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PubMed1985

Evaluation of a benchtop capillary gas chromatograph-mass spectrometer for clinical toxicology.

We evaluated the Hewlett-Packard 5995B benchtop capillary gas chromatograph-mass spectrometer (GC-MS) for its ability to identify drugs commonly detected and (or) measured in the clinical toxicology laboratory. Initial experiments indicated that the instrument as originally configured, with an isolation valve between the gas chromatograph and mass spectrometer, was unsatisfactory for the identification of hypnotics-sedatives. However, with the capillary inserted directly into the ion source, we could detect 10 ng of these drugs on a total-ion chromatogram. The software programs cause the instrument to be highly automated. In terms of ease of operation and speed it was found suitable for use in a routine clinical laboratory. Chromatography of urine extracts on the capillary gas chromatograph-mass spectrometer yielded excellent resolution of parent compounds and metabolites (e.g., diphenhydramine together with approximately four metabolites and propoxyphene with four metabolites). However, the manufacturer's computer program used to evaluate the quality of the match between the experimental mass spectra and the 375 drug reference spectra was only moderately successful in identifying unknown compounds. The ability of this capillary GC-MS to identify most compounds with a high degree of confidence will be increased by enlarging the library to include more drugs and metabolites and by using a more reliable computerized matching program.

Diphenhydramine↗

PubMed2003

Analysis of event-related fMRI data using best clustering bases.

We explore a new paradigm for the analysis of event-related functional magnetic resonance images (fMRI) of brain activity. We regard the fMRI data as a very large set of time series x(i)(t), indexed by the position i of a voxel inside the brain. The decision that a voxel i0 is activated is based not solely on the value of the fMRI signal at i0, but rather on the comparison of all time series x(i)(t) in a small neighborhood Wi0 around i0. We construct basis functions on which the projection of the fMRI data reveals the organization of the time-series x(i)(t) into "activated", and "non-activated" clusters. These "clustering basis functions" are selected from large libraries of wavelet packets according to their ability to separate the fMRI time-series into the activated cluster and a non activated cluster. This principle exploits the intrinsic spatial correlation that is present in the data.

Algorithms↗

PubMed1991

Application of robotics and image processing to automated colony picking and arraying.

We describe a system that applies image processing and robotic techniques to automatically pick individual colonies from square petri dishes and array them in 96-well microtiter plates. Digital images of the colony distribution in the dishes are acquired using a video camera and frame buffer. Commercial image processing software is used to identify individual colonies and determine their locations. A Hewlett-Packard Microassay System robot reads the resulting coordinate file for each dish, picks cells from each identified colony and transfers the cells into a microtiter plate well. A disposable pipet tip is used as the sterile implement for colony picking. Custom holders position the dishes accurately and provide common coordinate systems for imaging and picking. The system is calibrated to account for the depth of agar in the dishes. The robot can process up to 10 dishes and 20 plates (1920 colonies) in a single run. It has successfully arrayed a cosmid library of the S. pombe genome consisting of approximately 6000 colonies in 30 petri dishes in about 40 hours of robot time. Future enhancements to the system are discussed.

Cells, Cultured↗

PubMedDate not supplied

The primary structure of a basic (pI 9.0) fatty acid-binding protein from liver of Gallus domesticus.

The complete amino acid sequence of a basic (pI 9.0) fatty acid-binding protein purified from liver of Gallus domesticus was determined by automated Edman degradation of tryptic, CNBr/HFBA and Staphylococcus aureus protease peptides. The protein contains 125 amino acid residues which correspond to a molecular mass of 14094. The identification of the blocked N-terminus Ac-Ala required digestion of a SV-8 peptide with the acylamino acid-releasing enzyme prior to sequence analysis. Sequence comparison shows that chicken liver basic-FABP has a significant similarity to other proteins belonging to the superfamily of intracellular lipid molecule binding proteins. Moreover, these sequence data confirm that basic-FABP probably binds its substrate in a slightly different way when compared with other FABPs. Basic-FABP was submitted to the EMBL Data Library with an accession number of P80226.

Alkalies↗

PubMed2006

Hitting the SPOT: small-molecule macroarrays advance combinatorial synthesis.

The small-molecule macroarray represents a new tool to accelerate combinational library synthesis and screening. This array platform originates from the SPOT-synthesis technique, or the spatially addressed synthesis of peptides on cellulose supports. Recent advances in the field have expanded this technique beyond peptidic systems into the realm of complex small-molecule synthesis. Small-molecule macroarrays offer some significant advantages over traditional combinatorial synthesis platforms--these focused, 50-200 compound arrays are straightforward to synthesize, inexpensive, and amenable to numerous screening applications where the array compounds are either bound to or cleaved from the planar support. Critical advances in the small-molecule macroarray technique are highlighted herein, including the use of microwave-assisted organic reactions, multicomponent reactions, and automated spotting methods to further accelerate and broaden macroarray technology.

Combinatorial Chemistry Techniques↗

PubMed2004

Use of the internet for information and support: disclosure among persons with breast and prostate cancer.

The present study examined the feasibility of evaluating online communication of cancer patients using an automated content analysis program modified for application to cancer-related communication. Public messages posted to the Breast Cancer Discussion List and the Prostate Problems Mailing List were content analyzed uasing an augmented version of Linguistic Inquiry and Word Count to evaluate communication styles within these two cancer types. Breast cancer patients were more likely to submit multiple messages to the list and made greater use of words related to emotional disclosure and cognitive processing compared with prostate cancer patients. Prostate cancer patients were less likely to seek emotional support or repeated interaction with other patients, and more of their communication focused on cancer-related information. Use of cancer-specific word libraries significantly increased word identification within these samples. Content analysis of online communication appears to be a promising method for detecting communication differences among subgroups of cancer patients.

Adult↗

PubMed2000

Analysis of urine for drugs of abuse using mixed-mode solid-phase extraction and gas chromatography-mass spectrometry.

A method for the simultaneous analysis of urine for the major drugs of abuse is described. The analytical procedure uses solid-phase extraction (SPE), gas chromatography-mass spectrometry (GC-MS) and a semi-automated identification process. It allows simultaneous extraction, derivatization and analysis of acidic, neutral and basic drugs from urine. Urine samples were subjected to enzymatic hydrolysis followed by SPE using Bakerbond narc-2 columns. The eluant was selectively derivatized with N-methyl-bis-trifluoroacetamide (MBTFA) and N-methyl-N-trimethylsilyltrifluoroacetamide + 1% trimethylchlorosilane. Analysis was performed using a GC-MS system operating in full scan mode. A simple macro programme was written to enhance the mass spectra identification capabilities of the MS software by producing extracted ion chromatograms (EIC) for the drugs of interest. Once a suspect compound was indicated by EIC, the mass spectrum of the compound was searched manually against reference libraries for positive identification and the retention time checked against that of the standard. This procedure has increased both the amount and the reliability of information given to clinicians without increasing the cost per sample. The system has been in routine operation for 24 months, processing up to 40 urine samples per day, with a usual turn-around time of 48 h.

Evaluation Studies as Topic↗

PubMed2003

Comparative analyses of the dynamic properties of the rectum studied by cryo-sections of human cadavers and pelvic CT scans of patients.

Optimization of radiotherapy treatment plans based on dose-volume histograms relies on accurate organ delineation. Hollow organs, such as the rectum, are difficult and time-consuming to delineate owing to unclear visualization of the border between wall tissue and filling. Automated hollow organ delineation would be a valuable tool, but its development depends upon improved understanding of the dynamics of the rectum in response to filling. Two reasonable assumptions proposed in the literature are that (1) the rectal wall tissue along a constant length of the rectal cylinder is preserved over time and (2) the rectal wall tissue is distributed homogeneously along the cylinder. Therefore, variations in wall thickness can be explained by variable rectal filling. To investigate these assumptions, transversal cross-sectional areas enclosed by the outer contour (A(out)) and inner contour (A(in)) of the rectum were recorded from digital photographs of cadaver cryo-sections from the U.S. National Library of Medicine's Visible Human Project. In addition, A(out) and A(in) were recorded from 19 CT scans of 5 of our own patients. The transversal cross-sectional area of the wall of the rectum, A(wall)=A(out)-A(in), was calculated. The data derived both from cryo-sections and repetitive CT scans of patients, revealed that there was a significant correlation between A(wall) and A(out), in contradiction to assumption (1) stated above (male cryo-sections: p<0.001, female cryo-sections: p=0.03, repetitive CT scans p<0.001). Moreover, the mean A(wall) calculated from one CT scan differed significantly from the mean A(wall) from other CT scans and was correlated with the mean A(out), i.e. rectal filling (p<0.001). This finding was confirmed by careful analysis of another study (p=0.001) and opposes assumption (2). Hence, the amount of wall tissue within a constant length of rectum is not preserved over time, but increases with increased filling. This implies that the longitudinal length of the rectum decreases in response to distension of the organ.

Cadaver↗

PubMed2005

Analysis of cellular events using CellCard System in cell-based high-content multiplexed assays.

High-content screening technologies utilize assays that monitor and quantify multiple cellular events. These assays are typically performed on a single cell type with automated microscopy and image analysis. However, in order to better understand the selectivity of a compound across multiple cell lines, these types of assay must be run serially, which is time consuming. The CellCard System developed by Vitra Bioscience enables multiple cell types to be assayed within a single microtiter well, thereby enabling the simultaneous determination of cellular responses across ten cell types. This multiplexed approach could address the demand for assay capacity, increase the quality of the biologic data, reduce timelines, and improve cost-effectiveness in hit identification and lead evaluation. The authors have carried out an in-depth evaluation of this technology platform using ten cancer cell lines and a library of compounds that affect cellular growth through different mechanisms. Multiple assays were used to investigate the compound effects on membrane integrity, cell cycle progression and apoptosis. In this technology review, the authors discuss personal experience with assay validation, data analysis, results such as cell type-specific compound effects, and the potential application of the CellCard System in drug discovery.

Biological Assay↗

PubMed2002

Robust and sensitive nylon hybridization membrane suitable for high-throughput robotic arraying applications.

An important aspect of automated macroarraying is the suitability of the nylon membrane selected on which samples are to be arrayed. PerForma is a positively charged nylon membrane that has been developed specificallyfor automated macroarraying. Tests usingfluorescent hybridization detection methods have shown that immobilized DNA amounts as low as 0.25 pg can be detected and that positive signals are obtainable after 21 stripping cycles. This report describes the improved colony growth, improved handling characteristics, increased hybridization detection sensitivity, and increased stripping and reprobing capability obtained using PerForma.

Cells, Cultured↗

PubMed2006

bioNMF: a versatile tool for non-negative matrix factorization in biology.

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at http://www.dacya.ucm.es/apascual/bioNMF.

Algorithms↗

PubMed2000

Coherent membrane supports for parallel microsynthesis and screening of bioactive peptides.

Since its invention the SPOT-synthesis methodology has become one of the most efficient strategies for the miniaturized assembly of large numbers of peptides. The combination of a facile synthetic method with high throughput solid- and solution-phase screening assays qualifies the SPOT-technique as a valuable tool in biomedical research. Recent developments such as the introduction of novel polymeric surfaces, new linker and cleavage strategies as well as automated robot systems extended the scope of practical chemical reactions that can be accommodated as well as the numbers of compounds obtainable by this technique. Thus, highly complex spatially addressed compound arrays have become accessible. Together with the introduction of novel screening assays, the method is excellently suited to elucidate recognition events on the molecular level.

Adsorption↗

PubMed2003

GAMOLA: a new local solution for sequence annotation and analyzing draft and finished prokaryotic genomes.

Laboratories working with draft phase genomes have specific software needs, such as the unattended processing of hundreds of single scaffolds and subsequent sequence annotation. In addition, it is critical to follow the "movement" and the manual annotation of single open reading frames (ORFs) within the successive sequence updates. Even with finished genomes, regular database updates can lead to significant changes in the annotation of single ORFs. In functional genomics it is important to mine data and identify new genetic targets rapidly and easily. Often there is no need for sophisticated relational databases (RDB) that greatly reduce the system-independent access of the results. Another aspect is the internet dependency of most software packages. If users are working with confidential data, this dependency poses a security issue. GAMOLA was designed to handle the numerous scaffolds and changing contents of draft phase genomes in an automated process and stores the results for each predicted ORF in flatfile databases. In addition, annotation transfers, ORF designation tracking, Blast comparisons, and primer design for whole genome microarrays have been implemented. The software is available under the license of North Carolina State University. A website and a downloadable example are accessible under (http://fsweb2.schaub. ncsu.edu/TRKwebsite/index.htm).

Algorithms↗

PubMed1991

A mechanism for maintaining an up-to-date GenBank database via Usenet.

In this paper, we describe an automated system for distributing updates to the GenBank nucleic acid sequence database, using the Usenet news system as the underlying transport mechanism. Our system allows new loci to be distributed as soon as the sequences are available, over existing networks, using existing Usenet software and infrastructure currently available on a wide range of computer systems.

Amino Acid Sequence↗

PubMed1994

Facial plastic surgery database.

Every facial plastic surgeon accumulates a vast library of professional slides and photographs that document his work. Manual cataloguing of the clinical and operative documentation is time consuming and provides limited analysis capabilities. The facial plastic surgery database is a state-of-the-art computer programme that allows the surgeon to sort and locate slides and photographs. Designed for the computer novice, it utilises a simple coding system to permit rapid data input. The codes can be tailored to allow for new procedures or alternative practice styles. There are sophisticated searching routines to quickly find slides and photographs based on any combination of patients and operative criteria. The database also includes an online colour atlas and workspace for recording of presentations. There are automated routines to analyse patients' clinical features, operative trends, and surgical results. Ultimately, examination of this data can be used to facilitate peer review, research, and self-education.

Databases, Factual↗

PubMed2000

Automating parallel implementation of neural learning algorithms.

Neural learning algorithms generally involve a number of identical processing units, which are fully or partially connected, and involve an update function, such as a ramp, a sigmoid or a Gaussian function for instance. Some variations also exist, where units can be heterogeneous, or where an alternative update technique is employed, such as a pulse stream generator. Associated with connections are numerical values that must be adjusted using a learning rule, and and dictated by parameters that are learning rule specific, such as momentum, a learning rate, a temperature, amongst others. Usually, neural learning algorithms involve local updates, and a global interaction between units is often discouraged, except in instances where units are fully connected, or involve synchronous updates. In all of these instances, concurrency within a neural algorithm cannot be fully exploited without a suitable implementation strategy. A design scheme is described for translating a neural learning algorithm from inception to implementation on a parallel machine using PVM or MPI libraries, or onto programmable logic such as FPGAs. A designer must first describe the algorithm using a specialised Neural Language, from which a Petri net (PN) model is constructed automatically for verification, and building a performance model. The PN model can be used to study issues such as synchronisation points, resource sharing and concurrency within a learning rule. Specialised constructs are provided to enable a designer to express various aspects of a learning rule, such as the number and connectivity of neural nodes, the interconnection strategies, and information flows required by the learning algorithm. A scheduling and mapping strategy is then used to translate this PN model onto a multiprocessor template. We demonstrate our technique using a Kohonen and backpropagation learning rules, implemented on a loosely coupled workstation cluster, and a dedicated parallel machine, with PVM libraries.

Algorithms↗

PubMedDate not supplied

High-throughput investigation of osteoblast response to polymer crystallinity: influence of nanometer-scale roughness on proliferation.

A high-throughput method for analyzing cellular response to crystallinity in a polymer material is presented. Variations in crystallinity lead to changes in surface roughness on nanometer length scales, and it is shown that cells are exquisitely sensitive to these changes. Gradients of polymer crystallinity were fabricated on films of poly(L-lactic acid) using a gradient in annealing temperature. The resultant morphologies were characterized using an atomic force microscope. Root-mean-square (rms) roughness values ranging from 0.5 to 13 nm were created on a single sample. MC3T3-E1 osteoblastic cells were cultured for 1, 3 and 5 d, and the number of cells was measured using automated fluorescence microscopy. It is shown that the rate of proliferation on the smooth regions of the films is much greater than that on the rough regions, and a monotonic variation in rate is observed as a function of roughness. The critical rms roughness, above which a statistically significant reduction in rate of proliferation occurs, was approximately 1.1 nm. Fluorescence microscopy measurements on immunostained cells indicate there is no significant change in cell area, the number or type of adhesions formed, or the degree of actin polymerization. Results from enzyme-linked immunofluorescence assays indicated that there was no detectable change in adhesion protein accessibility, suggesting the cells directly respond to substrate topography. The use of the gradient library approach yielded the functional dependence of cell proliferation on nanometer-scale roughness and gave a sensitive estimate of the critical roughness for which a decrease in proliferation is observed.

3T3 Cells↗

PubMedDate not supplied

Multimedia in the radiology environment: current concept.

Multimedia has different meanings according to its context. Here, multimedia in the radiology environment is defined as the integration of multiple radiology and medical information systems to facilitate the practice of radiology. These information systems include the hospital information system, radiology information system, picture archiving and communication systems, voice reporting, library information systems, and electronic mail and file systems. The concept of multimedia within the context of integration of these database systems will be presented. An example is given on how to access these information systems by a radiologist's desktop personal computer.

Database Management Systems↗