer Applications in Health Care (CAHC 2006), Dijon, France, April 23 -27, 2006. Retrieved 6/21/2006 from http://www.ischool.drexel.edu/faculty/hhan/SAC2006_CAHC.pdf.Clinical medical records contain a wealth of information, largely in free-text form. Means to extract structured information from free-text records is an important research endeavor. In this paper, we describe a MEDical Information Extraction (MedIE) system that extracts and mines a variety of patient information with breast complaints from free-text clinical records. MedIE is a part of medical text mining project being conducted in Drexel University. Three approaches are proposed to solve different IE tasks and very good performance (precision and recall) was achieved. A graph-based approach which uses the parsing result of link-grammar parser was invented for relation extraction; high accuracy was achieved. A simple but efficient ontology-based approach was adopted to extract medical terms of interest. Finally, an NLP-based feature extraction method coupled with an ID3-based decision tree was used to perform text classification

Converting semi-structured clinical medical records into information and knowledge

Proceedings of the 21st International Conference on Data Engineering, ICDE 2005, pp. 1647765.Clinical medical records contain a wealth of information, largely in free-textual form. Thus, means to extract structured information from free-text records becomes an important research endeavor. In this paper, we propose and implement an information extraction system that extracts three types of information — numeric values, medical terms and categorical value — from semi-structured patient records. Three approaches are proposed to solve the problems posed by each of the three types of values, respectively, and very good performance (precision and recall) is achieved. A novel link-grammar based approach was invented to associate feature and number in a sentence, and extremely high accuracy was achieved. A simple but efficient approach, using POS-based pattern and domain ontology, was adopted to extract medical terms of interest. Finally, an NLPbased feature extraction method coupled with an ID3- based decision tree is used to classify and extract categorical cases. This preliminary approach to categorical fields has, so far, proven to be quite effective

Soft tissue elastic modulus measurement and tumor detection using piezoelectric fingers

2005 MRS Fall Meeting, 898, pp. 1-6.We have investigated probing breast tumor in a lumpectomy sample using a newly developed piezoelectric finger (PEF). PEF is a piezoelectric cantilever that consists of a top driving piezoelectric lead zirconate titanate (PZT) layer and a bottom sensing PZT layer sandwiched to a middle stainless steel layer. A PEF can both apply a force and detect the corresponding displacement in one single device by simple electrical means. Applying an electric field to the driving PZT layer causes the PEF to bend which in turn causes a measurable induced voltage across the sensing PZT layer that is proportional to the deflection of the PEF’s tip. Earlier studies have demonstrated that with the appropriate tip geometry, the PEF could accurately measure the elastic and shear moduli of a soft material. It could also differentiate and locate hard inclusions embedded in a soft matrix by the contrast of elastic moduli. In this study, we applied the PEF to probe a lumpectomy sample and located the tumor inside the sample using the spatial contrast of elastic moduli

Improving the efficacy of cellular therapy by magnetic cell targeting

Poster presented at Biomedical Technology Showcase 2006, Philadelphia, PA. Retrieved 18 Aug 2006 from http://www.biomed.drexel.edu/new04/Content/Biomed_Tech_Showcase/Poster_Presentations/Barbee.pdf.The hot topic of stem cell research has raised hopes for new treatments for a breadth of ailments. As the expectations continue to mount, most related engineering research has been focused around new tools for isolation and propagation of cell lines, with inadequate attention to effective delivery strategies. Invasive or systemic injections come with increased risk and poor efficiency, often wasting a vast majority of the total cellular dosage. We present a method for magnetic targeting of cells in the body with the use of a two-source method of magnetic drug delivery proposed previously in the literature

Floating electrode dielectric barrier discharge plasma in air promoting apoptotic behavior in Melanoma skin cancer cell lines

Plasma Chemistry and Plasma Processing, 27(2): pp. 163-176.Initiation of apoptosis, or programmed cell death, is an important issue in cancer treatment as cancer cells frequently have acquired the ability to block apoptosis and thus are more resistant to chemotherapeutic drugs. Targeted and perhaps selective destruction of cancerous tissue is desirable for many reasons, ranging from the enhancement of or aid to current medical methods to problems currently lacking a solution, i.e. lung cancer. Demonstrated in this publication is the inactivation (killing) of human Melanoma skin cancer cell lines, in vitro, by Floating Electrode Dielectric Barrier Discharge plasma. Not only are these cells shown to be killed immediately by high doses of plasma treatment,but low doses are shown to promote apoptotic behavior as detected by TUNEL staining and subsequent flow cytometry. It is shown that plasma acts on the cells directly and not by “poisoning” the solution surrounding the cells, even through a layer of such solution. Potential mechanisms of interaction of plasma with cells are discussed and further steps are proposed to develop an understanding of such systems

Leptospirosis during Dengue Outbreak, Bangladesh

We collected acute-phase serum samples from febrile patients at 2 major hospitals in Dhaka, Bangladesh, during an outbreak of dengue fever in 2001. A total of 18% of dengue-negative patients tested positive for leptospirosis. The case-fatality rate among leptospirosis patients (5%) was higher than among dengue fever patients (1.2%)

Marine ecosystem assessment for the Southern Ocean: birds and marine mammals in a changing climate

The massive number of seabirds (penguins and procellariiformes) and marine mammals (cetaceans and pinnipeds) – referred to here as top predators – is one of the most iconic components of the Antarctic and Southern Ocean. They play an important role as highly mobile consumers, structuring and connecting pelagic marine food webs and are widely studied relative to other taxa. Many birds and mammals establish dense breeding colonies or use haul-out sites, making them relatively easy to study. Cetaceans, however, spend their lives at sea and thus aspects of their life cycle are more complicated to monitor and study. Nevertheless, they all feed at sea and their reproductive success depends on the food availability in the marine environment, hence they are considered useful indicators of the state of the marine resources. In general, top predators have large body sizes that allow for instrumentation with miniature data-recording or transmitting devices to monitor their activities at sea. Development of scientific techniques to study reproduction and foraging of top predators has led to substantial scientific literature on their population trends, key biological parameters, migratory patterns, foraging and feeding ecology, and linkages with atmospheric or oceanographic dynamics, for a number of species and regions. We briefly summarize the vast literature on Southern Ocean top predators, focusing on the most recent syntheses. We also provide an overview on the key current and emerging pressures faced by these animals as a result of both natural and human causes. We recognize the overarching impact that environmental changes driven by climate change have on the ecology of these species. We also evaluate direct and indirect interactions between marine predators and other factors such as disease, pollution, land disturbance and the increasing pressure from global fisheries in the Southern Ocean. Where possible we consider the data availability for assessing the status and trends for each of these components, their capacity for resilience or recovery, effectiveness of management responses, risk likelihood of key impacts and future outlook