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At least 523 records · Page 29Linked to original sources
PubMed2002

Virtual reality surgical simulation for lower urinary tract endoscopy and procedures.

BACKGROUND AND PURPOSE: To provide a realistic experience of lower urinary tract endoscopic procedures, we have developed and continue to expand a computer-based surgical simulator that incorporates a surgical tool interface with anatomic detail and haptic feedback. METHODS: Surface-based geometric data for the lower urinary tract were generated from the National Library of Medicine Visible Human dataset. The three-dimensional texture map of the surface geometry was developed from recorded endoscopic video procedures. Geometry and associated texture maps were rendered in real time using the Silicon Graphics Extreme Impacts program. The surgical interface device incorporated all normal ranges of motion and resistance that occur within an actual operative environment. The hands-on endoscopic device attached to the interface device was provided by Circon-ACMI, Inc. Urologic residents evaluated the program for correlation with actual endoscopic procedures. RESULTS: Texture-mapped digitized images provided a close anatomic similarity to actual videoendoscopic images. Virtual endoscopy of the lower urinary tract was reproducible and closely simulated actual visual and tactile endoscopic experience. CONCLUSIONS: Virtual reality surgical simulation is feasible for a variety of lower urinary tract procedures. This system coordinates visual perception with appropriate haptic feedback in both longitudinal and rotational axes. These types of procedures may be incorporated into future educational experiences for urologists to introduce new techniques and to provide documentation of surgical experience.

Adult↗
PubMed1998

Three-dimensional determination of femoral-tibial contact positions under in vivo conditions using fluoroscopy.

OBJECTIVE: A method has been developed to accurately measure three-dimensional (3-D) femoral-tibial contact positions of artificial knee implants in vivo from X-ray fluoroscopy images using interactive 3-D computer vision algorithms. DESIGN: A computerized graphical (CAD) model of an implant component is displayed as an overlay on the original X-ray image. An image matching algorithm matches the silhouette of the implant component against a library of images, in order to estimate the position and orientation (pose) of the component. The operator further adjusts the pose of the graphical model to improve the accuracy of the match. BACKGROUND: Previous methods for in vivo measurement of joint kinematics make only indirect measurements of joint kinematics, require invasive procedures such as markers or pins, or make simplifying assumptions about imaging geometry which can reduce the accuracy of the resulting measurements. METHODS: Fluoroscopic videos are taken of implanted knees in subjects performing weight-bearing motion. Images from the videos are digitized and stored on a computer workstation. Using computerized model matching, the relative pose of the two knee implant components can be determined in each image. The resulting information can be used to determine where the two components are contacting, the area of the contact region, liftoff angle, and other kinematic data. RESULTS: Accuracy tests done on simulated imagery and in vitro real imagery show that the pose estimation method is accurate to less than 0.5 mm of error (RMS) for translations parallel to the image plane. Orientation error is less than or equal to 0.35 degrees about any axis. Errors are larger for translations perpendicular to the image plane (up to 2.25 mm). In a clinical study, the method was used to measure in vivo contact points, and characterize the kinematic patterns of two different knee implant designs. CONCLUSIONS: The ability to accurately measure knee kinematics in vivo is critical for the understanding of the behavior of knee implant designs and the ultimate development of new, longer lasting implants. RELEVANCE: This work shows that it is possible to accurately measure the three-dimensional position and orientation (pose) of artificial knee implants in vivo from X-ray fluoroscopy images using interactive 3-D computer graphics. The method can be applied to any joint when accurate CAD models are available. The resulting data can be used to characterize the kinematics of current knee implant designs.

Journal Article↗
PubMed1993

Restriction sites as identification tags for the gene catalog: a 2D gel model.

In our effort to collect, organize and assemble data from lymphocyte cDNA libraries, we assign DNA restriction sites collectively to the spots on two-dimensional (2D) gel patterns. In order to test the efficiency and reliability of such an approach, we have modeled the restriction analysis of cDNA libraries with a panel of restriction endonucleases. The work has two parts. In the first, we have chosen 255 proteins from the EMBL data base and determined whether or not their coding sequences contain restriction sites for the enzymes of our choice. In order to apply a sufficient discriminatory power we decided to use a relatively large number of cleaving enzymes with low and high cutting frequencies. In total, 13 restriction enzymes were chosen, which could distinguish 2(13) or 8192 different restriction site combinations. We have compiled a table in which the absence or presence of restriction sites yields a pattern of 'zeros' and 'ones'. Such a restriction pattern can be read as a binary number. The binary numbers with maximally 13 digits would uniquely assign each of the 255 proteins if the nucleotide sequences would be truly at random. As the restriction sites are not randomly distributed, the 'typing' does not yield a unique assignment. The choice of sequences was not random either. In fact, there are some human nucleotide sequences which possess the same cut number (the decimal equivalent of the binary number representing the restriction pattern). In spite of this redundancy, 141 coding sequences could uniquely be distinguished by the above treatment. In the second part of the project we have used the above mentioned coding sequences to prepare two-dimensional maps (plots of charge vs size) of the same kind as one obtains from experimental 2D gels and submitted such a map together with 13 maps of restriction enzyme treated populations to a computer image analysis. Ideally, one would expect results (cut numbers) congruent to those obtained in the first part of the work. In the modeled system we were confronted with 2D maps which closely resembled the experimental situation (e.g. some spots were close together and overlapping) and instances of incorrect spot detection yielding 'false cut numbers'. From 255 proteins we were able to assign unequivocally 161 proteins. To implement the model in an actual experiment we will perform the digestion with the restriction enzymes in duplicate, and only spots assigned the same cut number upon the two independent treatments will be considered as carrying a valid restriction tag.

Base Sequence↗
PubMed2004

Enhanced quality and quantity of retrieval of Critically Appraised Topics using the CAT Crawler.

As healthcare moves towards the implementation of Evidence-Based Medicine (EBM), Critically Appraised Topics (CATs) become useful in helping physicians to make clinical decisions. A number of academic and healthcare organizations have set up web-based CAT libraries. The primary objective of the presented work is to provide a one-stop search and download site that allows access to multiple CAT libraries. A web-based application, namely the CAT Crawler, was developed to serve physicians with an adequate access to available appraised topics on the Internet. Important information is extracted automatically and regularly from CAT websites, and consolidated by checking the uniqueness and availability. The principle of meta-search is incorporated into the implementation of the search engine, which finds relevant topics following keyword input. The retrieved result directs the physician to the original resource page. A full-text article of a particular topic can be converted into a proper format for downloading to Personal Digital Assistant (PDA) devices. In summary, the application provides physicians with a common interface to retrieve relevant CATs on particular clinical topics from multiple resources, and thus speeds up the decision making process.

Algorithms↗
PubMed2002

Comparison of rapid, automated ribotyping and DNA macrorestriction analysis of Burkholderia pseudomallei.

An automated ribotyping device (RiboPrinter) was used to determine the ribotypes of a collection of Burkholderia pseudomallei isolates. In a preliminary evaluation with the restriction enzymes BamHI and EcoRI, the protocol with EcoRI was more discriminating. The reproducibilities of the ribotypes obtained with EcoRI (EcoRI ribotypes) were determined by testing three levels of bacterial loads. The performance of the manufacturer's software was assessed by comparing the machine-optimized ribotypes with the type determined from the original gel image analyzed with Bionumerics software. The library of B. pseudomallei EcoRI ribotypes was then compared with the ribotypes obtained by DNA macrorestriction analysis of XbaI digests by pulsed-field gel electrophoresis. The typeability of B. pseudomallei by EcoRI ribotyping was 100%, and the discrimination index was 0.94. The slightly greater discrimination provided by DNA macrorestriction analysis (0.96) was achieved at the expense of a significantly longer processing time of 6 days, although the method was only half the cost of automated ribotyping. Typeability by macrorestriction analysis was lower (97%) unless a thiourea step was added to neutralize the action of Tris-dependent endonucleases. The digital record of B. pseudomallei isolates analyzed thus far provides a useful resource for future epidemiological studies and will help shorten the response time in the event of a further melioidosis outbreak or the deliberate release of B. pseudomallei as a biohazard.

Automation↗
PubMed2026

VIJB: a companion of the JBROWSE genome browser for the visually impaired people.

MOTIVATION: The availability of touch-sensitive and haptic devices has been a keystone development for the inclusion of visually impaired people (VIPs) in modern, highly digitized work environments. Braille displays have proven efficient and versatile enough to parse large and complex text files, making bioinformatics and text-heavy programming accessible to VIPs. However, the complex graphical objects -combining numerous datasets- typically generated during data integration remain challenging, even with the aid of descriptive AI. This is particularly true in functional genomics. Here, we present VIJB, a simple application that displays the multilayered output of the JBROWSE genome browser on a Braille reader, enabling VIPs to fully participate in data integration in functional genomics. AVAILABILITY AND IMPLEMENTATION: VIJB is programmed in Python and relies on the scientific library NumPy, the braillegraph and pyBigWig libraries, and the TABIX software. The architecture is summarized in Supplementary Material 1, available as supplementary data at Bioinformatics online. VIJB is available for download at the GitHub repository https://GitHub.com/NiBuMNHN/VIJB and is licenced under the GPL 3.0.

Persons with Visual Disabilities↗
PubMed1989

Fluorescence digital microscopy of interstitial macromolecular diffusion in burn injury.

Computer vision techniques implemented on an IBM PC/AT have been applied to the study of microvascular permeability and interstitial diffusion in dorsal skin flap chamber preparations of hamsters. Experimental data was obtained for the leakage of fluorescent labelled dextran (70,000 daltons) after a precisely controlled mild degree of localized thermal trauma and compared with control data acquired prior to burn injury. Computer vision analysis techniques were applied to convert the fluorescent images into two-dimensional concentration maps. Interstitial diffusion coefficient values were computed from measured extravascular concentration profiles around a vessel of interest, assuming cylindrical or rectangular geometry, and optimally fitting a diffusion model to the data. An increase in the apparent diffusivity after mild thermal trauma was observed. Novel techniques were applied to solve hardware problems related to data acquisition and analysis, and a new library of software was developed to handle specific image processing requirements.

Animals↗
PubMed1989

Selective presence of ubiquitin in intracellular inclusions.

The authors have shown previously that ubiquitin, a protein involved in the degradation of short-lived and abnormal proteins, is present in several cytoplasmic inclusions of neurons. This study used a library of antibodies to ubiquitin and immunohistochemically examined for the presence of ubiquitin in nonviral intracytoplasmic inclusions that form in different cell types under various pathologic conditions. Membrane-bound lysosomal and nonlysosomal inclusions such as those of storage disease, Russell bodies, alpha-1-antitrypsin and alpha-fetoprotein as well as nonmembrane-bound inclusions were examined. Ubiquitin epitopes were detected in some of the nonmembrane-bound inclusions only. The ubiquitin-containing inclusions were the Rosenthal fibers, Mallory bodies, Crooke bodies, Lafora bodies, amyloid bodies, and the giant axons of giant axonal neuropathy. Nemaline bodies and the inclusions of juvenile digital fibromatosis, both of which contain actin and actinbinding proteins, did not show immunoreaction. These findings, as well as those of the previous study, show that the presence of ubiquitin in cellular inclusions is selective. The ubiquitin-containing inclusions are not membrane bound; they are fibrillary and most contain also intermediate filament-related proteins. The role of ubiquitin in the formation of these inclusions remains to be elucidated.

Cell Nucleus↗
PubMed1991

Videodocumentation in digital dacryocystography.

The digital dacryocystography proved to be the optimum method of X-ray diagnostics in obstructions of the lacrimal pathways. The examination was performed with a computer controlled X-ray unit with a C-arc coupled to an image intensifier tv-system. In the study the advantages of this technique were combined with the advantages of modern videotechnique. A nonionic water soluble contrast medium was used. The bilateral contrast medium filling process was registrated and the findings were recorded on videotape concurrently. The videocassettes, marked with the data of the patients and the date of examination, are stored in a video-tape library. This provides an always repeatable diagnostic documentation and it is also an excellent base for scientific analyses. The technique and the results of the examinations, performed with 18 patients, are described.

Adult↗
PubMed1988

Imaging system for morphometric assessment of absorption or fluorescence in stained cells.

An image acquisition and processing system has been developed for quantitative microscopy of absorption or fluorescence in stained cells. Three different light transducers are used in the system to exploit the best characteristics of these sensors for different biological measurements. A digital scanner, in the form of a linear array charge-coupled device (CCD), acquires data with high spatial and photometric resolution. A color (RGB) camera is employed when spectral information is required for the segmentation of cellular subcomponents. An image-intensified charged-injection device (CID) camera provides for very low light intensity measurements, primarily for fluorescence-labeled cells. Properties of these transducers, such as contrast transfer function, linearity, and photo-response nonuniformity, have been measured. Two dedicated image processing units were incorporated into the system. The front-end processor, based on a digital signal processor, provides functions such as object detection, raw image calibration, compression, artifact removal, and filtering. The second image processor is associated with the frame memory and includes a histogram processor, a dedicated arithmetic logic unit for image processing functions, and a graphics module for one-bit overlay functions. An interactive program was developed to acquire cell images and to experiment with a range of segmentation algorithms, feature extractions, and other image processing functions. The results of any image operation are displayed on the video monitor. Once a desired processing sequence is determined, the sequence may be stored to become part of a command library and can be executed thereafter as a single instruction.

Algorithms↗
PubMed2026

Artificial intelligence-driven advancements in agricultural biotechnology.

The need for faster and more informative data processing for better decision-making is driving the adoption of artificial intelligence (AI) in the agricultural sector. Thanks to recent advancements in computer science and the increase in computational powers of modern computers, AI is not only augmenting traditional solutions, but also helping in developing novel solutions to existing challenging matters. AI-driven models have an exceptional ability to identify patterns and combine a diverse collection of data together and make inference. The increasing pressure on farmlands posed by the growing global population and climate change is lessening growth, yield, and productivity ultimately posing risk to food security worldwide. Incorporation of AI in agriculture has the potential to drive farming efficiency to new heights. This comprehensive review critically evaluates the evolution of AI in agricultural biotechnology from a theoretical concept to a global phenomenon. A comprehensive literature search was performed using major scientific databases, including PubMed, Web of Science, Embase, Scopus, Lens and the Cochrane Library. In this review, we empirically demonstrate the fields advancement toward more capable AI systems and discuss the current applications of AI across crop improvement and precision agriculture such as crop improvement and genetic engineering, genomic selection and plant breeding, pest and disease detection, precision agriculture and smart farming, soil health and nutrient management, climate resilient crop development, livestock biotechnology, challenges and ethical considerations in AI based agricultural biotechnology. Furthermore, this review addresses the exponential growth of commercial intellectual property in the field and contrast it with academic publication outputs. Finally, we critically assess the ethical challenges impeding equitable adoption of AI including data sovereignty and digital divide, while projecting future frontiers involving quantum computing. This review will help build sustainable agricultural systems capable of adapting to climate change, contribute to the development of climate-resilient and high-yielding crops, and address global food security challenges.

Agriculture↗
PubMed2005

Creating computer aided 3D model of spleen and kidney based on Visible Human Project.

OBJECTIVE: To investigate the efficacy of computer aided 3-dimensional (3D) reconstruction technique on visualization and modeling of gross anatomical structures with an affordable methodology applied on the spleen and kidney. METHODS: From The Visible Human Project Dataset cryosection images, developed by the National Library of Medicine, the spleen and kidney sections were preferred to be used due to their highly distinct contours. The software used for the reconstruction were SurfDriver 3.5.3 for Mac and Cinema 4D XL version 7.1 for Mac OS X. This study was carried out in May 2004 at the Department of Anatomy, Hacettepe University, Ankara, Turkey. RESULTS: As a result of this study, it is determined that these 2 programs could be effectively used both for 3D modeling of the mentioned organs and volumetric analyses on these models. It is also seen that it is possible to hold the physical models of these gross anatomical digital ones with stereolithography technique by means of the data exchange file format provided by the program and present such images as anaglyph. CONCLUSION: SurfDriver 3.5.3 for Mac OS and Cinema 4 DXL version 7.1 for Mac OS X can be used effectively for reconstruction of gross anatomical structures from serial parallel sections with distinct contours such as spleen and kidney and the animation of models. These software constitute a highly effective way of getting volumetric calculations, spatial relations and morphometrical measurements of reconstructed structures.

Computer Simulation↗
PubMed2004

New directions in medical e-curricula and the use of digital repositories.

Medical educators involved in the growth of multimedia-enhanced e-curricula are increasingly aware of the need for digital repositories to catalogue, store and ensure access to learning objects that are integrated within their online material. The experience at the Faculty of Medicine at McGill University during initial development of a mainstream electronic curriculum reflects this growing recognition that repositories can facilitate the development of a more comprehensive as well as effective electronic curricula. Also, digital repositories can help to ensure efficient utilization of resources through the use, re-use, and reprocessing of multimedia learning, addressing the potential for collaboration among repositories and increasing available material exponentially. The authors review different approaches to the development of a digital repository application, as well as global and specific issues that should be examined in the initial requirements definition and development phase, to ensure current initiatives meet long-term requirements. Often, decisions regarding creation of e-curricula and associated digital repositories are left to interested faculty and their individual development teams. However, the development of an e-curricula and digital repository is not predominantly a technical exercise, but rather one that affects global pedagogical strategies and curricular content and involves a commitment of large-scale resources. Outcomes of these decisions can have long-term consequences and as such, should involve faculty at the highest levels including the dean.

Cataloging↗
PubMed2005

Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii.

Blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. Its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. To contribute to the understanding of the complexity of the B. emersonii genome, we present here a survey of expressed sequence tags (ESTs) from various stages of the fungal development. Nearly 20,000 cDNA clones from 10 different libraries were partially sequenced from their 5' end, yielding 16,984 high-quality ESTs. These ESTs were assembled into 4,873 putative transcripts, of which 48% presented no matches with existing sequences in public databases. As a result of Gene Ontology (GO) project annotation, 1,680 ESTs (35%) were classified into biological processes of the GO structure, with transcription and RNA processing, protein biosynthesis, and transport as prevalent processes. We also report full-length sequences, useful for construction of molecular phylogenies, and several ESTs that showed high similarity with known proteins, some of which were not previously described in fungi. Furthermore, we analyzed the expression profile (digital Northern analysis) of each transcript throughout the life cycle of the fungus using Bayesian statistics. The in silico approach was validated by Northern blot analysis with good agreement between the two methodologies.

Amino Acid Sequence↗
PubMed1997

An open medical imaging workstation architecture for platform-independent 3-D medical image processing and visualization.

A need for an entirely new medical workstation design was identified to increase the deployment of 3-D medical imaging and multimedia communication. Recent wide acceptance of the Word Wide Web (WWW) as a general communication service within the global network has shown how big the impact of standards and open systems can be. Information is shared among heterogeneous systems and diverse applications on various hardware platforms only by agreeing on a common format for information distribution. For medical image communications, the Digital Imaging and Communication in Medicine (DICOM) standard is possibly anticipating such a role. Logically, the next step is open software: platform-independent tools, which can as easily be transferred and used on multiple platforms. Application of the platform-independent programming language Java enables creation of plug-in tools, which can easily extend the basic system. Performance problems inherent to all interpreter systems can be circumvented by using a hybrid approach. Computationally intensive functions like image processing functions can be integrated into a natively implemented optimized image processing kernel. Plug-in tools implemented in Java can utilize the kernel functions via a Java-wrapper library. This approach is comparable to the implementation of computationally intensive operations in hardware.

Computer Communication Networks↗
PubMed2002

HIV-1 Tat protein-mediated transactivation of the HIV-1 long terminal repeat promoter is potentiated by a novel nuclear Tat-interacting protein of 110 kDa, Tip110.

Human immunodeficiency virus type 1 (HIV-1) gene expression and replication is highly dependent on and modulated by interactions between viral and host cellular factors. Tat protein, encoded by one of the HIV-1 regulatory genes, tat, is essential for HIV-1 gene expression. A number of host cellular factors have been shown to interact with Tat in this process. During our attempts to determine the molecular mechanisms of Tat interaction with brain cells, we isolated a cDNA clone that encodes a novel Tat-interacting protein of 110 kDa or Tip110 from a human fetal brain cDNA library. GenBank BLAST search revealed that Tip110 was almost identical to a previously cloned KIAA0156 gene with unknown functions. In vivo binding of Tip110 with Tat was confirmed by immunoprecipitation and Western blotting, in combination with mutagenesis. The yeast three-hybrid RNA-protein interaction assay indicated no direct interaction of Tip110 with Tat transactivating response element RNA. Nevertheless, Tip110 strongly synergized with Tat on Tat-mediated chloramphenicol acetyltransferase reporter gene expression and HIV-1 virus production, whereas down-modulation of constitutive Tip110 expression inhibited HIV-1 virus production. Northern blot analysis showed that Tip110 mRNA was expressed in a variety of human tissues and cells. Moreover, digital fluorescence microscopic imaging revealed that Tip110 was expressed exclusively in the nucleus, and within a nuclear speckle structure that has recently been described for human cyclin T and CDK9, two critical components for Tat transactivation function on HIV-1 long terminal repeat promoter. Taken together, these data demonstrate that Tip110 regulates Tat transactivation activity through direct interaction, and suggest that Tip110 is an important cellular factor for HIV-1 gene expression and viral replication.

Amino Acid Sequence↗
PubMed2003

Expression profiling using cDNA microarrays.

Microarray technology has become increasingly useful in measuring expression levels of a large number of genes and part of a repertoire of functional genomic tools. We describe the methods of cDNA microarray preparation, the use, data collection, and initial data processing. The cDNA fragments are first prepared by polymerase chain reaction (PCR), and then attached to a solid substrate, such as a chemically treated glass slide. Robotic machines spot the prepared cloned cDNA samples in a miniaturized gridded pattern, so that nanoliter amounts of tens of thousands cDNA samples are bound to a single 7.5 x 2.5 cm glass slide. Probes are generated from RNA samples of test and control tissues by incorporating Cyanine dyes (Cy3 or Cy5) in reverse-transcribed products. Probes from a test sample are labeled with one of two Cy dyes and mixed in equal amounts with probes from a control sample labeled with the second dye. The glass slides containing the cDNA microarray are hybridized with the mixed Cy-labeled probes, washed, dried, and scanned using laser scanners with an optimized wavelength to excite each Cy dye. The emission image patterns for each dye are captured by a digital camera using micro-optics and processed into numerical values that positively correlate with quantitative levels of mRNA for each cDNA spot on the slide. The collected data is then further processed, normalized across experiments, and examined via numerous statistical and mathematical approaches to infer changes in expression levels of particular genes due to the treatment tested.

DNA, Complementary↗
PubMed1991

Software and hardware integration of a microprogrammable state machine for NMR imaging.

We have integrated a commercially available microprogrammable state machine (Tecmag PULSkit) for use as a magnetic resonance pulse programmer. Providing the capability for active research environment imaging protocols, it features timing resolution of 100 nsec, ten 16-bit loop counters, and individually addressable look-up tables. This integration involved hardware and software integration with a VAX 11/750 at several levels. Hardware: Each of the three gradient channels employs three digital-to-analog converters (DACs). An 8-bit, 4-quadrant, multiplying DAC generates the gradient waveform shape. A 12-bit DAC generates the multiplying DAC scaling voltage, controlling gradient amplitude and sign. A third 12-bit DAC produces a gradient offset (shim) voltage. An eddy current compensation network is present for each gradient channel. Software: The software design philosophy was to create a flexible interface (interactive window environment), while not constraining complex manipulation of the hardware (direct use of the pulse-sequence compiler primitives and microprogramming). The software levels include (a) pulse-sequence microprogramming, (b) pulse-sequence compiler, (c) interactive parameter specification, and (d) canned pulse-sequence microcode library.

Computer Systems↗