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PubMed2025

Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence.

MOTIVATION: The Open Targets Platform (https://platform.opentargets.org) is a unique, comprehensive, open-source resource supporting systematic identification and prioritisation of targets for drug discovery. The Platform combines, harmonizes and integrates data from >20 diverse sources to provide target-disease associations, covering evidence derived from genetic associations, somatic mutations, known drugs, differential expression, animal models, pathways and systems biology. An in-house target identification scoring framework weighs the evidence from each data source and type, contributing to an overall score for each of the 7.8M target-disease associations. However, the old infrastructure did not allow user-led dynamic adjustments in the contribution of different evidence types for target prioritisation, a limitation frequently raised by our user community. Furthermore, the previous Platform user interface did not support navigation and exploration of the underlying target-disease evidence on the same page, occasionally making the user journey counterintuitive. RESULTS: Here, we describe 'Associations on the Fly' (AOTF), a new Platform feature-developed with a user-centred vision-that enables the user to formulate more flexible therapeutic hypotheses through dynamic adjustment of the weight of contributing evidence from each source, altering the prioritisation of targets. AVAILABILITY AND IMPLEMENTATION: The codebases that power the Platform-including our pipelines, GraphQL API, and React UI-are all open source and licensed under the APACHE LICENSE, VERSION 2.0. You can find all of our code repositories on GitHub at https://github.com/opentargets and on Zenodo at https://zenodo.org/records/14392214. This tool was implemented using React v18 and its code is accessible here: (https://github.com/opentargets/ot-ui-apps). The tools are accessible through the Open Targets Platform web interface (https://platform.opentargets.org/) and GraphQL API (https://platform-docs.opentargets.org/data-access/graphql-api). Data is available for download here: (https://platform.opentargets.org/downloads) and from the EMBL-EBI FTP: (https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/).

Software↗

PubMed2006

Bioelectric properties of chloride channels in human, pig, ferret, and mouse airway epithelia.

The development of effective therapies for cystic fibrosis (CF) requires animal models that can appropriately reproduce the human disease phenotype. CF mouse models have demonstrated cAMP-inducible, non-CF transmembrane conductance regulator (non-CFTR) chloride transport in conducting airway epithelia, and this property is thought to be responsible for the lack of a spontaneous CF-like phenotype in the lung. Thus, an understanding of species diversity in airway epithelial electrolyte transport and CFTR function is critical to developing better models for CF. Two species currently being used in attempts to develop better animal models of CF include the pig and ferret. In the study reported here, we sought to comparatively characterize the bioelectric properties of in vitro polarized airway epithelia--from human, mouse, pig and ferret--grown at the air-liquid interface (ALI). Bioelectric properties analyzed include amiloride-sensitive Na(+) transport, 4,4'-diisothiocyanato-stilbene-2,2'-disulfonic acid (DIDS)-sensitive Cl(-) transport, and cAMP-sensitive Cl(-) transport. In addition, as an index for CFTR functional conservation, we evaluated the ability of four CFTR inhibitors, including glibenclamide, 5-nitro-2-(3-phenylpropyl-amino)-benzoic acid, CFTR (inh)-172, and CFTR(inh)-GlyH101, to block cAMP-mediated Cl(-) transport. Compared with human epithelia, pig epithelia demonstrated enhanced amiloride-sensitive Na(+) transport. In contrast, ferret epithelia exhibited significantly reduced DIDS-sensitive Cl(-) transport. Interestingly, although the four CFTR inhibitors effectively blocked cAMP-mediated Cl(-) secretion in human airway epithelia, each species tested demonstrated unique differences in its responsiveness to these inhibitors. These findings suggest the existence of substantial species-specific differences at the level of the biology of airway epithelial electrolyte transport, and potentially also in terms of CFTR structure/function.

Amino Acid Sequence↗

PubMed2002

A novel soluble analog of the HIV-1 fusion cofactor, globotriaosylceramide (Gb(3)), eliminates the cholesterol requirement for high affinity gp120/Gb(3) interaction.

We have analyzed the interaction of adamantyl Gb(3) (adaGb(3)), a semi-synthetic soluble analog of Gb(3), with HIV-1 surface envelope glycoprotein gp120. In this analog, which was orginally designed to inhibit verotoxin binding to its glycolipid receptor, Gb(3), the fatty acid chain is replaced with a rigid globular hydrocarbon frame (adamantane). Despite its solubility, adaGb(3) forms monolayers at an air-water interface. Compression isotherms of such monolayers demonstrated that the adamantane substitution resulted in a larger minimum molecular area and a more rigid, less compressible film than Gb(3). Insertion of gp120 into adaGb(3) monolayers was exponential whereas the gp120/Gb(3) interaction curve was sigmoidal with a lag phase of 40 min. Adding cholesterol into authentic Gb(3) monolayers abrogated the lag phase and increased the initial rate of interaction with gp120. This effect of cholesterol was not observed with phosphatidylcholine or sphingomyelin. In addition, verotoxin-bound adaGb(3) or Gb(3) plus cholesterol was recovered in fractions of comparable low density after ultracentrifugation through sucrose-density gradients in the presence of Triton X-100. The unique biological and physico-chemical properties of adaGb(3) suggest that this analog may be a potent soluble mimic of Gb(3), providing a novel concept for developing GSL-derived viral fusion inhibitors.

Adamantane↗

PubMed1991

The Medline/full-text research project.

This project was designed to test the relative efficacy of index terms and full-text for the retrieval of documents in those MEDLINE journals for which full-text searching was also available. The full-text files used were MEDIS from Mead Data Central and CCML from BRS Information Technologies. One hundred clinical medical topics were searched in these two files as well as the MEDLINE file to accumulate the necessary data. It was found that full-text identified significantly more relevant articles than did the indexed file, MEDLINE. The full-text searches, however, lacked the precision of searches done in the indexed file. Most relevant items missed in the full-text files, but identified in MEDLINE, were missed because the searcher failed to account for some aspect of natural language, used a logical or positional operator that was too restrictive, or included a concept which was implied, but not expressed in the natural language. Very few of the unique relevant full-text citations would have been retrieved by title or abstract alone. Finally, as of July, 1990 the more current issue of a journal was just as likely to appear in MEDLINE as in one of the full-text files.

Abstracting and Indexing↗

PubMed1992

HOME: highly optimized microscope environment.

The Highly Optimized Microscope Environment (HOME) is a computerized microscope designed to assist pathologists and cytotechnicians in clinical routine tasks. The prototype system consists of a IBM-PC compatible computer and a light microscope in which a built-in high-resolution computer display image is superimposed on the optical image of the specimen. Also, a manually operated encoding stage and objective turret encoder are used to provide continuous monitoring of the stage coordinates and microscope magnification to the computer. This allows any position on a slide to be uniquely defined and makes it possible to measure interactively lengths and areas larger than the size of the microscope field. Software, written in the C language and operating under the MS-DOS/MS-Windows environment, is controlled by means of a mouse-driven cursor moving over menu light-buttons displayed on the microscope image. The HOME microscope workstation is potentially useful in a wide range of applications such as i) tagging information on particular cells and tissue structures that can thus be accurately located and relocated, ii) performing morphometric measurement, differential counting, and stereological assessment of biological specimens, and iii) training and educating laboratory personnel. Finally, HOME will offer in the near future a user-friendly interface for automatic image processing of cells and tissue entities in interactively selected specimen areas.

Animals↗

PubMed2000

Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.

The 2.25 A resolution crystal structure of a pol alpha family (family B) DNA polymerase from the hyperthermophilic marine archaeon Thermococcus sp. 9 degrees N-7 (9 degrees N-7 pol) provides new insight into the mechanism of pol alpha family polymerases that include essentially all of the eukaryotic replicative and viral DNA polymerases. The structure is folded into NH(2)- terminal, editing 3'-5' exonuclease, and polymerase domains that are topologically similar to the two other known pol alpha family structures (bacteriophage RB69 and the recently determined Thermococcus gorgonarius), but differ in their relative orientation and conformation. The 9 degrees N-7 polymerase domain structure is reminiscent of the "closed" conformation characteristic of ternary complexes of the pol I polymerase family obtained in the presence of their dNTP and DNA substrates. In the apo-9 degrees N-7 structure, this conformation appears to be stabilized by an ion pair. Thus far, the other apo-pol alpha structures that have been determined adopt open conformations. These results therefore suggest that the pol alpha polymerases undergo a series of conformational transitions during the catalytic cycle similar to those proposed for the pol I family. Furthermore, comparison of the orientations of the fingers and exonuclease (sub)domains relative to the palm subdomain that contains the pol active site suggests that the exonuclease domain and the fingers subdomain of the polymerase can move as a unit and may do so as part of the catalytic cycle. This provides a possible structural explanation for the interdependence of polymerization and editing exonuclease activities unique to pol alpha family polymerases. We suggest that the NH(2)-terminal domain of 9 degrees N-7 pol may be structurally related to an RNA-binding motif, which appears to be conserved among archaeal polymerases. The presence of such a putative RNA- binding domain suggests a mechanism for the observed autoregulation of bacteriophage T4 DNA polymerase synthesis by binding to its own mRNA. Furthermore, conservation of this domain could indicate that such regulation of pol expression may be a characteristic of archaea. Comparion of the 9 degrees N-7 pol structure to its mesostable homolog from bacteriophage RB69 suggests that thermostability is achieved by shortening loops, forming two disulfide bridges, and increasing electrostatic interactions at subdomain interfaces.

Amino Acid Motifs↗

PubMed2006

Novel biophysical techniques for investigating long-term cell adhesion dynamics on biomaterial surfaces.

Cell adhesion on biomaterial surface is crucial for the regeneration and function of clinically viable cell and tissues. In turn, the cellular phenotypes, following the mechanochemical transduction of adherent cells on biomaterials, are directly correlated to the biophysical responses of cells. However, the lack of an integrated bio-analytical system for probing the cell-substrate interface poses significant obstacles to understanding the behavior of cells on biomaterial surface. We have developed a novel method, based on the principle of confocal reflectance interference contrast microscopy (C-RICM) that has enabled us to study the biomechanical deformation of cells on biomaterial surfaces. In this article, we would like to describe our recent development of the C-RICM system that integrates a confocal fluorescence microscope, phase contrast microscope and GFP expression system. We shall demonstrate the system by determining the adhesion contact kinetics, initial deformation rate, cytoskeleton structures of adherent cells on extracellular matrices (e.g., collagen and fibronectin) and biodegradable polymer (e.g., poly(lactic acid)) during long-term culture. We shall demonstrate that this unique approach could provide valuable biophysical information necessary for designing optimized biomaterial surfaces for cell/tissue regeneration applications.

Animals↗

PubMed2004

Human fatty acid synthase: structure and substrate selectivity of the thioesterase domain.

Human fatty acid synthase is a large homodimeric multifunctional enzyme that synthesizes palmitic acid. The unique carboxyl terminal thioesterase domain of fatty acid synthase hydrolyzes the growing fatty acid chain and plays a critical role in regulating the chain length of fatty acid released. Also, the up-regulation of human fatty acid synthase in a variety of cancer makes the thioesterase a candidate target for therapeutic treatment. The 2.6-A resolution structure of human fatty acid synthase thioesterase domain reported here is comprised of two dissimilar subdomains, A and B. The smaller subdomain B is composed entirely of alpha-helices arranged in an atypical fold, whereas the A subdomain is a variation of the alpha/beta hydrolase fold. The structure revealed the presence of a hydrophobic groove with a distal pocket at the interface of the two subdomains, which constitutes the candidate substrate binding site. The length and largely hydrophobic nature of the groove and pocket are consistent with the high selectivity of the thioesterase for palmitoyl acyl substrate. The structure also set the identity of the Asp residue of the catalytic triad of Ser, His, and Asp located in subdomain A at the proximal end of the groove.

Amino Acid Sequence↗

PubMedDate not supplied

Coordinate transformation as a primary representation of radiotherapy beam geometry.

An approach to both geometric specification of radiotherapy beams and computerized solution of geometric treatment planning problems using coordinate transformations is presented. It is demonstrated that the specification of the geometric relationship of a treatment beam to a patient can be uniquely given by a 4 x 4 coordinate transformation matrix, and that the matrix representation can be translated from (and to) the more conventional machine-based specification of geometry. This approach enables a compact representation of the patient/beam geometry which is independent of the specific labeling conventions of the treatment machine and which can be directly exploited in the solution of treatment planning problems. Beam geometry can be easily described either in terms of the natural degrees of freedom of a therapy machine or in terms of alternative, problem-specific frames of reference. The ability to use these various frames of reference interchangeably allows the designer of treatment design software to present appropriate task-specific user interfaces for arbitrarily complex tasks, and thus reduce the cognitive burden on users of the software.

Humans↗

PubMed2004

A knowledgebase system to enhance scientific discovery: Telemakus.

BACKGROUND: With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged. METHODS: Case study. RESULTS: The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports. CONCLUSION: Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.

Journal Article↗

PubMed1989

Telerobotics and orbital laboratories: an end-to-end analysis and demonstration.

A preliminary analysis of the United States Laboratory (USL) module of the International Space Station has been completed. A major conclusion was that one of the most limited resources within the USL will be crew time. A laboratory robot would alleviate these constraints, improve safety, and reduce operational costs. A laboratory experiment manipulator system (LEMS) is proposed, made up of an on-board mobile manipulator and a computer-assisted operator control station. The on-board manipulator concept was tested with an Intelledex 660 industrial robot. Operator joystick command capability and delayed video feedback were added to simulate a Space Station Teleoperation system. The implementation of a unique predictive display was chosen for further evaluation because of its promise as a partial solution to the classical problem of robot remote control in the presence of time delay. The incorporation of various correction factors to calibrate the robot predictor model, including geometric distortion and spherical aberration caused by the video optics, is described.

Calibration↗

PubMed2002

Deletion and insertion of a 192-residue peptide in the active-site domain of glycosyl hydrolase family-2 beta-galactosidases.

The monomeric multimetal-binding beta-galactosidase of Saccharopolyspora rectivirgula (srbg), a glycosyl hydrolase family-2 enzyme, has a unique sequence consisting of 192 amino acid residues with no similarity to known proteins. This 192-residue sequence (termed the "iota [iota] sequence") appears to be inserted into a sequence homologous to the active-site domain of the Escherichia coli lacZ enzyme (lacZbg). To assess the effects of the t sequence at specific sites of beta-galactosidase on the catalytic functioning and molecular properties of beta-galactosidase, deletion or insertion mutants of beta-galactosidases were constructed, expressed in LacZ- E. coli strains, and characterized: srbgdelta in which the iota sequence was deleted from srbg, and lacZbgI, in which the 192-residue iota sequence was inserted into the corresponding position (between Asp591 and Phe592) in the active-site domain of lacZbg. srbgdelta was a catalytically inactive, dimeric protein which retained multimetal-binding characteristics, suggesting that the iota sequence is very important for maintaining the structure necessary for the catalytic functioning and the monomeric structure of srbg but is not responsible for the unique metal ion requirements of srbg. On the other hand, lacZbgI existed as a mixture of a monomer, a tetramer, and higher multimers. The monomeric species was inactive, whereas the tetramer and other multimers were catalytically active (V(max )K(m) value, 25% of that of lacZbg) and highly specific for beta-D-galactoside. The tetrameric lacZbgI was activated by Mg2+ and Mn2+ with lowered metal affinities, and the stoichiometry of metal binding was unchanged from that of lacZbg. These results, along with the published stereo structure of lacZbg, suggest that, in lacZbgI, the inserted 192-residue iota peptide could fold independently of the lacZbg domains into a "sub-domain," lying distant from the active site and subunit interfaces.

Journal Article↗

PubMed1996

Human amnion contains a novel laminin variant, laminin 7, which like laminin 6, covalently associates with laminin 5 to promote stable epithelial-stromal attachment.

Stable attachment of external epithelia to the basement membrane and underlying stroma is mediated by transmembrane proteins such as the integrin alpha6beta4 and bullous pemphigoid antigen 2 within the hemidesmosomes along the basolateral surface of the epithelial cell and their ligands that include a specialized subfamily of laminins. The laminin 5 molecule (previously termed kalinin/nicein/epiligrin) is a member of this epithelial-specific subfamily. Laminin 5 chains are not only considerably truncated within domains III-VI, but are also extensively proteolytically processed in vitro and in vivo. As a result, the domains expected to be required for the association of laminins with other basement membrane components are lacking in the mature laminin 5 molecule. Therefore, the tight binding of laminin 5 to the basement membrane may occur by a unique mechanism. To examine laminin 5 in tissue, we chose human amnion as the source, because of its availability and the similarity of the amniotic epithelial basement membrane with that of skin. We isolated the laminin 5 contained within the basement membrane of human amnion. In addition to monomeric laminin 5, we find that much of the laminin 5 isolated is covalently adducted with laminin 6 (alpha3beta1gamma1) and a novel laminin isotype we have termed laminin 7 (alpha3beta2gamma1). We propose that the association between laminin 5 and laminins 6 and 7 is a mechanism used in amnion to allow stable association of laminin 5 with the basement membrane. The beta2 chain is seen at the human amniotic epithelial-stromal interface and at the dermal-epidermal junction of fetal and adult bovine skin by immunofluorescence, but is not present, or only weakly present, in neonatal human skin.

Adult↗

PubMed1994

Predicting protein function: a versatile tool for the Apple Macintosh.

A tool is presented that helps to find biological functions for new protein sequences. Running on any Macintosh computer system, MacPattern provides a unique combination of different algorithms, speed and user-friendliness. It supports searches for protein patterns using the PROSITE database, protein block searches with the BLOCKS database, and the identification of statistically significant protein segments. MacPattern allows batch processing of sequences and automatic translations of nucleotide sequence data. It is particularly suited for genome analysis or cDNA sequencing projects.

Algorithms↗

PubMed2001

Administrative relationships between medical schools and community preceptors.

PURPOSE: To determine the current administrative relationships between medical schools and community preceptors, with special emphasis on arrangements for academic appointment, review, and promotion. METHOD: In 1999, administrative contacts at all 126 U.S. allopathic medical schools were mailed a ten-item questionnaire to elicit information concerning the current practices of the schools regarding community preceptors, who were defined as volunteer or part-time physician faculty, primarily practicing at non-university-owned facilities, who contribute to medical students' and/or residents' education in various specified ways. RESULTS: Responses were received from 71 (56%) of the schools; they were in general a representative sample of U.S. medical schools. The numbers of preceptors per school ranged from 40 to 3,500. Sixty-seven percent of reporting schools identified clinical departments as the main administrative interface with preceptors. Only three schools used a central office; none exclusively used a regionalized system. Forty-four schools (63.8%) reported using formal written criteria for all preceptor appointments. Sixty-six schools (93%) used consistent academic titling systems, with 83.3% using titles including the word "clinical." Thirty-three schools (47.8%) reported that their departments conducted regular preceptor reviews; an additional 28 reported reviews by some departments. Preceptors were eligible for promotion at 94.4% of the responding schools. At 46.8%, specific promotion criteria exist; four schools were developing such criteria. Preceptors' interest in academic promotion was perceived to be moderate or low. CONCLUSION: A substantial proportion of U.S. medical schools have taken action to recognize preceptors as a unique faculty group. The comments received indicate that this is an active area of development in faculty affairs policy.

Personnel Management↗

PubMed2003

Physical characteristics of polyaxial-headed pedicle screws and biomechanical comparison of load with their failure.

STUDY DESIGN: Pedicle screw strength or load to failure was biomechanically evaluated, and the geometric characteristics of pedicle screw instrumentation systems were compared. OBJECTIVES: To compare the features of pedicle screw systems, and to demonstrate the failure point of the polyaxial pedicle screw head. SUMMARY OF BACKGROUND DATA: Many pedicle screw instrumentation systems are currently available to the spine surgeon. Each system has its unique characteristics. It is important for the surgeon to understand the differences in these pedicle screw systems. Pedicle screw load to failure has not been subjected to a comparison study. METHODS: The physical characteristics of each pedicle screw instrumentation system were determined. Features of rods, instruments, and pedicle screws were cataloged. Biomechanical testing of the pedicle screw construct was performed to determine the site and force of the load to failure. Nine pedicle screw systems were evaluated. Testing was performed with a pneumatic testing system under load control. Three polyaxial screws were used for each test at a load rate of 100 N/second. The load failure value was the force at which the pedicle screw or polyaxial head-screw interface initially deflected. RESULTS: Biomechanical testing demonstrated in all instances that the polyaxial head coupling to the screw was the first failure point. Although there have been subtle design differences in the instruments over time, the features of the pedicle screw instrument sets have become remarkably similar. CONCLUSIONS: Biomechanical pedicle screw load-to-failure data demonstrated that the polyaxial head coupling to the screw is the first to fail and may be a protective feature of the pedicle screw, preventing pedicle screw breakage. Knowing the physical characteristics of the available pedicle screw instrumentation systems may allow the choice of pedicle screw best suited for a given clinical situation.

Biomechanical Phenomena↗

PubMed2001

Case study: a data warehouse for an academic medical center.

The clinical data repository (CDR) is a frequently updated relational data warehouse that provides users with direct access to detailed, flexible, and rapid retrospective views of clinical, administrative, and financial patient data for the University of Virginia Health System. This article presents a case study of the CDR, detailing its five-year history and focusing on the unique role of data warehousing in an academic medical center. Specifically, the CDR must support multiple missions, including research and education, in addition to administration and management. Users include not only analysts and administrators but clinicians, researchers, and students.

Academic Medical Centers↗

PubMed2003

Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: mapping the nuclear proteome of human fibroblasts.

Miniaturized liquid chromatography nanoseparation in combination with minigel fractionation of human primary cell nuclei is presented. We obtained high-sensitivity and high-throughput identification of expressed proteins by subcellular fractionation and nanocapillary liquid chromatography interfaced to both electrospray ionization (ESI)- and matrix-assisted laser desorption/ionisation (MALDI) tandem mass spectrometry. The reversed-phase nanocapillary eluents were applied directly onto the MALDI target plate as discrete crystal spots using in-line matrix infusion. When working with primary cells, only a limited amount of sample is available. To maximize the number of identified proteins from a restricted amount of sample, miniaturized sample preparation protocols and nanoflow separation is a necessity, especially when working with low-abundant proteins. From the same isolated nuclear sample, complementary separation of intact proteins by two-dimensional (2-D) gel electrophoresis was made. In total 594 gene products from the nuclear preparations were identified out of which 261 were unique. Several proteins involved in transcriptional events were identified such as TATA-binding protein, EBNA-co-activator, and interleukin enhancer binding proteins, indicating that sufficient proteomic depth is obtained to study transcriptional controlling events. Our results suggest that by sample prefractionation and downscaled nanoflow separation along with a combined mass spectrometry strategy, it is possible to identify a large number of nuclear proteins from human primary cells. These findings are of particular importance due to the disease link of these targets cells.

Cell Nucleus↗