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Bioinformatics and Bioengineering Conference, 2001. Proceedings of the IEEE 2nd International Symposium on

Date 4-6 Nov. 2001

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Displaying Results 1 - 25 of 37
  • Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)

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    Freely Available from IEEE
  • Author index

    Page(s): 278 - 279
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    Freely Available from IEEE
  • Querying phylogenies visually

    Page(s): 3 - 10
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (116 KB) |  | HTML iconHTML  

    Querying and visualization of phylogenetic databases remain a great challenge due to their inherent complex structures. Popular phylogenetic databases such as Tree of Life and TreeBASE do not support flexible querying through query languages for the exploration of their contents. The query facility employed in these databases is usually limited to complex interfaces or is too limited to be useful for many applications. The most striking shortcoming of these systems is that they do not treat phylogenies (trees) as first citizens. In this paper, we introduce a novel visual query language for phylogenetic databases in which trees are recognized as basic units. We also introduce a Web based query interface, based on this language, for querying any tree like structure, either on the Web (e.g. Tree of Life), or in traditional relational databases (e.g. TreeBASE). As an aside, the mapping technique used in our system makes it possible to interoperate between a variety of heterogeneous phylogenetic databases. Finally, we demonstrate that the basic tree manipulation operators proposed in this paper can be used to form unlimited types of tree queries that were not possible in popular phylogenetic databases until now View full abstract»

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  • Registration of multi-modal brain images using the rigidity constraint

    Page(s): 217 - 222
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (137 KB) |  | HTML iconHTML  

    A template-matching approach to registration of volumetric images is described. The process automatically selects about a dozen highly detailed and unique templates (cubic or spherical subvolumes) from the target volume and locates the templates in the reference volume. The centroids of four correspondences best satisfying the rigidity constraint are then used to determine the transformation matrix that resamples the target volume to overlay the reference volume. Different similarity measures used in template matching are discussed and experimental results are presented. The proposed registration method produces a median error of 2.8 mm when registering Venderbilt brain image data sets and an average registration time of 2.5 minutes on a 400 MHz PC View full abstract»

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  • Searching online journals for fluorescence microscope images depicting protein subcellular location patterns

    Page(s): 119 - 128
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (232 KB) |  | HTML iconHTML  

    There is extensive interest in automating the collection, organization and analysis of biological data. Data in the form of images present special challenges for such efforts. Since fluorescence microscope images are a primary source of information about the location of proteins within cells, we have set as a long-term goal the building of a knowledge base system that can interpret such images in online journals. To this end, we first developed a robot that searches online journals and finds fluorescence microscope images of individual cells. We then characterized the applicability of pattern classification methods we have previously used on images obtained under controlled conditions to images from different sources and to images subjected to manipulations commonly performed during publication. The results indicate the feasibility of developing search engines to find fluorescence microscope images depicting particular subcellular patterns View full abstract»

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  • TRUFFLER: programs to study microbial community composition and flux from fluorescent DNA fingerprinting data

    Page(s): 129 - 135
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    Terminal-restriction fragment length polymorphism (T-RFLP) and length heterogeneity-polymerase chain reaction (LH-PCR) are DNA fingerprinting technologies which use PCR amplification of a gene of interest e.g. small subunit rRNA gene, to study microbial community structure and dynamics. Either one or both of the forward and reverse strand primers used to amplify the gene are fluorescently labelled. The products of restriction endonuclease digestion are electrophoresed with an automated sequencer that detects only the terminal (labelled) restriction fragments (T-RFs). In LH-PCR, products are electrophoresed without digestion, with different fragment lengths being due to inherent variation in the amplified sequence. A novel software system, TRUFFLER, has been developed to mimic this process in silico allowing comparison of experimental data against databases of theoretically determined T-RFs. As a given combination of forward and reverse primers and restriction endonuclease can yield identical T-RFs across a number of species, combinations of different endonucleases (and/or primers) are typically used In addition to fragment length data, data on fluorescence levels is also available. Computationally, this can be viewed as a constraint satisfaction problem which can be solved to allow identification of the dominant members of the microbial community, often down to individual species or at least genus level, and their relative proportions View full abstract»

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  • An algebra for semantic interoperability of information sources

    Page(s): 174 - 182
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (118 KB) |  | HTML iconHTML  

    Resolving heterogeneity among the various biological information systems is a crucial problem if we wish to gain value from the many distributed resources available to us. For example, information from multiple protein databases (e.g., Swiss-Prot and PDB) might need to be composed to answer queries posed by end-users. Problems of heterogeneity in hardware, operating systems, interfaces and data structures have been widely addressed, but issues of diverse semantics have been handled mainly in an ad-hoc fashion. This paper highlights the ONION (ONtology compositION) system that enables semantic interoperation among various information sources by articulating the ontologies associated with them. An articulation focuses on the semantically relevant intersection of information resources. Although the generation of articulations (semantic correspondences between the ontologies) cannot be fully automated, we take a semi-automatic approach. ONION uses heuristic algorithms for the automatic generation of suggested articulations. This paper outlines an algebra for ontology composition based on their articulations. We show the properties of the algebraic operators and how they depend upon the articulation functions that generate the articulations. Query optimization is enabled based on the properties of the algebraic operators View full abstract»

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  • Utilizing multiple bioinformatics information sources: an XML database approach

    Page(s): 73 - 80
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (49 KB) |  | HTML iconHTML  

    Biological databanks have proven useful to bioscience researchers, especially in the analysis of raw data. Computational tools for sequence identification, structural analysis, and visualization have been built to access these databanks. This paper describes a way to utilize these resources (both data and tools) by integrating different biological databanks into a unified XML framework. An interface to access the embedded bioinformatic tools for this common model is built by leveraging the query language of XML database management system. The proposed framework has been implemented with the emphasis of reusing the existing bioinformatic data and tools. This paper describes the overall architecture of this prototype and some design issues View full abstract»

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  • Interrelated two-way clustering: an unsupervised approach for gene expression data analysis

    Page(s): 41 - 48
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (169 KB) |  | HTML iconHTML  

    DNA arrays can be used to measure the expression levels of thousands of genes simultaneously. Most research is focusing on interpretation of the meaning of the data. However, the majority of methods are supervised, with less attention having been paid to unsupervised approaches which are important when domain knowledge is incomplete or hard to obtain. In this paper we present a new framework for unsupervised analysis of gene expression data which applies an interrelated two-way clustering approach to the gene expression matrices. The goal of clustering is to find important gene patterns and perform cluster discovery on samples. The advantage of this approach is that we can dynamically use the relationships between the groups of genes and samples while iteratively clustering through both gene-dimension and sample-dimension. We illustrate the method on gene expression data from a study of multiple sclerosis patients. The experiments demonstrate the effectiveness of this approach View full abstract»

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  • Investigation of ultrasound image based correction of intraoperative brain shift

    Page(s): 254 - 261
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (168 KB) |  | HTML iconHTML  

    Stereotactic navigational systems are being incorporated into an increasing number of neurosurgical procedures. Preoperatively acquired 3D images are used for planning the procedure, and are also employed in intraoperative navigations to help localize and resect brain lesions. However, as the operation progresses, multiple factors contribute to changes that limit the accuracy of the navigation based on pre-operative images alone. Our method to correct for brain shift involves the use of ultrasound intraoperatively to update patient specific pre-operative MRI scans using a physics based dynamic model. To validate the imaging and modeling process, a phantom was designed that simulates the brain and its shifting patterns resulting from several of the clinical factors present during a brain operation. MRI and ultrasound datasets were acquired for several permutations of phantom parameters. Deformation algorithms were then applied to the phantom data to demonstrate the efficacy of this approach as a method to effectively update the pre-operatively acquired MRI data during an operation View full abstract»

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  • PocketMol: a molecular visualization tool for the Pocket PC

    Page(s): 11 - 14
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (60 KB) |  | HTML iconHTML  

    Molecular visualization programs are available on many platforms. They allow a user to visualize and manipulate molecular structures. PocketMol provides the same functionality on a Pocket PC handheld computer. Using standard protein data bank (pdb) files, the user can move, rotate, and scale a protein to explore its structure and function. The user can choose from a standard backbone view or a simplified view using only alpha carbon atoms. PocketMolGX uses the Microsoft Game API to provide fast animation that is quite smooth. PocketMol is designed as an aid for those wishing to explore or demonstrate protein structures without the availability of a full-size computer View full abstract»

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  • Knowledge discovery in biological data sets using a hybrid Bayes classifier/evolutionary algorithm

    Page(s): 236 - 245
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (108 KB) |  | HTML iconHTML  

    A key element of bioinformatics research is the extraction of meaningful information from large experimental data sets. Various approaches, including statistical and graph theoretical methods, data mining, and computational pattern recognition, have been applied to this task with varying degrees of success. We have previously shown that a genetic algorithm coupled with a k-nearest-neighbors classifier performs well in extracting information about protein-water binding from X-ray crystallographic protein structure data. Using a novel classifier based on the Bayes discriminant function, we present a hybrid algorithm that employs feature selection and extraction to isolate salient features from large biological data sets. The effectiveness of this algorithm is demonstrated on various biological and medical data sets View full abstract»

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  • Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways

    Page(s): 209 - 216
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (131 KB) |  | HTML iconHTML  

    This paper extends previously described automated techniques by automatically integrating the information about automatically derived co-transcribed gene-groups, functionally similar gene-groups derived using automated pair-wise genome comparisons and automatically derived orthologs (functionally equivalent genes) to derive microbial metabolic pathways. The method integrates automatically derived co-transcribed gene-groups with orthologous and homologous gene-groups (http://www.mcs.kent.edu/~arvind/orthos.html), the biochemical pathway template available at the KEGG database. (http://www.genome.ad.jp), the enzyme information derived from the SwissProt enzyme database (http://expasy.hcuge.ch/) and Ligand database (http://www.genome.ad.jp). The technique refines existing pathways (based upon network of reactions of enzymes) by associating corresponding non-enzymatic, regulatory, and cotranscribed proteins to enzymes. The technique has been illustrated by deriving a major pathway of M. tuberculosis by comparison with seven microbial genomes including E coli and B. subtilis - two microbes well explored in wet laboratories View full abstract»

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  • Profile combinatorics for fragment selection in comparative protein structure modeling

    Page(s): 271 - 278
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (115 KB) |  | HTML iconHTML  

    Sequencing of the human genome was a great stride towards modeling cellular complexes, massive systems whose key players are proteins and DNA. A major bottleneck limiting the modeling process is structure and function annotation for the new genes. Contemporary protein structure prediction algorithms represent the sequence of every protein of known structure with a profile to which the profile of a protein sequence of unknown structure is compared for recognition. We propose a novel approach to increase the scope and resolution of protein structure profiles. Our technique locates equivalent regions among the members of a structurally similar fold family, and clusters these region by structural similarity. Equivalent substructures can then be swapped on the common regions to generate an array of profiles which represent hypothetical structures to supplement profiles of known structures. Strategies for a specific implementation of the strategy are discussed, including application to multiple template comparative modeling View full abstract»

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  • An intelligent assistant for navigation of visually impaired people

    Page(s): 230 - 235
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (92 KB) |  | HTML iconHTML  

    This paper presents the navigation methodology employed by an intelligent assistant (agent) for people with disabilities. In particular, the intelligent assistant, called Tyflos, would help a visually impaired user to be partially independent and able to walk and work in a 3D dynamic environment. The Tyflos system carries two vision cameras and captures images from the surrounding 3D environment, either by the user's command or in a continuous mode (video), then it converts these images into verbal descriptions for each image into a verbal communication with the user. In other words the system plays the role of human assistant, who describes to the user the 3D visual environment View full abstract»

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  • A fast pruning algorithm for optimal sequence alignment

    Page(s): 49 - 56
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    Sequence alignment is an important operation in computational biology. Both dynamic programming and A* heuristic search algorithms for optimal sequence alignment are discussed and evaluated Presented here are two new algorithms for optimal pairwise sequence alignment which outperform traditional methods on very large problem instances (hundreds of thousands of characters, for example). The technique combines the benefits of dynamic programming and A* heuristic search, with a minimal amount of additional overhead. The dynamic programming matrix is traversed along antidiagonals, bounding the computation to exclude portions of the matrix that cannot contain optimal paths. An admissible heuristic assists in pruning away unnecessary areas of the matrix, while preserving optimal solutions for any given scoring function. Since memory requirements are a major concern for large sequence alignment problems, it is shown how the standard algorithm (requiring quadratic space) can be reformulated as a divide and conquer algorithm (requiring only linear space, at the cost of some recomputuation) View full abstract»

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  • An XML application for genomic data interoperation

    Page(s): 97 - 103
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (166 KB) |  | HTML iconHTML  

    As the eXtensible Markup Language (XML) becomes a popular or standard language for exchanging data over the Internet/Web, there are a growing number of genome Web sites that make their data available in XML format. Publishing genomic data in XML format alone would not be that useful if there is a lack of development of software applications that could take advantage of the XML technology to process these XML-formatted data. This paper illustrates the usefulness of XML in representing and interoperating genomic data between two different data sources (Snyder's laboratory at Yale and SGD at Stanford). In particular, we compare the locations of transposon insertions in the yeast DNA sequences that have been identified by BLAST searches with the chromosomal locations of the yeast open reading frames (ORFs) stored in SGD. Such a comparison allows us to characterize the transposon insertions by indicating whether they fall into any ORFs (which may potentially encode proteins that possess essential biological functions). To implement this XML-based interoperation, we used NCBIs "blastall" (which gives an XML output option) and SGD's yeast nucleotide sequence dataset to establish a local blast server. Also, we converted the SGD's ORF location data file (which is available in tab-delimited formal) into an XML document based on the BIOML (BIOpolymer Markup Language) standard View full abstract»

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  • Thinking nonlinearly about brain dynamics: a neurocommentary

    Page(s): 112 - 118
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    Despite significant progress over the past several decades in neural research there still remains an ingrained tendency to approach the field using overly reductionistic as well as linear theories and methods. We are just beginning to appreciate the complexity of the brain. A further shift in our "consciousness" about neural dynamics is needed to take the next steps in brain research. We need to use more reflexively what we have learned about the nonlinear dynamical and complex nature of the brain to attempt to "bootstrap" our own thinking processes about neural science itself View full abstract»

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  • Medical applications of radiation micro-force

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    The general direction of this research is measurement of sound and vibration in response to a micro-force. The main hypothesis is that by measuring the sound and/or vibration resulting from such small forces we will be able to obtain important information about the object. The micro-force, which is in mN range, is produced by the radiation force of ultrasound, and the resulting vibration is in nanometer or angstrom range. The stress field is confined to a small region with a few hundred microns in diameter. We have shown that by measuring the acoustic field resulting from such vibrations, which are in low (kHz) frequency range, we can estimate some of the mechanical properties of objects. We have also used this method to image tissue at high resolutions and detect small particles. This imaging technology promises a wide range of medical applications, including imaging organs, detection of arterial calcifications and breast microcalcifications, and evaluation of the structural integrity of implants View full abstract»

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  • Comparing trees in a phylogenetic relationship repository

    Page(s): 166 - 173
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (328 KB) |  | HTML iconHTML  

    Scientists are able to use many different phylogenetic analysis tools to assist them in their research. The data collection and data analysis processes can take days or weeks to complete. Having this data available in a repository would reduce this process time and allow researchers to spend more time analyzing data instead of collecting it. We collected data for 21 completely sequenced genomes and created an intuitive interface for browsing the genomes. The interface allows users to search this data including the pre-calculated phylogenetic trees that are stored in the database. We have also developed a new method for comparing a large set of phylogenetic trees so users can search the database based on a user given hypothesis tree View full abstract»

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  • PSST... the probabilistic sequence search tool

    Page(s): 33 - 40
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (443 KB) |  | HTML iconHTML  

    Whole genome comparison and clustering cannot be routinely performed without access to significant resources. If as expected, repositories continue to grow at the current rate, increasingly large and expensive systems will be required in order to maintain the status quo. The high-proportion of uncharacterised gene-sequences, combined with the fact that the majority of sequence analysis techniques are alignment-based, raises the possibility that alternative approaches might be able to identify relationships that have otherwise been missed. There is a need for alternative ways to predict function. PSST is an analysis tool with parallels to both pairwise algorithms and multiple motif-based pattern approaches. It is significantly faster than BLAST, and for some families including GPCRs, the tool is more sensitive and selective as well. For others it is worse. This paper describes the algorithm, its implementation, its evaluation against a diverse set of protein families, and discusses the reasons behind its behaviour View full abstract»

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  • Mining genome variation to associate disease with transcription factor binding site alteration

    Page(s): 153 - 160
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    During the post genome era, single nucleotide polymorphism (SNP) analysis becomes the crossroad of bioinformatics, bioengineering and human health care. We have developed a data mining system, rSNP-Guide, http://wwmgs.bionet.nsc.ru/mgs/systems/rsnp/, devoted to predict the transcription factor (TF) binding sites on DNA, alterations of which are associated with disease. rSNP-Guide formalizes the disease-referred experimental data on the alterations in the DNA binding to unknown TF, estimates the abilities of the DNA with mutations associated with disease to bind to each known TFs examined so that to separate one of them, which TF site is altered by the mutations in the best consistence with that of the unknown TF experimentally associated with diseases. The rSNP-Guide has been control tested on the SNPs with known site-disease relationships. Two TF sites associated with diseases were predicted and confirmed experimentally, namely: GATA site in K-ras gene (lung tumor) and YY1 site in TDO2 gene (mental disorders) View full abstract»

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  • Optimized seamless integration of biomolecular data

    Page(s): 23 - 32
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (75 KB) |  | HTML iconHTML  

    Today, scientific data is inevitably digitized, stored in a variety of heterogeneous formats, and is accessible over the Internet. Scientists need to access an integrated view of multiple remote or local heterogeneous data sources. They then integrate the results of complex queries and apply further analysis and visualization to support the task of scientific discovery. Building a digital library for scientific discovery requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web, as well as data that is locally materialized in warehouses or is generated by software. We consider several tasks to provide optimized and seamless integration of biomolecular data. Challenges to be addressed include capturing and representing source capabilities; developing a methodology to acquire and represent metadata about source contents and access costs; and decision support to select sources and capabilities using cost based and semantic knowledge, and generating low cost query evaluation plans View full abstract»

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  • Supporting remote user defined functions in heterogeneous biological databases

    Page(s): 144 - 152
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (357 KB) |  | HTML iconHTML  

    Similar to most scientific studies, biological analyses demand a great deal of computations and simulations involving sophisticated tools that are often found geographically distributed over the Internet. A worldwide effort in genomics research has resulted in a powerful collection of publicly available sequence analysis tools. These tools often require specialized local services and domain knowledge to function correctly, rendering them unlikely candidates for integration into remote database applications. Thus, integration of heterogeneous "functions" still remains an open problem. Providing a reasonable framework for seamless integration of these tools with database query engines will enable application developers to exploit and harness the power of these effective analysis tools. In this paper, we present an integration framework for such tools by enabling access to them in a user transparent way as part of database queries. In our system, such online tools are abstracted as remote user defined functions (RUDF). An extended SQL DDL language, called the Internet Function Definition Language (IFDL), is presented for the specification and definition of RUDFs. The interface between database system and the Internet is implemented using a layer based on a language called the Hypertext Query Language (HTQL). The separation of IFDL, DDL, HTQL and SQL DML offers several optimization opportunities and makes it possible to develop an architecture for interoperability of heterogeneous databases with RUDFs in more simple and efficient ways View full abstract»

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  • Development of a robotic device for MRI-guided interventions in the breast

    Page(s): 201 - 208
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (379 KB) |  | HTML iconHTML  

    The objective of this work was to develop a robotic apparatus for MR-guided biopsy and therapeutic interventions in the breast. This device facilitates (i) conditioning of the breast, by setting the orientation and degree of compression, (ii) definition of the interventional probe trajectory, by setting the height and angulation of a probe guide and (iii) positioning of an interventional probe, by setting the depth of insertion. The apparatus is fitted with appropriate computer-controlled degrees of freedom for optimal approach for delivering and monitoring interventions with MR-guidance, such as diagnostic or therapeutic trans-cannula or subcutaneous minimally invasive procedures. The entire device is constructed of MR compatible material, i.e. non-magnetic and non-conductive, to eliminate artifacts and distortion of the local magnetic field. The apparatus is remotely controlled by means of ultrasonic actuators and a graphics user interface, providing real-time MR-guided planning and monitoring of the operation View full abstract»

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