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PubMed1999

The development and evaluation of CADMIUM: a prototype system to assist in the interpretation of mammograms.

We have developed CADMIUM, a novel approach for the design of systems to assist in the interpretation of medical images. CADMIUM uses symbolic reasoning to relate information obtained from image processing to the decisions radiologists take. The approach is based on a symbolic decision procedure which has already been used successfully in a variety of nonimaging clinical decision systems. In CADMIUM this decision procedure is extended with models of three generic image interpretation tasks: detection, measurement and classification of image features. The extended procedure is used to construct the lines of reasoning needed in each task and to control the acquisition of information by image processing. CADMIUM has been evaluated as an aid to the differential diagnosis of microcalcifications on mammographic images. Radiographers who had been trained to interpret images performed better when using the advice provided by the system.

Artificial Intelligence↗
PubMed1999

Inter-individual differences in the metabolism of environmental toxicants: cytochrome P450 1A2 as a prototype.

Cytochrome P450 (P450) 1A2 provides an interesting paradigm for inter-individual differences in the metabolism of pro-carcinogens. The enzyme is known to vary 40-fold among individuals and may contribute to cancers caused by heterocyclic amines and other chemicals. Rat and human P450 1A2 are known to be 75% identical and were compared for several catalytic activities. The human enzyme was an order of magnitude more efficient in the N-hydroxylation of two heterocyclic amines. Further, the levels of P450 1A2 expressed in human livers show a 40-fold variation, with some as high as 0.25 nmol P450 1A2 per milligram microsomal protein. Some human liver samples are more active (than those isolated from polychlorinated biphenyl-treated rats) in the activation of heterocyclic amines. A bacterial genotoxicity assay has been developed in which human P450 1A2 and NADPH-P450 reductase are expressed within Escherichia coli and bacterial mutants can be assayed using reversion to lac prototrophy. A random mutagenesis strategy for human P450 1A2 has been developed and used to examine the changes in catalytic activity seen with many single-amino acid substitutions. These results may be of relevance in consideration of genetic polymorphisms. Further, the findings pose a challenge to molecular epidemiology effort in that results with one substrate do not necessarily predict those for others. Some dinitropyrenes are P450 1A2 substrates but others are not. 6-Nitrochrysene can be activated by human P450 1A2 but the (mono) nitropyrenes examined were not; these were oxidized by P450 3A4 instead.

Amino Acid Substitution↗
PubMed2001

Decision support for infectious diseases--a working prototype.

This paper presents a decision support system for nosocomial infections and its integration in the large HIS of the University Hospital of Giessen. The system comprises five different engines and a data dictionary. It is designed to detect hospital acquired infections even in a situation where only a restricted amount of clinical data is available (the data is split up in different information systems). Furthermore the model prevents time consuming manual data entry. The five engines split the main task into: (1) a preselection, which sorts out patients who definitely do not have a nosocomial infection; (2) a rule based reasoning process which detects patients likely to have such an infection; (3) an alarm process which is responsible for the presentation of the alert; (4) an explanation process to follow up the reasoning; and (5) statistic tools to answer specific hygienic questions. A data dictionary supplies the controlled vocabulary, which is required to understand data structures used in the different clinical subsystems and may those with each other.

Artificial Intelligence↗
PubMed1998

Improving clinical pathway design: lessons learned from a computerised prototype.

Increasing costs of health care, fuelled by demand for high quality, cost-efficient health care has propelled hospitals to restructure their patient care delivery systems. One such effort is the adaptation of an engineering project management methodology, the critical path method (CPM), as a tool to organise, standardise and improve the quality of healthcare delivery and hence patient outcomes. However, the two-dimensional nature and the size of paper impose severe limitations on the manual clinical pathways currently in use by hospitals. This paper analyses these inherent limitations and discusses some of the problems encountered in an attempt in early 1996 to create an electronic care map planner (CMP) based on the precedence diagramming method (PDM) model. It also reports on a current project to create a computerised clinical pathway tool to resolve the identified problems.

Cost-Benefit Analysis↗
PubMed2002

Distinct BH3 domains either sensitize or activate mitochondrial apoptosis, serving as prototype cancer therapeutics.

The "BH3-only" proteins of the BCL-2 family require "multidomain" proapoptotic members BAX and BAK to release cytochrome c from mitochondria and kill cells. We find short peptides representing the alpha-helical BH3 domains of BID or BIM are capable of inducing oligomerization of BAK and BAX to release cytochrome c. Another subset characterized by the BH3 peptides from BAD and BIK cannot directly activate BAX, BAK but instead binds antiapoptotic BCL-2, resulting in the displacement of BID-like BH3 domains that initiate mitochondrial dysfunction. Transduced BAD-like and BID-like BH3 peptides also displayed synergy in killing leukemic cells. These data support a two-class model for BH3 domains: BID-like domains that "activate" BAX, BAK and BAD-like domains that "sensitize" by occupying the pocket of antiapoptotic members.

Animals↗
PubMed1999

Pathbreaking verbs in syntactic development and the question of prototypical transitivity.

The first verbs to participate in VO and SVO combinations, and the temporal parameters of the spread of these combinatory patterns over different verbs were investigated. The longitudinal language observations of 16 children, one acquiring English, the others Hebrew, were examined. The children were observed once a week for 3-12 months, the observations starting when the children were still in the single-word stage (1.1-2.1) and ending when they were well into multiword speech (1.8-2.7). The results indicate that the more verbs children already know to combine in a certain pattern, the faster they learn new ones. Apparently children induce from individual word-combinations some general principles that facilitate further learning. The 'pathbreaking verbs' that begin the acquisition of a novel syntactic rule tend to be generic verbs expressing the relevant combinatorial property in a relatively pure fashion: the same verbs that children first combine with direct objects, are typical grammaticalized markers of transitivity in many languages. These verbs do not have HIGH TRANSITIVITY as defined by Hopper & Thompson (1980). Rather, they express fundamental 'object relations' of incorporation into, and ejection from the personal. Crosslinguistic evidence indicates that this may be the basic transitivity construct in languages. The results raise the possibility that lexical-specific learning of positional patterns is sufficient to account for the formation of syntactic abstractions.

Age Factors↗
PubMed2002

Prototyping of microfluidic devices in poly(dimethylsiloxane) using solid-object printing.

A solid-object printer was used to produce masters for the fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS). The printer provides an alternative to photolithography for applications where features of > 250 microm are needed. Solid-object printing is capable of delivering objects that have dimensions as large as 250 x 190 x 200 mm (x, y, z) with feature sizes that can range from 10 cm to 250 microm. The user designs a device in 3-D in a CAD program, and the CAD file is used by the printer to fabricate a master directly without the need for a mask. The printer can produce complex structures, including multilevel features, in one unattended printing. The masters are robust and inexpensive and can be fabricated rapidly. Once a master was obtained, a PDMS replica was fabricated by molding against it and used to fabricate a microfluidic device. The capabilities of this method are demonstrated by fabricating devices that contain multilevel and tall features, devices that cover a large area (approximately 150 cm2), and devices that contain nonintersecting, crossing channels.

Animals↗
PubMed2002

A prototype two-dimensional capillary electrophoresis system fabricated in poly(dimethylsiloxane).

A method for carrying out 2D gel electrophoresis in a capillary format is presented. In this method, separation in the first dimension is carried out in a 1D capillary, with this system physically isolated from the capillaries that provide the separation in the second dimension. After completion of the first separation, the 1D channel is physically connected to the 2D capillaries, and a second separation is carried out in an orthogonal set of parallel capillaries. The ability of poly(dimethylsiloxane) (PDMS) to support the fabrication of 3D microfluidic systems makes it possible to produce membranes that both enclose the gel used in the first separation in a capillary and provide passages for the proteins to migrate into the array of orthogonal capillaries. The elastomeric nature of PDMS makes it possible to make reversible connections between pieces of PDMS. The feasibility of this system is demonstrated using a protein mixture containing fluorescein-conjugated carbonic anhydrase, fluorescein-conjugated BSA, and Texas Red-conjugated ovalbumin. This work suggests one type of design that might form the basis for a microfabricated device for 2D capillary electrophoresis.

Carbonic Anhydrases↗
PubMed2004

Rapid prototyping of thermoset polyester microfluidic devices.

This paper presents a simple procedure for the fabrication of thermoset polyester (TPE) microfluidic systems and discusses the properties of the final devices. TPE chips are fabricated in less than 3 h by casting TPE resin directly on a lithographically patterned (SU-8) silicon master. Thorough curing of the devices is obtained through the combined use of ultraviolet light and heat, as both an ultraviolet and a thermal initiator are employed in the resin mixture. Features on the order of micrometers and greater are routinely reproduced using the presented procedure, including complex designs and multilayer features. The surface of TPE was characterized using contact angle measurements and X-ray photoelectron spectroscopy (XPS). Following oxygen plasma treatment, the hydrophilicity of the surface of TPE increases (determined by contact angle measurements) and the proportion of oxygen-containing functional groups also increases (determined by XPS), which indicates a correlated increase in the charge density on the surface. Native TPE microchannels support electroosmotic flow (EOF) toward the cathode, with an average electroosmotic mobility of 1.3 x 10(-4) cm(2) V(-1) s(-1) for a 50-microm square channel (20 mM borate at pH 9); following plasma treatment (5 min at 30 W and 0.3 mbar), EOF is enhanced by a factor of 2. This enhancement of the EOF from plasma treatment is stable for days, with no significant decrease noted during the 5-day period that we monitored. Using plasma-treated TPE microchannels, we demonstrate the separation of a mixture of fluorescein-tagged amino acids (glycine, glutamic acid, aspartic acid). TPE devices are up to 90% transparent (for approximately 2-mm-thick sample) to visible light (400-800 nm). The compatibility of TPE with a wide range of solvents was tested over a 24-h period, and the material performed well with acids, bases, alcohols, cyclohexane, n-heptane, and toluene but not with chlorinated solvents (dichloromethane, chloroform).

Microfluidic Analytical Techniques↗
PubMed1999

A prototype electrochemical chromatographic column for use with proteins.

We developed electrochemical hardware and media targeted for protein chromatography. Two types of stationary phases were investigated. The first comprised gold-plated stainless 316L beads coated with a self-assembled monolayer of 6-mercaptohexan-1-ol and was expected to behave like an ion-exchange resin in the presence of an electric field. The secondary stationary phase comprised the first stationary phase with further functionalization with immobilized heme moieties and was expected to behave like immobilized metal affinity resin. We tested apparatus with both stationary phases using ribonuclease A as a model protein and applied potentials from -0.3 to +0.3 V versus the saturated calomel electrode. Despite low binding capacities, we demonstrated that protein retention on both stationary phases could be controlled with an applied potential. The greatest extent of electromodulation was achieved with the mercaptohexanol-based ion-exchange media.

Chromatography↗
PubMed2000

Prototyping of masks, masters, and stamps/molds for soft lithography using an office printer and photographic reduction

This paper describes a practical method for the fabrication of photomasks, masters, and stamps/molds used in soft lithography that minimizes the need for specialized equipment. In this method, CAD files are first printed onto paper using an office printer with resolution of 600 dots/in. Photographic reduction of these printed patterns transfers the images onto 35-mm film or microfiche. These photographic films can be used, after development, as photomasks in 1:1 contact photolithography. With the resulting photoresist masters, it is straightforward to fabricate poly(dimethylsiloxane) (PDMS) stamps/molds for soft lithography. This process can generate microstructures as small as 15 microm; the overall time to go from CAD file to PDMS stamp is 4-24 h. Although access to equipment-spin coater and ultraviolet exposure tool-normally found in the clean room is still required, the cost of the photomask itself is small, and the time required to go from concept to device is short. A comparison between this method and all other methods that generate film-type photomasks has been performed using test patterns of lines, squares, and circles. Three microstructures have also been fabricated to demonstrate the utility of this method in practical applications.

Journal Article↗
PubMed1993

Structure of the altromycin B (N7-guanine)-DNA adduct. A proposed prototypic DNA adduct structure for the pluramycin antitumor antibiotics.

Altromycin B belongs to the pluramycin family of antitumor antibiotics, which also includes kidamycin, hedamycin, pluramycin, neopluramycin, DC92-B, and rubiflavin A. These potent antitumor compounds react with DNA in as yet imprecisely determined ways. In the present investigation, we have used gel electrophoresis methods in combination with nuclear magnetic resonance and mass spectrometry to determine the structure of the altromycin B-DNA adduct. High-resolution gel electrophoresis demonstrated that guanine was the reactive base, and N7 was implicated from experiments in which N7-deazaguanine was used in place of guanine in a strand breakage assay. Experiments using supercoiled DNA demonstrated that altromycin B and related drugs intercalated into DNA, which implicated this as a common mechanism for binding of the pluramycin antibiotics to DNA. The altromycin B-guanine adduct was isolated from calf thymus DNA after thermal depurination of the alkylated DNA. Mass spectrometry confirmed that altromycin alkylated DNA through guanine, and 1H- and 13C-NMR was used to confirm the covalent linkage sites between altromycin B and guanine. On the basis of these results, we propose that altromycin B first intercalates into DNA via a threading mechanism, reminiscent of nogalamycin, to insert the disaccharide into the minor groove and position the epoxide in the major groove in proximity to N7 of guanine. Nucleophilic attack from N7 of guanine leads to an acid-catalyzed opening of the epoxide, resulting in the altromycin B-DNA adduct. On the basis of these results, a general mechanism for the interaction of the pluramycin family of antibiotics with DNA is proposed.

Alkylation↗
PubMed2000

Distinctive cognate sequence discrimination, bound DNA conformation, and binding modes in the E2 C-terminal domains from prototype human and bovine papillomaviruses.

The C-terminal DNA binding domain of the E2 protein is involved in transcriptional regulation and DNA replication in papillomaviruses. At low ionic strength, the domain has a tendency to form aggregates, a process readily reversible by the addition of salt. While fluorescence anisotropy measurements show a 1:1 stoichiometry at pH 5.5, we observed that a second HPV-16 E2 C-terminal dimer can bind per DNA site at pH 7.0. This was confirmed by displacement of bis-ANS binding, tryptophan fluorescence, native electrophoresis, and circular dichroism. The two binding events are nonequivalent, with a high-affinity binding involving one E2C dimer per DNA molecule with a K(D) of 0.18 +/- 0.02 nM and a lower affinity binding mode of 2.0 +/- 0.2 nM. The bovine (BPV-1) E2 C-terminal domain binds to an HPV-16 E2 site with 350-fold lower affinity than the human cognate domain and binds 7-fold less tightly even to a bovine-derived DNA site. The ability to discriminate between cognate and noncognate sequences is 50-fold higher for the human domain, and the latter is 180-fold better than the bovine at discriminating specific from nonspecific DNA. A substantial conformational change in bound DNA is observed by near-UV circular dichroism. The bovine domain imposes a different DNA conformation than that caused by the human counterpart, which could be explained by a more pronounced bent. Structure-function differences and biochemical properties of the complexes depend on the protein domain rather than on the DNA, in line with crystallographic evidence. Despite the strong sequence homology and overall folding topology, the differences observed may explain the distinctive transcriptional regulation in bovine and human viruses.

Adenovirus E2 Proteins↗
PubMed1984

Purification and characterization of the rat liver microsomal cytochrome P-450 involved in the 4-hydroxylation of debrisoquine, a prototype for genetic variation in oxidative drug metabolism.

Genetic polymorphism in oxidative drug metabolism is perhaps best exemplified in the case of debrisoquine 4-hydroxylase activity, where the incidence of deficient metabolism ranges from 1% to 30% in various populations and this defect is also linked to an impaired ability to metabolize a number of other drugs effectively. Sprague-Dawley (SD) rats possess this activity, but females of the DA strain do not, although total cytochrome P-450 (P-450) levels are similar. We have purified, by using debrisoquine 4-hydroxylase activity as an assay, a minor P-450 to electrophoretic homogeneity from male SD rats and designate this as P-450UT-H. P-450UT-H differs from eight other purified rat liver P-450s as judged by peptide mapping and immunochemical analysis and thus appears to be isozymic with these other P-450s. P-450UT-H exhibited considerably more debrisoquine 4-hydroxylase activity than any of the other purified P-450s and, on a total P-450 basis, more than total microsomal P-450. Antibodies raised against P-450UT-H specifically recognized P-450UT-H and inhibited more than 90% of the debrisoquine hydroxylase activity present in SD rat liver microsomes. The level of P-450UT-H in SD rat liver microsomes accounted for less than 10% of the total P-450, as judged by immunochemical quantitation. These assays also indicated that the level of P-450UT-H in female DA rat liver microsomes is only about 5% of that in male or female SD rat liver microsomes, consonant with the view that deficiency of this form of P-450 is responsible for the defective debrisoquine 4-hydroxylase activity in the former animals.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1980

New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures.

A new family of high-affinity buffers and optical indicators for Ca2+ is rationally designed and synthesized. The parent compound is 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), a relative of the well-known chelator EGTA [ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid] in which methylene links between oxygen and nitrogen are replaced by benzene rings. BAPTA and its derivatives share the high (greater than 10(5)) selectivity for Ca2+ over Mg2+ of EGTA but are very much less affected by pH changes and are faster at taking up and releasing Ca2+. The affinity of the parent compound for Ca2+ (dissociation constant 1.1 x 10(-7) M in 0.1 M KCl) may be strengthened or weakened by electron-releasing or -withdrawing substituents on the aromatic rings. The Ca2+ and Mg2+ affinities may further be altered by replacing the ether oxygens by heterocyclic nitrogen atoms. The compounds described are fluorescent Ca2+ indicators absorbing in the ultraviolet region; the very large spectral shifts observed on binding Ca2+ fit the prediction that complexation should hinder the conjugation of the nitrogen lone-pair electrons with the aromatic rings. Derivatives with quinoline nuclei are notable for their high sensitivity of fluorescent quantum yield to the binding of Ca2+ but not of Mg2+. Preliminary biological tests have so far revealed little or no binding to membranes or toxic effects following intracellular microinjection.

Calcium↗
PubMed2001

Monomeric solution structure of the prototypical 'C' chemokine lymphotactin.

Lymphotactin, the sole identified member of the C class of chemokines, specifically attracts T lymphocytes and natural killer cells. This 93-residue protein lacks 2 of the 4 conserved cysteine residues characteristic of the other 3 classes of chemokines and possesses an extended carboxyl terminus, which is required for chemotactic activity. We have determined the three-dimensional solution structure of recombinant human lymphotactin by NMR spectroscopy. Under the conditions used for the structure determination, lymphotactin was predominantly monomeric; however, pulsed field gradient NMR self-diffusion measurements and analytical ultracentrifugation revealed evidence of dimer formation. Sequence-specific chemical shift assignments were determined through analysis of two- and three-dimensional NMR spectra of (15)N- and (13)C/(15)N-enriched protein samples. Input for the torsion angle dynamics calculations used in determining the structure included 1258 unique NOE-derived distance constraints and 60 dihedral angle constraints obtained from chemical-shift-based searching of a protein conformational database. The ensemble of 20 structures chosen to represent the structure had backbone and heavy atom rms deviations of 0.46 +/- 0.11 and 1.02 +/- 0.14 A, respectively. The results revealed that human lymphotactin adopts the conserved chemokine fold, which is characterized by a three-stranded antiparallel beta-sheet and a C-terminal alpha-helix. Two regions are dynamically disordered as evidenced by (1)H and (13)C chemical shifts and [(15)N]-(1)H NOEs: residues 1-9 of the amino terminus and residues 69-93 of the C-terminal extension. A functional role for the C-terminal extension, which is unique to lymphotactin, remains to be elucidated.

Amino Acid Sequence↗