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At least 325 records · Page 18Linked to original sources
PubMed2004

Comprehensive EST analysis of tomato and comparative genomics of fruit ripening.

A large tomato expressed sequence tag (EST) dataset (152 635 total) was analyzed to gain insights into differential gene expression among diverse plant tissues representing a range of developmental programs and biological responses. These ESTs were clustered and assembled to a total of 31 012 unique gene sequences. To better understand tomato gene expression at a plant system level and to identify differentially expressed and tissue-specific genes, we developed and implemented a digital expression analysis protocol. By clustering genes according to their relative abundance in the various EST libraries, expression patterns of genes across various tissues were generated and genes with similar patterns were grouped. In addition, tissues themselves were clustered for relatedness based on relative gene expression as a means of validating the integrity of the EST data as representative of relative gene expression. Arabidopsis and grape EST collections were also characterized to facilitate cross-species comparisons where possible. Tomato fruit digital expression data was specifically compared with publicly available grape EST data to gain insight into molecular manifestation of ripening processes across diverse taxa and resulted in identification of common transcription factors not previously associated with ripening.

Arabidopsis↗
PubMed1998

Use of approximate entropy measurements to classify ventricular tachycardia and fibrillation.

Implantable cardiac devices which treat arrhythmias require automated detection to decide when to deliver therapy and, in some devices like the implantable cardioverter-defibrillator (ICD), to determine which therapy to deliver. This type of detection often requires the separation of fibrillatory chaotic rhythms from coherent tachycardias. In the ICD, multiple rate zones can be programmed for detection of ventricular tachycardia (VT) and ventricular fibrillation (VF) and for delivery of therapy: antitachycardia pacing and cardioversion for VT, and defibrillation for VF. Previous research determined that current technology is unable to uniquely classify VF. Analysis of typical settings of the ICD revealed that 40% to 80% of VTs were misclassified as VF (depending on device/setting). Improved detection of VF must be sought in order to capitalize on the cost effectiveness of low-energy VT therapies, potentially saving up to 20% of the life of the battery. In this study, a statistical measure of variability, called approximate entropy (ApEn), has been applied to separate fibrillatory and nonfibrillatory rhythms. Although standard deviation is often used as a measure of variability, it fails to capture the level of regularity or complexity. ApEn improves upon standard deviation by quantifying differences between random and regular signals. ApEn was tested on a small patient set containing VF, VT, and sinus rhythm (SR). Intracardiac recordings (bipolar, ventricular) were selected from the Ann Arbor Electrogram Library (Ann Arbor, MI) where filtering (1-500 Hz), amplification (approximately 1000), and digitization (1000 Hz) are tightly controlled. Results demonstrated that ApEn has the ability to quantify subtle differences between VF and other rhythms.

Cost-Benefit Analysis↗
PubMedDate not supplied

Measurement of volume changes after sinus floor augmentation with a phycogenic hydroxyapatite.

PURPOSE: The purpose of this study was the determination of time-dependent volumetric changes of particulate sinus inlay grafts. A mixture of phycogenic hydroxyapatite (Algipore/C-Graft) and autologous bone collected from the surgical access area was used as the grafting material. MATERIALS AND METHODS: Thirty-three sinus floor augmentations using phycogenic hydroxyapatite combined with autologous bone collected at the augmentation site and venous blood were performed on 18 patients aged 57.4 +/- 12.5 years (mean +/- SD) with severe atrophy of the posterior maxilla. Graft volume was measured 1 to 14 days postoperatively and before the placement of dental implants 6.1 +/- 2.1 months later (mean +/- SD; range, 4 to 11 months) to evaluate the amount of time-dependent resorption of the implanted material on computerized tomographic (CT) images of the augmented region. The images were put into Digital Imaging and Communications in Medicine (DICOM) format and evaluated using the software library Analyze. The implanted bone replacement material was plotted manually on each CT slice, and the volume of the implanted material was calculated. RESULTS: The average volume loss of the bone replacement material during the observation period was 13.9% +/- 1.9% (mean +/- SEM). All sinus floor augmentations healed without complications except for delayed membrane exposure in 2 cases. DISCUSSION: The results indicate that the graft material, a mixture of Algipore, bone chips from the access area, and venous blood, exhibited a small volume loss over a period of approximately 6 months, thus providing predictable height for second-stage implant surgery. CONCLUSION: Further investigations are needed to evaluate long-term stability and implant success.

Adult↗
PubMedDate not supplied

[Video documentation in forensic practice].

The authors report in part 1 about their experiences with the Canon Ex1 Hi camcorder and the possibilities of documentation with the modern video technique. Application examples in legal medicine and criminalistics are described autopsy, scene, reconstruction of crimes etc. The online video documentation of microscopic sessions makes the discussion of findings easier. The use of video films for instruction produces a good resonance. The use of the video documentation can be extended by digitizing (Part 2). Two frame grabbers are presented, with which we obtained good results in digitizing of images captured from video. The best quality of images is achieved by online use of an image analysis chain. Corel 5.0 and PicEd Cora 4.0 allow complete image processings and analysis. The digital image processing influences the objectivity of the documentation. The applicabilities of image libraries are discussed.

Equipment Design↗
PubMed1991

Analog-to-digital clinical data collection on networked workstations with graphic user interface.

An innovative respiratory examination system has been developed that combines physiological response measurement, real-time graphic displays, user-driven operating sequences, and networked file archiving and review into a scientific research and clinical diagnosis tool. This newly constructed computer network is being used to enhance the research center's ability to perform patient pulmonary function examinations. Respiratory data are simultaneously acquired and graphically presented during patient breathing maneuvers and rapidly transformed into graphic and numeric reports, suitable for statistical analysis or database access. The environment consists of the hardware (Macintosh computer, MacADIOS converters, analog amplifiers), the software (HyperCard v2.0, HyperTalk, XCMDs), and the network (AppleTalk, fileservers, printers) as building blocks for data acquisition, analysis, editing, and storage. System operation modules include: Calibration, Examination, Reports, On-line Help Library, Graphic/Data Editing, and Network Storage.

Analog-Digital Conversion↗
PubMed2005

The information needs of perioperative staff: a preparatory study for a proposed specialist library for theatres (NeLH).

AIMS/OBJECTIVES: To undertake an information-needs analysis of operating theatre staff in order to inform the development of a specialist library of the National Electronic Library of Health (NeLH). SETTING: Three hospitals in an NHS Trust in a rural county in the north of England. METHODS: In-depth interviews, during which staff were questioned in regard to their job roles and information needs, information-seeking behaviour, access to computers, use and perceptions of the NeLH, and what they would like from a specialist library. RESULTS: Information needs were found to concern direct care, professional and academic development, medical devices knowledge and administration. Currency and speed of delivery were the key information requirements. Poor communication appeared to be a major problem for many staff and inhibited efficient information exchange. When using the Web, both clinical and non-clinical staff searched in a similar fashion to health consumers generally, despite their need for highly specialist information. Most respondents reacted warmly to the idea of the proposed National Electronic Library for Theatre Staff (NeLTS) and made several practical suggestions for suitable material. However, access was problematic for nurses and might prove to be an obstacle to take-up of the Specialist Library. CONCLUSIONS: Communication difficulties, the fragmentation of data in the field and the consequent difficulties of finding information point to the need for an NeLTS. However, for this library to embrace and succeed with all the various groups that constitute the operating theatre staff, issues of access and digital literacy need to be addressed.

England↗
PubMed2002

[Establishment of biopanning model of phage display peptide library in the blood vessels of excised human osteosarcoma vasculature and its significance].

OBJECTIVE: To establish an in vivo biopanning model of phage display peptide library in the blood vessels contained in surgically removed human osteosarcoma. METHOD: In 28 patients with osteosarcoma, digital subtraction angiography (DSA) of the involved limb was performed preoperatively to understand the approximate status of the arteries in the tumors. The tumors were then surgically removed and carefully trimmed, perfused via a simulated Langendorff perfusion apparatus with the indexes as the pH value, temperature and O2 partial pressure monitored in the blood vessels. A 12-meres phage display peptide library was biopanned to isolate peptides capable of homing specifically to the excised osteosarcoma. RESULTS: In vivo biopanning models were successfully established in all the excised tumors, which could be directly used in perfusion experiment and the indexes monitored in the blood vessels in the tumors were comparable to those of living tissues. Some high-affinity peptides specific to the blood vessels in osteosarcoma were obtained with the motif of RLTR. CONCLUSION: In vivo biopanning model simulating the Langendorff perfusion apparatus can be easily established which is instrumental for the application of phage display technology in human living tissues and may facilitate the study of targeted chemotherapy of osteosarcoma.

Adolescent↗
PubMedDate not supplied

Improved video documentation of endoscopic sinus surgery made possible with desktop digital video.

Endoscopic cameras in endoscopic sinus surgery (ESS) allow for easy video documentation of surgery. This often leads to the build-up of extensive videocassette libraries where the prospective viewer is subjected to a lengthy and cumbersome videotape search before accessing a sequence of interest. Footage is difficult to use for educational purposes. New techniques for storing, retrieving, and presenting ESS video footage were developed. Desktop computer systems were used to digitize video footage. Short video sequences containing highlights of interesting ESS cases were prepared using video-editing programs. The resulting images were stored in individual segments on recordable CD-ROM disks. This technique was used to archive all video footage from our ESS procedures for a 6-month period. Archiving footage on CD-ROM rather than videotape has made the storage of large quantities of information possible while now allowing for the random access of segment(s) of interest. It has simplified preparation of video projects, reduced production time 10-fold and has eliminated the need for professional video-editing services. These techniques have also been adapted for the development of an educational CD-ROM demonstrating the component steps of ESS, which can be played back on any CD-ROM-equipped computer.

CD-ROM↗
PubMed2004

Mobile phone interference with medical equipment and its clinical relevance: a systematic review.

OBJECTIVE: To conduct a systematic review of studies on clinically relevant digital mobile phone electromagnetic interference with medical equipment. DATA SOURCES: MEDLINE and SUMSEARCH were searched for the period 1966-2004. The Cochrane Library and Database of Abstracts of Reviews of Effects were also searched for systematic reviews. STUDY SELECTION: Studies were eligible if published in a peer-reviewed journal in English, and if they included testing of digital mobile phones for clinically relevant interference with medical equipment used to monitor or treat patients, but not implantable medical devices. DATA SYNTHESIS: As there was considerable heterogeneity in medical equipment studied and the conduct of testing, results were summarised rather than subjected to meta-analysis. RESULTS: Clinically relevant electromagnetic interference (EMI) secondary to mobile phones potentially endangering patients occurred in 45 of 479 devices tested at 900 MHz and 14 of 457 devices tested at 1800 MHz. However, in the largest studies, the prevalence of clinically relevant EMI was low. Most clinically relevant EMI occurred when mobile phones were used within 1 m of medical equipment. CONCLUSIONS: Although testing was not standardised between studies and equipment tested was not identical, it is of concern that at least 4% of devices tested in any study were susceptible to clinically relevant EMI. All studies recommend some type of restriction of mobile phone use in hospitals, with use greater than 1 m from equipment and restrictions in clinical areas being the most common.

Australia↗
PubMed2005

Sam68-like mammalian protein 2, identified by digital differential display as expressed by podocytes, is induced in proteinuria and involved in splice site selection of vascular endothelial growth factor.

Podocytes, the glomerular epithelial cells of the kidney, share important features with neuronal cells. In addition to phenotypical and functional similarities, a number of gene products have been found to be expressed exclusively or predominantly by both cell types. With the hypothesis of a common transcriptome shared by podocytes and neurons, digital differential display was used to identify novel podocyte-expressed gene products. Comparison of brain and kidney cDNA libraries with those of other organs identified Sam68-like mammalian protein 2 (SLM-2), a member of the STAR family of RNA processing proteins, as expressed by podocytes. SLM-2 expression was found to be restricted in the kidney to podocytes. In proteinuric diseases, SLM-2, a known regulator of neuronal mRNA splice site selection, was found significantly upregulated on mRNA and protein levels. Knockdown of SLM-2 by short interfering RNA in podocytes was performed to evaluate its biologic role. RNA splicing of vascular endothelial growth factor (VEGF), a key regulator of the filtration barrier and expressed as functionally distinct splice isoforms, was evaluated. VEGF(165) expression was found to be reduced by 25% after SLM-2 knockdown. In vivo, the glomerular expression of SLM-2 correlated with the mRNA levels of VEGF(165). This study demonstrates the power of digital differential display to predict cell type-specific gene expression by hypothesis-driven analysis of tissue cDNA libraries. SLM-2-dependent VEGF splicing indicates the importance of mRNA splice site selection for glomerular filtration barrier function.

Animals↗
PubMed1997

The significance of digital gene expression profiles.

Genes differentially expressed in different tissues, during development, or during specific pathologies are of foremost interest to both basic and pharmaceutical research. "Transcript profiles" or "digital Northerns" are generated routinely by partially sequencing thousands of randomly selected clones from relevant cDNA libraries. Differentially expressed genes can then be detected from variations in the counts of their cognate sequence tags. Here we present the first systematic study on the influence of random fluctuations and sampling size on the reliability of this kind of data. We establish a rigorous significance test and demonstrate its use on publicly available transcript profiles. The theory links the threshold of selection of putatively regulated genes (e.g., the number of pharmaceutical leads) to the fraction of false positive clones one is willing to risk. Our results delineate more precisely and extend the limits within which digital Northern data can be used.

Actins↗
PubMed2006

Preparing digitized cervigrams for colposcopy research and education: determination of optimal resolution and compression parameters.

OBJECTIVE: Visual assessment of digitized cervigrams through the Internet needs to be optimized. The National Cancer Institute and National Library of Medicine are involved in a large effort to improve colposcopic assessment and, in preparation, are conducting methodologic research. MATERIALS AND METHODS: We selected 50 cervigrams with diagnoses ranging from normal to cervical intraepithelial neoplasia 3 or invasive cancer. Those pictures were scanned at 5 resolution levels from 1,550 to 4,000 dots per inch (dpi) and were presented to 4 expert colposcopists to assess image quality. After the ideal resolution level was determined, pictures were compressed at 7 compression ratios from 20:1 to 80:1 to determine the optimal level of compression that permitted full assessment of key visual details. RESULTS: There were no statistically significant differences between the 3,000 and 4,000 dpi pictures. At 2,000 dpi resolution, only one colposcopist found a slightly statistically significant difference (p = 0.02) compared with the gold standard. There was a clear loss of quality of the pictures at 1,660 dpi. At compression ratio 60:1, 3 of 4 evaluators found statistically significant differences when comparing against the gold standard. CONCLUSIONS: Our results suggest that 2,000 dpi is the optimal level for digitizing cervigrams, and the optimal compression ratio is 50:1 using a novel wavelet-based technology. At these parameters, pictures have no significant differences with the gold standard.

Biomedical Research↗
PubMedDate not supplied

A client/server system for Internet access to biomedical text/image databanks.

Internet access to mixed text/image databanks is finding application in the medical world. An example is a database of medical X-rays and associated data consisting of demographic, socioeconomic, physician's exam, medical laboratory and other information collected as part of a nationwide health survey conducted by the government. Another example is a collection of digitized cryosection images, CT and MR taken of cadavers as part of the National Library of Medicine's Visible Human Project. In both cases, the challenge is to provide access to both the image and the associated text for a wide end user community to create atlases, conduct epidemiological studies, to develop image-specific algorithms for compression, enhancement and other types of image processing, among many other applications. The databanks mentioned above are being created in prototype form. This paper describes the prototype system developed for the archiving of the data and the client software to enable a broad range of end users to access the archive, retrieve text and image data, display the data and manipulate the images. System design considerations include; data organization in a relational database management system with object-oriented extensions; a hierarchical organization of the image data by different resolution levels for different user classes; client design based on common hardware and software platforms incorporating SQL search capability, X Window, Motif and TAE (a development environment supporting rapid prototyping and management of graphic-oriented user interfaces); potential to include ultra high resolution display monitors as a user option; intuitive user interface paradigm for building complex queries; and contrast enhancement, magnification and mensuration tools for better viewing by the user.

Anatomy, Cross-Sectional↗
PubMed2002

Digital analysis of cDNA abundance; expression profiling by means of restriction fragment fingerprinting.

BACKGROUND: Gene expression profiling among different tissues is of paramount interest in various areas of biomedical research. We have developed a novel method (DADA, Digital Analysis of cDNA Abundance), that calculates the relative abundance of genes in cDNA libraries. RESULTS: DADA is based upon multiple restriction fragment length analysis of pools of clones from cDNA libraries and the identification of gene-specific restriction fingerprints in the resulting complex fragment mixtures. A specific cDNA cloning vector had to be constructed that governed missing or incomplete cDNA inserts which would generate misleading fingerprints in standard cloning vectors. Double stranded cDNA was synthesized using an anchored oligo dT primer, uni-directionally inserted into the DADA vector and cDNA libraries were constructed in E. coli. The cDNA fingerprints were generated in a PCR-free procedure that allows for parallel plasmid preparation, labeling, restriction digest and fragment separation of pools of 96 colonies each. This multiplexing significantly enhanced the throughput in comparison to sequence-based methods (e.g. EST approach). The data of the fragment mixtures were integrated into a relational database system and queried with fingerprints experimentally produced by analyzing single colonies. Due to limited predictability of the position of DNA fragments on the polyacrylamid gels of a given size, fingerprints derived solely from cDNA sequences were not accurate enough to be used for the analysis. We applied DADA to the analysis of gene expression profiles in a model for impaired wound healing (treatment of mice with dexamethasone). CONCLUSIONS: The method proved to be capable of identifying pharmacologically relevant target genes that had not been identified by other standard methods routinely used to find differentially expressed genes. Due to the above mentioned limited predictability of the fingerprints, the method was yet tested only with a limited number of experimentally determined fingerprints and was able to detect differences in gene expression of transcripts representing 0.05% of the total mRNA population (e.g. medium abundant gene transcripts).

Journal Article↗
PubMed2005

Crossing the digital divide: the contribution of information technology to the professional performance of malaria researchers in Africa.

BACKGROUND: The US National Library of Medicine supports the Multilateral Initiative on Malaria (MIM) through the design, implementation, and operation of the Multilateral Initiative on Malaria Communications Network (MIMCom.) MIMCom makes possible enhanced access to the Internet and to medical literature. OBJECTIVES: The main objectives of the present study were to examine the use of MIMCom supported information technology (IT) by scientists, students, and administrative personnel to facilitate communication, retrieve information, obtain documents, write proposals, and prepare papers for publication; and to determine the contribution of this intervention to their professional performance. METHODS: The authors analyzed the contribution of enhanced Internet connectivity and access to electronic information resources to the performance of malaria research staff and their institutes through a cross-sectional questionnaire survey of 181 respondents at 14 health research centers in Africa. Separate reviews of bandwidth usage, requests for document delivery, and publications in peer reviewed journals support the data of the survey. RESULTS: The MIMCom network makes a positive contribution to the performance of malaria researchers and support staff at the sites reviewed by improving e-mail exchange, access to published literature, and research proposal development and submission. Implications of these findings are discussed. CONCLUSION: By providing full access to the Internet and the resources of the WorldWide Web, MIMCom has been shown to be invaluable to malaria researchers and their institutes in Africa. This access has increased visibility of scientists in their respective institutions and provided opportunities for stronger engagement with the international scientific community.

Access to Information↗
PubMed2003

Teaching and learning gross anatomy using modern electronic media based on the visible human project.

This article reviews online (Internet) anatomy projects and multimedia productions (books and CD-ROMs) based on the Visible Human Project (VHP) of the United States National Library of Medicine. The focus of these projects and productions is on the teaching of 3D anatomy using the digitized sections of the visible human male and female. The article also provides information about the VHP, its goals and what it has achieved thus far.

Anatomy↗