SEARCH · PubMed Health

Results for “Unique interface”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,783 records · Page 99Linked to original sources

PubMed2005

Digital microfluidics using soft lithography.

Although microfluidic chips have demonstrated basic functionality for single applications, performing varied and complex experiments on a single device is still technically challenging. While many groups have implemented control software to drive the pumps, valves, and electrodes used to manipulate fluids in microfluidic devices, a new level of programmability is needed for end users to orchestrate their own unique experiments on a given device. This paper presents an approach for programmable and scalable control of discrete fluid samples in a polydimethylsiloxane (PDMS) microfluidic system using multiphase flows. An immiscible fluid phase is utilized to separate aqueous samples from one another, and a novel "microfluidic latch" is used to precisely align a sample after it has been transported a long distance through the flow channels. To demonstrate the scalability of the approach, this paper introduces a "general-purpose" microfluidic chip containing a rotary mixer and addressable storage cells. The system is general purpose in that all operations on the chip operate in terms of unit-sized aqueous samples; using the underlying mechanisms for sample transport and storage, additional sensors and actuators can be integrated in a scalable manner. A novel high-level software library allows users to specify experiments in terms of variables (i.e., fluids) and operations (i.e., mixes) without the need for detailed knowledge about the underlying device architecture. This research represents a first step to provide a programmable interface to the microfluidic realm, with the aim of enabling a new level of scalability and flexibility for lab-on-a-chip experiments.

Computers↗

PubMed2005

GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists.

Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for computational genome-wise analyses. We developed and made available through GFINDer web server an original approach for the analysis of genetic disorder related genes by exploiting the information on genetic diseases and their clinical phenotypes present in textual form within the Online Mendelian Inheritance in Man (OMIM) database. Because several synonyms for the same name and different names for overlapping concepts are often used in OMIM, we first normalized phenotype location descriptions reducing them to a list of unique controlled terms representing phenotype location categories. Then, we hierarchically structured them and the correspondent genetic diseases according to their topology and granularity of description, respectively. Thus, in GFINDer we could implement specific Genetic Disorders modules for the analysis of these structured data. Such modules allow to automatically annotate user-classified gene lists with updated disease and clinical information, classify them according to the genetic syndrome and the phenotypic location categories, and statistically identify the most relevant categories in each gene class. GFINDer is available for non-profit use at http://www.bioinformatics.polimi.it/GFINDer/.

Data Interpretation, Statistical↗

PubMed2006

EMAGE: a spatial database of gene expression patterns during mouse embryo development.

EMAGE (http://genex.hgu.mrc.ac.uk/Emage/database) is a freely available, curated database of gene expression patterns generated by in situ techniques in the developing mouse embryo. It is unique in that it contains standardized spatial representations of the sites of gene expression for each gene, denoted against a set of virtual reference embryo models. As such, the data can be interrogated in a novel and abstract manner by using space to define a query. Accompanying the spatial representations of gene expression patterns are text descriptions of the sites of expression, which also allows searching of the data by more conventional text-based methods.

Animals↗

PubMedDate not supplied

Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires.

Studies of antibodies of known three-dimensional structure have revealed that insertion and deletion of amino acids at the hypervariable loops change the canonical structures, thus generating differences in the antigen-binding site topography. Such differences determine the size of the antigen with which the antibody interacts. Here, 59 unique antibodies determined at a resolution of 3.0 A or below, including 19 in complex with proteins, 18 with peptides and 22 with haptens, were analyzed to identify and characterize differences in the residues that are directly involved in the interaction with antigen, so-called specificity-determining residues (SDRs). It was found that antibodies use a similar number of SDRs to recognize proteins and peptides but contact haptens with five SDRs less. By using a score of SDR usage, differences in the location of the SDRs, depending on the type of antigen recognized, were then identified with precision. An analysis of the surface generated by the SDRs usage indicates that the differences found correlate well with the size of the antigen. Anti-protein antibodies have the largest SDR surface, with SDRs of high usage located in the edge of the surface. The SDR surface of anti-hapten antibodies is the smallest, with hot spots of contacts in the interior of the binding surface and buried in the V(L):V(H) interface. The SDR surface of anti-peptide antibodies has a size in between anti-protein and anti-hapten antibodies, with the SDRs of high usage located in the interior of the antigen-binding site but do not buried as in anti-hapten antibodies. These findings led to a fine-tuning of the model correlating differences in the antigen-binding site topography with its preference to recognize antigens of different size. Therefore, it is discussed how this knowledge should help to design antibody repertoires biased toward the recognition of antigens of predefined size.

Amino Acid Sequence↗

PubMedDate not supplied

Determination of burn depth with noncontact ultrasonography.

Early excision and grafting is the current treatment of choice for deep dermal and full-thickness burn wounds that will not heal spontaneously within 3 weeks. The time needed for the burn wound to heal is estimated with clinical assessment of the burn depth; this is often an inaccurate method. Therefore we have developed a new and unique noncontact ultrasonographic method to estimate burn depth. This study was designed to determine the practical utility and accuracy of noncontact ultrasonography for the assessment of burn depth. Seventy-eight burn sites and 42 normal skin sites (control sites) of 15 patients (age, 18-63 years) with burns of 2% to 35% total body surface area were evaluated. The burn sites were scanned with a prototype noncontact ultrasonographic system 1 and 3 days after the burn injuries. The probe was held 1 inch from the skin, and the time spent on each site was approximately 5 minutes. The ultrasonographic results were interpreted by an investigator who was blinded to the clinical findings. Clinical assessment of the burn wounds was made on the same days by 2 experienced physicians who were blinded to the results of the ultrasonography. The investigators were asked to categorize the burn wounds into those that would heal within 3 weeks and those that would not. With this method, we were able to visualize the epidermis, dermis, and dermal-fat interface in normal skin. The destruction of the dermal-fat interface was interpreted as a deep burn, which would not heal within 3 weeks. The overall accuracy of the noncontact ultrasonography in the prediction of which burn wounds would heal within 3 weeks was 96%. The results of this study show that noncontact ultrasonography will allow for the rapid evaluation of burn depth with high accuracy, without contacting the patient, and without causing pain or discomfort.

Adult↗

PubMed1996

Kinetics and crystallographic analysis of human glutathione reductase in complex with a xanthene inhibitor.

We have determined the crystal structure of a complex between the noncompetitive inhibitor (Kis = 27 microM, Kii = 48 microM with respect to oxidized glutathione (GSSG) and Kis = 144 microM, Kii = 176 microM with respect to NADPH) 6-hydroxy-3-oxo-3H-xanthene-9-propionic acid (XAN) and human glutathione reductase (hGR). The structure, refined to an R-factor of 0.158 at 2.0 A resolution, reveals XAN bound in the large cavity present at the hGR dimer interface where it does not overlap the glutathione binding site. The inhibitor binding causes extensive local structural changes that primarily involve amino acid residues from a 30-residue alpha-helix that lines the cavity and contributes to the active site of hGR. Despite the lack of physical overlap of XAN with the GSSG binding site, no GSSG binding is seen in soaks carried out with high XAN and GSSG concentrations, suggesting that some subtle interaction between the sites exists. An earlier crystallographic analysis on the complex between hGR and 3,7-diamino-2,8-dimethyl-5-phenyl-phenazinium chloride (safranin) showed that safranin bound at this same site. We have found that safranin also inhibits hGR in a noncompetitive fashion, but it binds about 16 times less tightly (Kis = 453 microM, Kii = 586 microM with respect to GSSG) than XAN and does not preclude the binding of GSSG in the crystal. Although in structure-based drug design competitive inhibitors are usually targetted, XAN's binding to a well defined site that is unique to glutathione reductase suggests that noncompetitive inhibitors could also serve as lead compounds for structure-based drug design, in particular as components of chimeric inhibitors.

Binding Sites↗

PubMed2002

EXProt--a database for EXPerimentally verified Protein functions.

EXProt (database for EXPerimentally verified Protein functions) is a new non-redundant database containing protein sequences for which the function has been experimentally verified. It is a selection of 3976 entries from the Prokaryotes section of the EMBL Nucleotide Sequence Database, Release 66, and 375 entries from the Pseudomonas Community Annotation Project (PseudoCAP). The entries in EXProt all have a unique ID number and provide information about the organism, protein sequence, functional annotation, link to entry in original database, and if known, gene name and link to references in PubMed/Medline. The EXProt web page (http://www.cmbi.nl/EXProt) provides further details of the database and a link to a BLAST search (blastp & blastx) of the database. The EXProt entries are indexed in SRS (http://www.cmbi.nl/srs/) and can be searched by means of keywords. Authors can be reached by email (exprot(cmbi.kun.nl).

Amino Acid Sequence↗

PubMed2000

Surface and bulk modifications to photocrosslinked polyanhydrides to control degradation behavior.

A unique class of surface-eroding polyanhydrides was developed and explored for use in medical applications requiring high-strength biomaterials (e.g., orthopedics). In particular, dimethacrylated anhydride monomers were synthesized that photopolymerize quickly to render densely crosslinked polymer networks that degrade from the surface only by hydrolysis of labile anhydride linkages. Previous research on these materials has shown that the rate of hydrolysis of the degradable linkages is dependent on the hydrophobicity of the network composition. This article demonstrates the versatility in controlling the degradation process and resulting cellular response in these materials through the incorporation of new chemistries and the formation of polymer-polymer composite structures. Specifically, the rate of mass loss was controlled by the addition of hydrophobic linear polymers [e.g., poly(methyl methacrylate)] or monovinyl monomers based on hydrophobic natural components (e.g., cholesterol, steric acid). In addition, a newly established photografting method was used to modify the network surface chemistry with cholesterol- and stearic acid-based polymer grafts to control the degradation front and cellular interactions at the polymer-tissue interface. Finally, a porogen leaching method was used to form porous polyanhydride constructs, which can be subsequently filled with osteoblasts photoencapsulated in a hydrogel, as potential synthetic allograft materials for tissue engineering bone.

Anhydrides↗

PubMed2002

Development of a web-based SEM specifically for K-12 education.

The scanning electron microscope (SEM) is uniquely suited for use in education due to its ability to produce clear three-dimensional-looking images of virtually any sample. Elementary and secondary science textbooks regularly contain SEM images of bugs, plants, human tissue, rocks, etc. as a means of illustrating the microscopic world to students. However, despite the widespread use of SEM images for educational purposes microscope companies have virtually ignored the area of education in their development and design of SEMs, due presumably to a perceived lack of marketing potential in this area. This article presents the results of a program aimed at developing a Web-based SEM that is specifically designed for educational use by students and teachers in pre-college classrooms. While virtually all companies tout some form of remote control, no concerted effort has been made to fully develop these capabilities for use by the education sector. The microscope under development, termed the WebSEM, seeks to remedy this situation and address this neglected market. Remote control of the WebSEM is possible by means of a simple web interface that allows the users a wide range of controls, depending on the skill of the operator at the remote site. The web interface is specifically designed to be simple and reliable such that little or no training is required for use. This joint effort between educators and a microscope manufacturer is the first attempt at the development of a truly education-oriented SEM suitable for use in the classroom.

Computer-Assisted Instruction↗

PubMed2003

Neuroactive steroids: mechanisms of action and neuropsychopharmacological properties.

Steroids influence neuronal function through binding to cognate intracellular receptors which may act as transcription factors in the regulation of gene expression. In addition, certain so-called neuroactive steroids modulate ligand-gated ion channels via non-genomic mechanisms. Especially distinct 3alpha-reduced metabolites of progesterone and deoxycorticosterone are potent positive allosteric modulators of gamma-aminobutyric acid type A (GABA(A)) receptors. However, also classical steroid hormones such as 17beta-estradiol, testosterone and progesterone are neuroactive steroids because they may act as functional antagonists at the 5-hydroxytryptamine type 3 (5-HT(3)) receptor, a ligand-gated ion channel or distinct glutamate receptors. A structure-activity relationship for the actions of a variety of steroids at the 5-HT(3) receptor was elaborated that differed considerably from that known for GABA(A) receptors. Although a bindings site for steroids at GABA(A) receptors is still a matter of debate, meanwhile there is also evidence that steroids interact allosterically with ligand-gated ion channels at the receptor membrane interface. On the other hand, also 3alpha-reduced neuroactive steroids may regulate gene expression via the progesterone receptor after intracellular oxidation into 5alpha-pregnane steroids. Animal studies showed that progesterone is converted rapidly into GABAergic neuroactive steroids in vivo. Progesterone reduces locomotor activity in a dose-dependent fashion in male Wistar rats. Moreover, progesterone and 3alpha-reduced neuroactive steroids produce a benzodiazepine-like sleep EEG profile in rats and humans. During major depression, there is a disequilibrium of such 3alpha-reduced neuroactive steroids which is corrected by successful treatment with antidepressant drugs. Neuroactive steroids may further be involved in the treatment of depression and anxiety with antidepressants in patients during ethanol withdrawal. Studies in patients with panic disorder suggest that neuroactive steroids may also play a role in modulating human anxiety. Both the genomic and non-genomic effects of steroids in the brain may contribute to the pathophysiology of psychiatric disorders and the mechanisms of action of antidepressants. Neuroactive steroids affect a broad spectrum of behavioral functions through their unique molecular properties and may represent a new treatment strategy for neuropsychiatric disorders.

Anesthesia↗

PubMed1986

Polysulfone corneal lenses.

Polysulfone is a thermoplastic compound first synthesized in 1965. A unique characteristic of polysulfone is its high refractive index (1.633), which allows very thin optical lenses to be manufactured. Over the last five years, D. Peter Choyce has surgically implanted over 40 polysulfone lenses into eyes of his patients. Analysis of his data indicates that polysulfone intraocular lenses are capable of correcting large refractive errors. Based on his work, a multicenter study was undertaken to evaluate the safety and efficacy of polysulfone as an intracorneal lens material in laboratory models. Four monkeys, eight baboons, and 24 cats were used as laboratory models; 5.0-mm to 6.0-mm diameter hyperopic (+28.5 diopter) and myopic (-17.0 and -25.5 diopter) lenses were surgically implanted within the corneal stroma in one eye of each of the laboratory models while a sham lamellar dissection was performed in the other eye. One hundred percent (4/4) of monkey eyes, 12.5% (1/8) of baboon eyes, and 70.0% (18/24) of cat eyes maintained clear media by ophthalmoscopic examination at follow-ups ranging from three to six months. Complications included both visually and nonvisually significant interface opacities, lens extrusion, anterior corneal necrosis, refractile particles, and epithelial thinning.

Animals↗

PubMed2004

Structural analysis of the human Golgi-associated plant pathogenesis related protein GAPR-1 implicates dimerization as a regulatory mechanism.

The plant pathogenesis related proteins group 1 (PR-1) and a variety of related mammalian proteins constitute a PR-1 protein family that share sequence and structural similarities. GAPR-1 is a unique family member as thus far it is the only PR-1 family member that is not co-translationally targeted to the lumen of the endoplasmic reticulum before trafficking to either vacuoles or secretion. Here we report that GAPR-1 may form dimers in vitro and in vivo, as determined by yeast two-hybrid screening, biochemical and biophysical assays. The 1.55A crystal structure demonstrates that GAPR-1 is structurally homologous to the other PR-1 family members previously solved (p14a and Ves V 5). Through an examination of inter-molecular interactions between GAPR-1 molecules in the crystal lattice, we propose a number of the highly conserved amino acid residues of the PR-1 family to be involved in the regulation of dimer formation of GAPR-1 with potential implications for other PR-1 family members. We show that mutagenesis of these conserved amino acid residues leads to a greatly increased dimer population. A recent report suggests that PR-1 family members may exhibit serine protease activity and further examination of the dimer interface of GAPR-1 indicates that a catalytic triad similar to that of serine proteases may be formed across the dimer interface by residues from both molecules within the dimer.

Amino Acid Sequence↗

PubMed2002

A model for the structure of the Escherichia coli SOS-regulated UmuD2 protein.

The ubiquitous Y-family of DNA polymerases, exemplified by the Escherichia coli UmuC protein (the catalytic subunit of DNA Pol V), possess the remarkable ability to replicate imperfect DNA templates that cannot be replicated by other types of DNA polymerases. Since this ability comes at the cost of a reduced fidelity, it is important that organisms manage these unique polymerases to coordinate their actions with those of the replication machinery. In E. coli, it is becoming evident that a sophisticated series of protein-protein interactions involving the two forms of the umuD gene product, UmuD and UmuD' and components of the replicative DNA polymerase serve to manage the actions of the umuC-encoded DNA polymerase. The purpose of this study was to better understand how structural differences between UmuD2 and UmuD2' help to determine which biological role the umuDC gene products will play; the UmuD2C complex functions as a DNA damage checkpoint effector, while the UmuD2'C complex participates in translesion DNA synthesis, which serves as the mechanistic basis for most chemical and UV light mutagenesis. Based on the results of a combination of disulfide cross-linking experiments, measurements of solvent accessibility and electron paramagnetic spin resonance (EPR) studies, we have developed a refined model for the structure of the UmuD2 homodimer. In the model that we are proposing, the N-terminal arms of UmuD (residues 1-39) form an extended interface in the UmuD2 homodimer by folding down over the globular domains of their intradimer partners. As a result, significant portions of the surface of each globular domain are buried in the UmuD2 homodimer. Based on the structure of the UmuD2' homodimer, both in the crystal and in solution, these same surfaces are exposed. Implications of these structural differences between the UmuD2 and the UmuD2' homodimers with respect to their roles in managing the actions of the umuC-encoded DNA polymerase are discussed.

Binding Sites↗

PubMed2003

Crystal structure of Escherichia coli thiol peroxidase in the oxidized state: insights into intramolecular disulfide formation and substrate binding in atypical 2-Cys peroxiredoxins.

Thioredoxin-dependent thiol peroxidase (Tpx) from Escherichia coli represents a group of antioxidant enzymes that are widely distributed in pathogenic bacterial species and which belong to the peroxiredoxin (Prx) family. Bacterial Tpxs are unique in that the location of the resolving cysteine (CR) is different from those of other Prxs. E. coli Tpx (EcTpx) shows substrate specificity toward alkyl hydroperoxides over H2O2 and is the most potent reductant of alkyl hydroperoxides surpassing AhpC and BCP, the other E. coli Prx members. Here, we present the crystal structure of EcTpx in the oxidized state determined at 2.2-A resolution. The structure revealed that Tpxs are the second type of atypical 2-Cys Prxs with an intramolecular disulfide bond formed between the peroxidatic (CP, Cys61) and resolving (Cys95) cysteine residues. The extraordinarily long N-terminal chain of EcTpx folds into a beta-hairpin making the overall structure very compact. Modeling suggests that, in atypical 2-Cys Prxs, the CR-loop as well as the CP-loop may alternately assume the fully folded or locally unfolded conformation depending on redox states, as does the CP-loop in typical 2-Cys Prxs. EcTpx exists as a dimer stabilized by hydrogen bonds. Its substrate binding site extends to the dimer interface. A modeled structure of the reduced EcTpx in complex with 15-hydroperoxyeicosatetraenoic acid suggests that the size and shape of the binding site are particularly suited for long fatty acid hydroperoxides consistent with its greater reactivity.

Amino Acid Sequence↗

PubMed2006

Chronic neural recordings using silicon microelectrode arrays electrochemically deposited with a poly(3,4-ethylenedioxythiophene) (PEDOT) film.

Conductive polymer coatings can be used to modify traditional electrode recording sites with the intent of improving the long-term performance of cortical microelectrodes. Conductive polymers can drastically decrease recording site impedance, which in turn is hypothesized to reduce thermal noise and signal loss through shunt pathways. Moreover, conductive polymers can be seeded with agents aimed at promoting neural growth toward the recording sites or minimizing the inherent immune response. The end goal of these efforts is to generate an ideal long-term interface between the recording electrode and surrounding tissue. The goal of this study was to refine a method to electrochemically deposit surfactant-templated ordered poly(3,4-ethylenedioxythiophene) (PEDOT) films on the recording sites of standard 'Michigan' probes and to evaluate the efficacy of these modified sites in recording chronic neural activity. PEDOT-coated site performance was compared to control sites over a six-week evaluation period in terms of impedance spectroscopy, signal-to-noise ratio, number of viable unit potentials recorded and local field potential recordings. PEDOT sites were found to outperform control sites with respect to signal-to-noise ratio and number of viable unit potentials. The benefit of reduced initial impedance, however, was mitigated by the impedance contribution of typical silicon electrode encapsulation. Coating sites with PEDOT also reduced the amount of low-frequency drift evident in local field potential recordings. These findings indicate that electrode sites electrochemically deposited with PEDOT films are suitable for recording neural activity in vivo for extended periods. This study also provided a unique opportunity to monitor how neural recording characteristics develop over the six weeks following implantation.

Action Potentials↗

PubMed2005

ECgene: genome annotation for alternative splicing.

ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. The gene-modeling algorithm combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. The website provides several viewers and applications that have many unique features useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. We also provide two unique ways of analyzing gene expression. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publically. Furthermore, the cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. It should be noted that the ECgene website provides annotation for the whole transcriptome, not just the alternatively spliced genes. Currently, ECgene supports the human, mouse and rat genomes. The ECgene suite of tools and programs is available at http://genome.ewha.ac.kr/ECgene/.

Algorithms↗

PubMedDate not supplied

Combining hierarchy and energy for drawing directed graphs.

We present an algorithm for drawing directed graphs which is based on rapidly solving a unique one-dimensional optimization problem for each of the axes. The algorithm results in a clear description of the hierarchy structure of the graph. Nodes are not restricted to lie on fixed horizontal layers, resulting in layouts that convey the symmetries of the graph very naturally. The algorithm can be applied without change to cyclic or acyclic digraphs and even to graphs containing both directed and undirected edges. We also derive a hierarchy index from the input digraph, which quantitatively measures its amount of hierarchy.

Algorithms↗

PubMed1984

Alveolyn--structure and source: a review.

Alveolyn is a unique secretory glycoprotein of 250,000 molecular weight (MW) that is found in distal pulmonary secretions. Several glycoproteins of 130,000 MW, 80,000 MW, 62,000 MW, and 36,000 MW have also been found to be present in the alveolar secretions, and it was found that these glycoproteins were proteolytic fragments of the much larger molecular glycoprotein. It is also a major protein in human amniotic fluid, presumably a product of alveolar secretions. It is also secreted by a clone of pulmonary fetal type II cells. Preliminary results indicate that two of the proteolytic fragments of 62,000 MW and 36,000 MW contain alternate collagenous and noncollagenous domains in the same polypeptide chain. The presence of collagenous domains in these glycoproteins was also confirmed by their susceptibility to digestion with collagenase and the presence of Gly-Pro-Hyp-Gly-type sequence in the peptide chain. Very little is known about the tertiary structure of the protein, except that its fragments bind phospholipids and probably facilitate transfer of the lipid to air-water interfaces.

Amino Acid Sequence↗