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At least 217 records · Page 12Linked to original sources
PubMed1998

Octamer-primed cycle sequencing using dye-terminator chemistry.

Octamer Sequencing Technology, OST, is a method of DNA sequencing using single octamer oligonucleotides to prime cycle sequencing reactions. This sequencing strategy is faster than a traditional primer-walking strategy, since access to this optimized octamer library eliminates delays associated with designing and synthesizing gene specific primers. In this report, OST has been optimized for fluorescent, dye-terminator cycle sequencing reactions to facilitate parallel processing of samples. The successful adaptation of OST to an automated sequencing platform and the design of and access to an octamer library are critical steps towards developing an efficient 'closed-loop' DNA sequencing system.

Animals↗
PubMed2000

Automated solid-phase synthesis of linear nitrogen-linked compounds.

A synthetic library motif has been developed to create linear, nitrogen-linked compounds as screening libraries to target structured RNA for drug discovery. Scaffolds were created in situ from suitably protected bifunctional compounds linked together either by acyl or amine links. Acyl links were created from amino acids, which also introduce one degree of functionality. Amine links from the amino acid nitrogen were created from an N-protected amino alcohol via Fukuyama Mitsunobu alkylation. Each amine site can then be used for introducing functionality or extending the scaffold. This synthetic scheme can be used to create a wide variety of modified-backbone PNA in situ, as shown by the synthesis of a PNA-type monomer. The synthesis steps have been enabled on a 96-well parallel-array synthesizer for high-throughput synthesis. The present study represents a versatile synthetic approach to a wide variety of potential RNA-binding molecules.

Amides↗
PubMed2002

Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory.

BACKGROUND: The development of DNA amplification for the direct detection of M. tuberculosis from clinical samples has been a major goal of clinical microbiology during the last ten years. However, the limited sensitivity of most DNA amplification techniques restricts their use to smear positive samples. On the other hand, the development of automated liquid culture has increased the speed and sensitivity of cultivation of mycobacteria. We have opted to combine automated culture with rapid genotypic identification (ARDRA: amplified rDNA restriction analysis) for the detection resp. identification of all mycobacterial species at once, instead of attempting direct PCR based detection from clinical samples of M. tuberculosis only. RESULTS: During 1998-2000 a total of approx. 3500 clinical samples was screened for the presence of M. tuberculosis. Of the 151 culture positive samples, 61 were M. tuberculosis culture positive. Of the 30 smear positive samples, 26 were M. tuberculosis positive. All but three of these 151 mycobacterial isolates could be identified with ARDRA within on average 36 hours. The three isolates that could not be identified belonged to rare species not yet included in our ARDRA fingerprint library or were isolates with an aberrant pattern. CONCLUSIONS: In our hands, automated culture in combination with ARDRA provides with accurate, practically applicable, wide range identification of mycobacterial species. The existing identification library covers most species, and can be easily updated when new species are studied or described. The drawback is that ARDRA is culture-dependent, since automated culture of M. tuberculosis takes on average 16.7 days (range 6 to 29 days). However, culture is needed after all to assess the antibiotic susceptibility of the strains.

Bacterial Typing Techniques↗
PubMed1995

Application of a unique automated synthesis system for solution-phase peptide synthesis.

An automated synthesis system, which is suitable for repetitive syntheses using similar reaction procedures, was used to synthesize systematically a library of all possible dipeptides (25) and tripeptides (125) from 5 protected amino acids. The apparatus has also been applied to the automated synthesis of 10 fragment tripeptide derivatives that are constituents of the hormone PACAP-27. The measured molecular optical rotation values of the library of 125 tripeptides were found to correlate well with calculated values obtained by summation of the molecular optical rotation values for the constituent amino acids.

Amino Acid Sequence↗
PubMed2026

The role of artificial intelligence in the diagnosis and prognosis of traumatic brain injury based on brain CT scans: a systematic review.

Traumatic brain injury (TBI) is a leading cause of emergency department visits and a major contributor to injury-related mortality and long-term neurological disability. Non-contrast computed tomography (CT) is the gold-standard imaging modality for the rapid diagnosis of TBI. Clinical outcomes depend strongly on early detection and prompt acute management. Artificial intelligence (AI)-based models may support faster automated identification of traumatic findings and early prediction of patient prognosis. A systematic literature search was conducted in PubMed/MEDLINE, Scopus, IEEE Xplore, ACM Digital Library, and the Cochrane Library in accordance with PRISMA 2020 guidelines to evaluate AI-based models for automated detection of TBI-related findings on CT and for prediction of clinical outcomes. Risk of bias and applicability were assessed using QUADAS-2 for diagnostic accuracy studies and PROBAST + AI for prediction model studies. Twenty-two studies were included. Sixteen studies evaluated diagnostic tasks and 10 evaluated prognostic outcomes, with four studies contributing to both categories. Diagnostic performance was generally high, with many studies reporting AUC values approaching or exceeding 0.90, particularly for larger lesion volumes.Prognostic performance was more variable, with moderate to high discrimination and substantial heterogeneity. Only 9 studies incorporated independent external validation, and performance was frequently lower in external cohorts. All prognostic model studies were judged to be at high overall risk of bias using PROBAST + AI, and most diagnostic accuracy studies also demonstrated high or unclear risk of bias in at least one QUADAS-2 domain, most frequently in patient selection. AI-based models applied to brain CT demonstrate strong technical performance for both diagnostic and prognostic tasks in TBI. However, most studies relied on retrospective designs and lacked independent external validation which limits models generalizability and raises concern for potential overfitting. Prospective, multicenter studies with standardized methodologies and rigorous external validation are required before widespread clinical implementation.

Humans↗
PubMed1995

A compilation of partial sequences of randomly selected cDNA clones from the rat incisor.

The formation of tooth organs is regulated by a series of developmental programs. We have initiated a genome project with the ultimate goal of identifying novel genes important for tooth development. As an initial approach, we constructed a unidirectional cDNA library from the non-calcified portion of incisors of 3- to 4-week-old rats, sequenced cDNA clones, and classified their sequences by homology search through the GenBank data base and the PIR protein data base. Here, we report partial DNA sequences obtained by automated DNA sequencing on 400 cDNA clones randomly selected from the library. Of the sequences determined, 51% represented sequences of new genes that were not related to any previously reported gene. Twenty-six percent of the clones strongly matched genes and proteins in the data bases, including amelogenin, alpha 1(I) and alpha 2(I) collagen chains, osteonectin, and decorin. Nine percent of clones revealed partial sequence homology to known genes such as transcription factors and cell surface receptors. A significant number of the previously identified genes were expressed redundantly and were found to encode extracellular matrix proteins. Identification and cataloging of cDNA clones in these tissues are the first step toward identification of markers expressed in a tissue- or stage-specific manner, as well as the genetic linkage study of tooth anomalies. Further characterization of the clones described in this paper should lead to the discovery of novel genes important for tooth development.

Amelogenesis↗
PubMed1997

IMAGE cDNA clones, UniGene clustering, and ACeDB: an integrated resource for expressed sequence information.

In this study we describe a new information resource that provides integrated access to information on IMAGE (integrated molecular analysis of genomes and their expression) cDNA library clones and derived expressed sequence tags (ESTs). We have developed an automated procedure that collates data from various public sources into a single ACeDB database. This database is a valuable tool for electronic cloning experiments and gene expression studies. It allows researchers to find information about cDNA libraries, plate addresses, insert sizes, and sequence data for IMAGE clones, the assignment of ESTs to UniGene clusters, and the chromosomal location of those genes in an efficient, graphically oriented manner.

Cloning, Molecular↗
PubMed1996

Sequenase sequence profiles used for HLA-DPB1 sequencing-based typing.

Sequencing-based HLA typing (SBT) is a PCR based high resolution HLA typing method in which polymorphic regions of the gene are sequenced and directly used for typing. Currently, for class II SBT, alleles are identified by comparison of the exon 2 sequence with their corresponding allele sequence library. Routine SBT requires reliable identification of heterozygosity, and automated assignment of the alleles. In sequencing strategies different enzymes can be used for primer extension. The most characteristic difference between sequences obtained by two protocols using Sequenaseregistered, or Taq-cycle sequencing, respectively, is a difference in incorporation of nucleotides in the primer extension leading to different sequence profiles. In Taq-cycling sequencing variable nucleotide incorporation results in irregular, but reproducible peak patterns, whereas Sequenase incorporates nucleotides in nearly equal amounts, resulting in more even peak patterns. In a previously published multi-center study we evaluated HLA-DPB1 SBT using Taq-cycle sequencing, and showed that typing can reliably be performed, considering the specific sequence profiles. In this study the applicability of Sequenase for HLA-DPB1 SBT was tested. A panel of samples were typed by SBT at five test sites which participate in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. The assignment of homozygosity and heterozygosity was validated by Multi-Sequence Analysis, performing cluster analysis of chromatographic data of all sequences at each position. Sequence characteristics were examined and considered for appropriate assignment. Data reveals that Sequenase sequencing can also reliably be used for HLA-DPB1 typing.

Bacteriophage T7↗
PubMed1998

A rare-earth phosphor containing one-dimensional chains identified through combinatorial methods

An unusual luminescent inorganic oxide, Sr2CeO4, was identified by parallel screening techniques from within a combinatorial library of more than 25,000 members prepared by automated thin-film synthesis. A bulk sample of single-phase Sr2CeO4 was prepared, and its structure, determined from powder x-ray diffraction data, reveals one-dimensional chains of edge-sharing CeO6 octahedra, with two terminal oxygen atoms per cerium center, that are isolated from one another by Sr2+ cations. The emission maximum at 485 nanometers appears blue-white and has a quantum yield of 0.48 +/- 0.02. The excited-state lifetime, electron spin resonance, magnetic susceptibility, and structural data all suggest that luminescence originates from a ligand-to-metal Ce4+ charge transfer.

Journal Article↗
PubMed2000

A solution-phase combinatorial synthesis of selective dopamine D4 ligands.

Utilizing combinatorial synthesis and a preparative LC-MS automated chromatography system we have prepared and purified a library of 4-[2-(1,2,4-oxadiazolyl)]piperidines that were designed to be novel and selective dopamine D4 ligands. In one round of synthesis we identified N-4-chlorobenzyl-4-[2-(3-(2-thienyl)-1,2, 4-oxadiazolyl)]piperidine with a Kd of 5 nM for the human D4 receptor.

Combinatorial Chemistry Techniques↗
PubMed1995

The availability of health information in South Africa.

The South African Medical Research Council (MRC) has provided access to on-line health and biomedical information since 1976, when the MRC became an international partner of NLM. This was done to support research and health care when the Institute of Biomedical Communication was established. The institute has since reorganized and is now the Information Systems Division in the Research Systems Support Group MRC. he MRC and medical libraries in South Africa are able to access various automated services via telecommunication. The major systems available are MEDLARS, DIALOG, DATASTAR and BRS, with ECRI being the latest addition; most used are MEDLARS and DIALOG. New technologies (e.g., CD-ROM) have given more people access. This technology is not available to many people working in Primary Health Care (PHC), as they do not have access to computer networks. Beyond on-line is statistical and printed information, called "Gray Literature," not accessible through on-line systems as it is not published in conventional sources used to build databases. With a shift to Essential National Health Research and the focus on PHC and preventative medicine, demand for health information and "gray literature" is growing. The MRC collects and produces this material and has its own database called SAMED, which is to be made available to others as our contribution to health. It is hoped to make this available for inclusion in the proposed African Index Medicus presently investigated by the World Health Organization. Africa as a continent, and South Africa as a country, are experiencing major changes in health care and medical practice, and inevitably, provision of health information services. With South Africa's re-entry into the global village and its acceptance by the rest of Africa, it can be a key player in information provision to the rest of the continent. The MRC, as a major provider of Health information, can play a vital role in the information flow throughout Africa by continuously improving and expanding its services. A large proportion of South Africans live in rural areas where health care is provided by clinics not linked to information networks. This does not mean these clinics are excluded from the use of information. The major challenge is to find the ways and means of getting the relevant information to these clinics. Information is needed to help with patient care and continuing education. With this in mind, the MRC is evaluating different formats in which information can be supplied. Due to the lack of computer literacy, facilities, and financial constraints, it is better to supply printed information. With the spread of technology through the country and continent, it can be assumed that information flow and transfer will be more rapid. Repackaging of information means that it is possible to get the relevant information to the right people at the right time. The first such package developed is for hospital managers. With the help from experts in the field of PHC, it is hoped to develop packages aimed specifically at the CHWs and other workers in the field. All packages developed by the MRC are backed by a document provision service, using the most cost-effective route to obtain documents. A printed product must comply with certain criteria; these are: 1) purpose for which the information is needed; 2) kind of information needed and the format in which it is needed; 3) when the information is needed; 4) is the information to be supplied on an ongoing basis i.e., updated with latest information; 5) cost involved; and 6) how to get the information to the relevant user.

Computer Communication Networks↗
PubMed1999

Automated semantic indexing of imaging reports to support retrieval of medical images in the multimedia electronic medical record.

This paper describes preliminary work evaluating automated semantic indexing of radiology imaging reports to represent images stored in the Image Engine multimedia medical record system at the University of Pittsburgh Medical Center. The authors used the SAPHIRE indexing system to automatically identify important biomedical concepts within radiology reports and represent these concepts with terms from the 1998 edition of the U.S. National Library of Medicine's Unified Medical Language System (UMLS) Metathesaurus. This automated UMLS indexing was then compared with manual UMLS indexing of the same reports. Human indexing identified appropriate UMLS Metathesaurus descriptors for 81% of the important biomedical concepts contained in the report set. SAPHIRE automatically identified UMLS Metathesaurus descriptors for 64% of the important biomedical concepts contained in the report set. The overall conclusions of this pilot study were that the UMLS metathesaurus provided adequate coverage of the majority of the important concepts contained within the radiology report test set and that SAPHIRE could automatically identify and translate almost two thirds of these concepts into appropriate UMLS descriptors. Further work is required to improve both the recall and precision of this automated concept extraction process.

Abstracting and Indexing↗
PubMedDate not supplied

Solid-phase synthesis of urea and amide libraries using the T2 triazene linker.

Starting from Merrifield resin, primary amines were immobilized in two steps by triazene linkage (T2-linker). While reaction with isocyanates gave rise to resin-bound urea derivatives, acylation by acid chlorides or anhydrides furnished amides bound to solid support via the nitrogen atom, therefore representing a novel backbone amide linker. Cleavage from the resin was conducted using dilute trimethylsilyl chloride or trifluoroacetic acid, respectively, to yield ureas and amines/amides in a library format (altogether 60 examples; manual synthesis: 17 ureas, 6 mono-alkylated ureas [including dihydroxylation and ozonolysis/Wittig reaction]; automated synthesis: 15 ureas, 15 amides) in high purities and good overall yields. The synthesis of a small library (4 x 4 member) was successfully conducted on a Bohdan Neptune synthesizer.

Journal Article↗
PubMed1976

Automated cataloging: the state of the art.

The art of cataloging is in a state of constant dynamic change. The capabilities of automation are causing changes in the tools we have at our disposal, the education and training we need to work with these tools, the caliber of staff we use at various stages of the cataloging process, and the physical form of the end product of the efforts of the catalog department. But perhaps of more importance is the cooperation and sharing between libraries on both the national and international level that become possible as the result of automated systems.

Automation↗
PubMed1996

Isotope or mass encoding of combinatorial libraries.

BACKGROUND: Combinatorial chemistry using solid-phase synthesis is a rapidly developing technology that can result in a significant reduction in the time required to find and optimize lead compounds. The application of this approach to traditional medicinal chemistry has led to the construction of libraries of small organic molecules on resin beads. A major difficulty in developing large combinatorial libraries is the lack of a facile encoding and decoding methodology to identify active compounds. RESULTS: Several encoding schemes are described which use the ability of mass spectrometry to ascertain isotopic distributions. Molecular tags are attached to resin beads in parallel or on the linker used for chemical library synthesis. The tags are encoded via a controlled ratio of a number of stable isotopes on the tagging molecules, and range from a single to a complex isotopic distribution. CONCLUSIONS: A novel coding scheme is described that is useful for the generation of large encoded combinatorial libraries. The code can be cleaved after assay and analyzed by mass spectrometry in an automated fashion. An important element of the combinatorial discovery process is the ability to extract the structure-activity relationship (SAR) information made available by library screening. The speed and sensitivity of the mass-encoding scheme has the potential to determine the full SAR for a given library.

Chemistry, Organic↗
PubMed1992

Cosmid linking clones localized to the long arm of human chromosome 11.

Molecular probes that contain DNA flanking CpG-rich restriction sites are extremely valuable in the construction of physical maps of chromosomes and in the identification of genes associated with hypomethylated HTF (HpaII tiny fragment) islands. We describe a new approach to the isolation and characterization of linking clones in arrayed chromosome-specific cosmid libraries through the large-scale semiautomated restriction mapping of cosmid clones. We utilized a cosmid library representing human chromosome 11q12-11qter and carried out automated restriction enzyme analysis, followed by regional localization to chromosome 11q using high-resolution in situ suppression hybridization. Using this approach, 165 cosmid linking clones containing one or more NotI, BssHII, SfiI, or SacII sites were identified among 960 chromosome-specific cosmids. Furthermore, this analysis allowed clones containing a single site to be distinguished from those containing clusters of two or more rare sites. This analysis demonstrated that more than 75% of cosmids containing a rare restriction site also contained a second rare restriction site, suggesting a high degree of CpG-rich restriction site clustering. Thirty chromosome 11q-specific cosmids containing rare CpG-rich restriction sites were regionally localized by high-resolution fluorescence in situ suppression hybridization, demonstrating that all of the CpG-rich sites detected by this method were located in bands 11q13 and 11q23. In addition, the distribution of (CA)n repetitive sequences was determined by hybridization of the arrayed cosmid library with oligonucleotide probes, confirming a random distribution of microsatellites among CpG-rich cosmid clones. This set of reagent cosmid clones will be useful for physical linking of large restriction fragments detected by pulsed-field gel electrophoresis and will provide a new and highly efficient approach to the construction of a physical map of human chromosome 11q.

Chromosomes, Human, Pair 11↗
PubMed2001

Sequence and structure of the mouse gene for RPE65.

PURPOSE: To determine the genomic organization of the mouse gene for the retinal pigment epithelium (RPE) specific protein RPE65. METHODS: A genomic clone containing the entire Rpe65 gene was isolated from a mouse genomic P1 library. Fragments of this clone were subcloned and sequenced by automated fluorescent dideoxy DNA sequencing and analyzed. Direct sequencing of PCR amplification products was used to complete the structure. Primer extension analysis was used to determine the transcription start site. RESULTS: Southern hybridization of restriction digests of mouse genomic DNA reveals a likely single autosomal gene for Rpe65 with no evidence of pseudogenes. Sequence analysis of the mouse P1 clone for Rpe65 and fragments thereof reveals 14 exons distributed over 27 kbp. The transcription start site is located 57 bp upstream of the initiation codon. The protein encoded by the mouse Rpe65 gene is highly conserved when compared with RPE65s from other species. CONCLUSIONS: RPE65 is a highly conserved protein and it appears that the genes for the mouse and human RPE65s, at least, are also conserved in overall structure.

Amino Acid Sequence↗
PubMed2001

Full-length cDNAs: more than just reaching the ends.

The development of functional genomic resources is essential to understand and utilize information generated from genome sequencing projects. Central to the development of this technology is the creation of high-quality cDNA resources and improved technologies for analyzing coding and noncoding mRNA sequences. The isolation and mapping of cDNAs is an entrée to characterizing the information that is of significant biological relevance in the genome of an organism. However, a bottleneck is often encountered when attempting to bring to full-length (or at least full-coding) a number of incomplete cDNAs in parallel, since this involves the nonsystematic, time consuming, and labor-intensive iterative screening of a number of cDNA libraries of variable quality and/or directed strategies to process individual clones (e.g., 5' rapid amplification of cDNA ends). Here, we review the current state of the art in cDNA library generation, as well as present an analysis of the different steps involved in cDNA library generation.

Automation↗