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PubMed2004

Enhancement of needle visibility in ultrasound-guided percutaneous procedures.

The visibility of a needle in ultrasound (US)-guided percutaneous procedures is often limited by dispersion of the needle's reflections away from the probe. A needle enhancement algorithm is developed that maximizes the received reflections by steering the US beam precisely perpendicular to the needle. The resulting image clearly depicts the needle as a bright line. The key is to automatically detect the needle in the image and maintain the appropriate beam steering angle during the procedure. The brightened needle in the steered image is then fused with the original image to produce an improved image. Implementation of the needle-enhancement algorithm was made possible by using the programmable ultrasound platform and interface library (PUPIL). PUPIL is capable of acquiring digital images, processing the images in real-time, controlling the beam angle, and displaying the fused image. The results demonstrate significantly improved needle visibility in both breast phantoms and turkey breast samples.

Algorithms↗

PubMed2001

Selective arterial distribution of cerebral hyperperfusion in Fabry disease.

Fabry disease is an X-linked recessive deficiency of lysosomal alpha-galactosidase A associated with an increased risk of early onset cerebrovascular disease. The disorder is reported to affect the posterior circulation predominantly. This hypothesis was investigated directly by the measurement of regional cerebral blood flow with positron emission tomography (PET). Resting regional cerebral blood flow (rCBF) in 26 hemizygous patients with Fabry disease and 10 control participants was examined using H(2)15O and PET. Statistical parametric mapping (SPM(t), SPM99) and PET images of patients and controls were produced. Significantly increased SPM(t) clusters were then color coded and blended with a coregistered T1 magnetic resonance imaging (MRI) template. Cerebral arterial territory maps were digitized and rescaled. Custom OpenGL and ImageVision Library C++ code was written to allow a first-order affine transformation of the blended SPM(t) and MRI template onto the arterial territory map. The affine transformation was constrained by choosing corresponding cerebral landmark "tie points" between the SPM(t) [symbol: see text] MRI template images and the cerebral arterial territory maps. The data demonstrated that the posterior circulation is the predominant arterial territory with a significantly increased rCBF in Fabry disease. No arterial distribution had a decreased rCBF.

Adult↗

PubMed1999

A high-throughput digital imaging screen for the discovery and directed evolution of oxygenases.

BACKGROUND: Oxygenases catalyze the hydroxylation of a wide variety of organic substrates. An ability to alter oxygenase substrate specificities and improve their activities and stabilities using recombinant DNA techniques would expand their use in processes such as chemical synthesis and bioremediation. Discovery and directed evolution of oxygenases require efficient screens that are sensitive to the activities of interest and can be applied to large numbers of crude enzyme samples. RESULTS: Horseradish peroxidase (HRP) couples the phenolic products of hydroxylation of aromatic substrates to generate colored and/or fluorescent compounds that are easily detected spectroscopically in high-throughput screening. Coexpression of the coupling enzyme with a functional mono- or dioxygenase creates a pathway for the conversion of aromatic substrates into fluorescent compounds in vivo. We used this approach for detecting the products of the toluene-dioxygenase-catalyzed hydroxylation of chlorobenzene and to screen large mutant libraries of Pseudomonas putida cytochrome P450cam by fluorescence digital imaging. Colors generated by the HRP coupling reaction are sensitive to the site of oxygenase-catalyzed hydroxylation, allowing the screen to be used to identify catalysts with new or altered regiospecificities. CONCLUSIONS: The coupled oxygenase-peroxidase reaction system is well suited for screening oxygenase libraries to identify mutants with desired features, including higher activity or stability and altered reaction specificity. This approach should also be useful for screening expressed DNA libraries and combinatorial chemical libraries for hydroxylation catalysts and for optimizing oxygenase reaction conditions.

Camphor 5-Monooxygenase↗

PubMed2005

Library as place: results of a delphi study.

OBJECTIVE: An expert consensus on the future of the library as place was developed to assist health sciences librarians in designing new library spaces. METHOD: An expert panel of health sciences librarians, building consultants, architects, and information technologists was asked to reflect on the likelihood, desirability, timing, and impact on building design of more than seventy possible changes in the use of library space. RESULTS: An expert consensus predicted that the roles librarians play and the way libraries are used will substantially change. These changes come in response to changes in technology, scholarly communication, learning environments, and the health care economy. CONCLUSIONS: How health sciences library space is used will be far less consistent by 2015, as space becomes more tailored to institutional needs. However, the manner in which health sciences libraries develop and deliver services and collections will drastically change in the next decade. Libraries will continue to exist and will provide support for knowledge management and clinical trials, provide access to digital materials, and play a host of other roles that will enable libraries to emerge as institutional change agents.

Delphi Technique↗

PubMed1995

Interpretation of emergency department radiographs by radiologists and emergency medicine physicians: teleradiology workstation versus radiograph readings.

PURPOSE: To compare accuracy of interpretation by radiologists and emergency medicine physicians of conventional radiographs and digitized images on a workstation. MATERIALS AND METHODS: One author selected 120 radiographs from the radiology department library, including 62 musculoskeletal, 20 abdominal, and 38 chest examinations. Analog radiographs were digitized. There were 60 positive and 60 control cases. Positive cases demonstrated clinically important disease and had a high degree of diagnostic difficulty. Thirty-one cases were judged to be critical to the patient's immediate care, requiring prompt accurate interpretation. Four groups of readers were used: staff radiologists and emergency medicine physicians and second-year radiology and emergency medicine residents. RESULTS: All reader groups performed better when interpreting conventional radiographs than digitized images. Differences in favor of radiograph reading were statistically significant for overall accuracy related to all cases and to critical cases (P < .05, one-tailed test). CONCLUSION: Results with the teleradiology system were found unacceptable for primary interpretation of the spectrum of radiographs seen in an emergency department.

Baltimore↗

PubMed2004

Being there: the library as place.

The value of the library as place is examined in this Janet Doe Lecture. The lecture, which is intended to focus on the history or philosophy of health sciences librarianship, presents an overview of the library as a place in society from ancient times to the present. The impact of information technology and changes in the methods of scholarly publication from print to digital are addressed as well as the role of the library as the repository of the written historical record of cultures. Functions and services of libraries are discussed in light of the physical library facility of the future. Finally, librarians are asked to remember the enduring values of librarianship in planning libraries of the future.

Egypt↗

PubMed2000

The development of a digital image database of clinical photographs.

At the end of December 1998, the traditional clinical slide library at the Media Resources Centre University Hospital of Wales and University of Wales College of Medicine was closed to new acquisitions. This paper describes how a digital image database (Image AXS) has been customized to provide a source of rapidly accessible and easily searchable images, suitable for teaching and reference purposes. The basic functions of the program are explained and areas such as data integrity, image capture, storage, archiving and the impact that this technology has had on departmental workflow are discussed.

Databases as Topic↗

PubMed2003

Digital extractor: analysis of digital differential display output.

Digital Extractor is a program for the high-throughput processing of data sets derived from digital differential display-based comparisons of EST libraries. These comparisons can be utilized to identify discrete subsets of genes whose expression is restricted to distinct tissue types. The program facilitates these investigations by permitting parallel annotation of genes identified as being differentially expressed.

Database Management Systems↗

PubMed1965

MEDLARS: PERFORMANCE, PROBLEMS, POSSIBILITIES.

Operational experience during the first year of MEDLARS is described in relation to the Library's primary objectives of index publication, recurring bibliographies, and demand search services. Progress toward the implementation of two secondary objectives-the input of cataloging copy and the decentralization of the system-is also reported. MEDLARS has been intensively tested during its first operational year, its strengths and weaknesses have been identified, and it is now prepared to develop its service potential.

Bibliographies as Topic↗

PubMed2004

Search for epithelial-specific mRNAs in peripheral blood of patients with colon cancer by RT-PCR.

Research has widely supported the efficacy of screening for colorectal cancer in reducing mortality. A blood-based assay potentially represents a more accessible early detection tool for the identification of solid tumor cells originating from a primary tumor site in the body. We demonstrate a relatively easy and highly reproducible technique for the detection of mRNA expression of genes as markers of malignancy in blood samples of patients with colon cancer. The present study aims to identify a set of specific mRNAs expressed in epithelial cells but not in blood cells, which may be useful as markers for early detection of circulating colon cancer cells by a simple, qualitative RT-PCR assay following semi-automated RNA extraction from peripheral blood samples. Our approach includes a systematic search for candidate markers using digital differential display, search on UniGene colon EST libraries and analysis of published data on colon cancer gene expression. A final list included the following genes: bone morphogenetic protein 4 (BMP4), cyclin D (CycD), family with sequence similarity 3, member D (FAM3D), gastrin (GAS), glycoprotein A33 transmembrane (GPA33), glutathione peroxidase 2 gastrointestinal (GPX2), galactoside-binding, soluble, 4 (galectin 4) (LGALS4), non-SMC, structural maintenance of chromosomes, element 1 protein (NSE1), tumor-associated calcium signal transducer 1 (TACSTD1), telomerase reverse transcriptase (hTERT), trefoil factor 3 intestinal (TFF3), transmembrane 4 superfamily member 3 (TM4SF3), UDP glycosyltransferase 1 family, polypeptide A9 (UGT1A9), villin 1 (VIL1), and the novel gene FLJ20127. The mRNA expression of these genes was evaluated in a pool of 16 samples from subjects diagnosed with colon cancer and from 16 normal-controls. We observed expression in 13 of the 15 investigated genes from the blood samples of the vast majority of patients considered, but also in a certain percentage of the controls (from 14.3 to 100%). This finding confirms that the extreme sensitivity of RT-PCR is able to detect minimal amounts of mRNA expressed in a non tissue-specific manner ('illegitimate transcription'). On the contrary, NSE1 and GAS mRNAs were not detected either in patient or in control blood samples; however, they were abundantly expressed in normal and cancerous colon mucosa, encouraging further search for useful markers able to detect epithelial cells in peripheral blood.

Aged↗

PubMed2005

Molecular cloning and primary functional analysis of a novel human testis-specific gene.

In this study, a new data mining tool called Digital Differential Display (DDD) from the NCBI was used to predict testis-specific expressed genes from the expressed sequence tag (EST) database. DDD (digital differential display) was performed between nine testis libraries and seventy libraries derived from other tissues. We identified a new contig of ESTs (HS. 326528) which was from testis libraries. To validate the use of bioinformatic approaches in gene discovery, the ESTs (HS. 326528), which were predicted to be testis-specific, were chosen for further study. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) analysis of matched sets of cDNAs from testis and other tissues indicated that the ESTs were specifically expressed in testis. This result was further validated by multi-tissue Northern blot. The full-length cDNA encompassing the entire open reading frame was cloned and, in view of its apparent specificity to testis, the gene was termed homo sapiens spermatogenesis-related gene 8---SRG8 (GenBank accession number: AY489187). The gene whose full cDNA length is 1 044 bp containing 3 exons and 2 introns is located in human chromosome 15q26.2, the cDNA encodes a novel protein of 105 amino acides with a theoretical molecular weight of 11.7 kD and isoelectric point of 10.09 which shares no significant homology with any known proteins in database. Real time PCR analysis of testis of different developmental periods revealed that SRG8 gene is significantly expressed in adult testis. The green fluorescent protein produced by pEGFP-C3/SRG8 was detected in the nucleus of HeLa cells after 24 h post-transfection. Cell cycle analysis showed that SRG8 can accelerate HeLa cells to traverse the S-phase and enter the G2-phase compared with the control without transfection of SRG8, which suggested that this gene plays an important role in the development of testis. The discovery of SRG8 showed that DDD combined with experiments is a feasible, time-saving strategy to identify new candidate genes for testis-specific development

Adult↗

PubMedDate not supplied

The visible human male: a technical report.

The National Library of Medicine's Visible Human Male data set consists of digital magnetic resonance (MR), computed tomography (CT), and anatomic images derived from a single male cadaver. The data set is 15 gigabytes in size and is available from the National Library of Medicine under a no-cost license agreement. The history of the Visible Human Male cadaver and the methods and technology to produce the data set are described.

Adult↗

PubMed2005

A new approach to fetal echocardiography: digital casts of the fetal cardiac chambers and great vessels for detection of congenital heart disease.

OBJECTIVE: The purpose of this study was to describe a method of 4-dimensional (4D) reconstruction of the cardiac chambers and outflow tracts using a combination of spatiotemporal image correlation, "inversion mode," and "B-flow" imaging. METHODS: Spatiotemporal image correlation and the inversion mode were used in the examination of the volume data sets of 23 fetuses with congenital heart anomalies. A subset was also examined with B-flow imaging using the gradient light algorithm. Digital reconstructions from abnormal hearts were compared with a library obtained from fetuses without abnormalities. RESULTS: Rendered images of the 4-chamber view using the inversion mode were characterized by: (1) echogenic chambers; (2) sharp delineation of chamber contours when compared with 2-dimensional (2D) images; and (3) distinct display of the myocardium, interventricular septum, interatrial septum, and mitral and tricuspid valves as anechoic structures. Ventricular septal defects, abnormal differential insertion of the atrioventricular valves, and valve atresia were well visualized with the inversion mode. The application of inversion mode or B-flow imaging to 4D rendering of the outflow tracts resulted in "digital casts" displaying the spatial relationships between the outflow tracts as well as the connections between the great arteries and ventricular chambers. The spatial relationships and communications among cardiac structures cannot be visualized with conventional 2D ultrasonography. CONCLUSIONS: The application of spatiotemporal image correlation, inversion mode, and B-flow imaging generates information about the anatomy and pathologic characteristics of the fetal heart (digital casts) that cannot be obtained with 2D fetal echocardiography. We propose that these modalities enhance the information provided by ultrasonographic interrogation of the fetal heart and will improve prenatal diagnosis.

Echocardiography, Four-Dimensional↗

PubMed1997

Benchmark test cases for evaluation of computer-based methods for detection of setup errors: realistic digitally reconstructed electronic portal images with known setup errors.

PURPOSE: The purpose of this investigation was to develop methods and software for computing realistic digitally reconstructed electronic portal images with known setup errors for use as benchmark test cases for evaluation and intercomparison of computer-based methods for image matching and detecting setup errors in electronic portal images. METHODS AND MATERIALS: An existing software tool for computing digitally reconstructed radiographs was modified to compute simulated megavoltage images. An interface was added to allow the user to specify which setup parameter(s) will contain computer-induced random and systematic errors in a reference beam created during virtual simulation. Other software features include options for adding random and structured noise, Gaussian blurring to simulate geometric unsharpness, histogram matching with a "typical" electronic portal image, specifying individual preferences for the appearance of the "gold standard" image, and specifying the number of images generated. The visible male computed tomography data set from the National Library of Medicine was used as the planning image. RESULTS: Digitally reconstructed electronic portal images with known setup errors have been generated and used to evaluate our methods for automatic image matching and error detection. Any number of different sets of test cases can be generated to investigate setup errors involving selected setup parameters and anatomic volumes. This approach has proved to be invaluable for determination of error detection sensitivity under ideal (rigid body) conditions and for guiding further development of image matching and error detection methods. Example images have been successfully exported for similar use at other sites. CONCLUSIONS: Because absolute truth is known, digitally reconstructed electronic portal images with known setup errors are well suited for evaluation of computer-aided image matching and error detection methods. High-quality planning images, such as the visible human CT scans from the National Library of Medicine, are essential for producing realistic images. Sets of test cases with systematic and random errors in selected setup parameters and anatomic volumes are suitable for use as standard benchmarks by the radiotherapy community. In addition to serving as an aid to research and development, benchmark images may also be useful for evaluation of commercial systems and as part of a quality assurance program for clinical systems. Test cases and software are available upon request.

Computer Simulation↗

PubMed2004

Prediction of the coding sequences of mouse homologues of FLJ genes: the complete nucleotide sequences of 110 mouse FLJ-homologous cDnas identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries.

We have been conducting a mouse cDNA project to predict protein-coding sequences of mouse KIAA-homologous genes since 2001. As an extension of this project, we also started to accumulate mouse cDNA clones homologous to the human FLJ cDNA clones which are another long cDNA resource produced in our institute. We have isolated the cDNA clones from size-fractionated cDNA libraries derived from five different mouse tissues and natural killer T-cells. Although the human FLJ cDNA clones were originally derived from human spleen libraries, one-third of their mouse homologues were obtained from the brain library. We designated these homologues "mFLJ" plus a 5-digit number and herein characterized 110 mFLJ cDNA clones. We assigned an integrity of the CDSs from the comparison of the 110 cDNA clones with the corresponding human FLJ cDNA clones. The average size of the 110 mouse cDNA sequences was 3.8 kb and that of the deduced amino acid sequences from their longest CDS in each cDNA was 663 amino acid residues. Homology and/or motif search against public databases revealed new domains and/or motifs in 26 mFLJ gene products which provide additional speculation regarding the function of FLJ genes.

Animals↗

PubMed2006

A community-based participatory health information needs assessment to help eliminate diabetes information disparities.

This article describes the participatory research process, results, action plan, and implications of the community health information needs assessment conducted within the African American community in two South Carolina counties. The REACH 2010: Charleston and Georgetown Diabetes Coalition library program is a partnership among community organizations, public and health sciences libraries, and lay community health advisors. A planning committee studied digital divide issues related to health information, designed and implemented a survey, held focus groups, analyzed data, identified needs and assets, and formulated an action plan to increase the dissemination of diabetes information. Key survey findings show that older (older than 60) and less educated (fewer than 12 years of education) African Americans in Charleston and Georgetown counties lack skills to access Internet and library services and suffer disparities in health information. Based on assessment evidence, the community plans to increase Internet access points and provide a train-the-trainer program to teach people skills for using Internet and library resources to get high-quality information about diabetes and its complications. This process taps community resources, builds local capacities and technical skills, educates about health, and empowers participants as active partners in their own health and their community's health.

Adult↗

PubMed2026

Host-aware Identification of Intrinsic Gene Expression Biopart Parameters using Combinatorial Libraries.

Model-based design in synthetic biology is limited because bioparts are typically characterised by relative metrics that vary across genetic and physiological contexts. To address this, we introduce a host-aware framework for quantitatively characterising bioparts in combinatorial libraries of plasmid-based constitutive expression constructs. The approach integrates a digital twin of Escherichia coli, conditioned on measured growth rate, with model-in-the-loop parameter identification to separate biopart-associated properties from host-dependent effects. Using structured combinatorial libraries, we identify mechanistically interpretable, transferable parameters for plasmid origins, promoters and ribosome binding sites. In particular, we define an intrinsic translation initiation capacity that captures the dominant RBS-associated contribution to translation while context-dependent expression emerges from host physiology and local sequence context. The resulting parameterisation accurately predicts protein synthesis across physiological conditions, supports incremental library expansion, and reveals localised failures of modularity, providing a scalable foundation for predictive host-aware design in synthetic biology.

Escherichia coli↗

PubMed2002

Gene expression profiling in developing human hippocampus.

The gene expression profile of developing human hippocampus is of particular interest and importance to neurobiologists devoted to development of the human brain and related diseases. To gain further molecular insight into the developmental and functional characteristics, we analyzed the expression profile of active genes in developing human hippocampus. Expressed sequence tags (ESTs) were selected by sequencing randomly selected clones from an original 3'-directed cDNA library of 150-day human fetal hippocampus, and a digital expression profile of 946 known genes that could be divided into 16 categories was generated. We also used for comparison 14 other expression profiles of related human neural cells/tissues, including human adult hippocampus. To yield more confidence regarding differential expression, a method was applied to attach normalized expression data to genes with a low false-positive rate (<0.05). Finally, hierarchical cluster analysis was used to exhibit related gene expression patterns. Our results are in accordance with anatomical and physiological observations made during the developmental process of the human hippocampus. Furthermore, some novel findings appeared to be unique to our results. The abundant expression of genes for cell surface components and disease-related genes drew our attention. Twenty-four genes are significantly different from adult, and 13 genes might be developing hippocampus-specific candidate genes, including wnt2b and some Alzheimer's disease-related genes. Our results could provide useful information on the ontogeny, development, and function of cells in the human hippocampus at the molecular level and underscore the utility of large-scale, parallel gene expression analyses in the study of complex biological phenomena.

Adult↗