Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Data Storage And Retrieval”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,729 records · Page 96Linked to original sources
PubMedDate not supplied

Fast and reliable collision culling using graphics hardware.

We present a reliable culling algorithm that enables fast and accurate collision detection between triangulated models in a complex environment. Our algorithm performs fast visibility queries on the GPUs for eliminating a subset of primitives that are not in close proximity. In order to overcome the accuracy problems caused by the limited viewport resolution, we compute the Minkowski sum of each primitive with a sphere and perform reliable 2.5D overlap tests between the primitives. We are able to achieve more effective collision culling as compared to prior object-space culling algorithms. We integrate our culling algorithm with CULLIDE [1] and use it to perform reliable GPU-based collision queries at interactive rates on all types of models, including nonmanifold geometry, deformable models, and breaking objects.

Algorithms↗
PubMedDate not supplied

HDR VolVis: high dynamic range volume visualization.

In this paper, we present an interactive high dynamic range volume visualization framework (HDR VolVis) for visualizing volumetric data with both high spatial and intensity resolutions. Volumes with high dynamic range values require high precision computing during the rendering process to preserve data precision. Furthermore, it is desirable to render high resolution volumes with low opacity values to reveal detailed internal structures, which also requires high precision compositing. High precision rendering will result in a high precision intermediate image (also known as high dynamic range image). Simply rounding up pixel values to regular display scales will result in loss of computed details. Our method performs high precision compositing followed by dynamic tone mapping to preserve details on regular display devices. Rendering high precision volume data requires corresponding resolution in the transfer function. To assist the users in designing a high resolution transfer function on a limited resolution display device, we propose a novel transfer function specification interface with nonlinear magnification of the density range and logarithmic scaling of the color/ opacity range. By leveraging modern commodity graphics hardware, multiresolution rendering techniques and out-of-core acceleration, our system can effectively produce an interactive visualization of large volume data, such as 2,048(3).

Algorithms↗
PubMedDate not supplied

Multifocal projection: a multiprojector technique for increasing focal depth.

In this paper, we describe a novel multifocal projection concept that applies conventional video projectors and camera feedback. Multiple projectors with differently adjusted focal planes, but overlapping image areas are used. They can be either differently positioned in the environment or can be integrated into a single projection unit. The defocus created on an arbitrary surface is estimated automatically for each projector pixel. If this is known, a final image with minimal defocus can be composed in real-time from individual pixel contributions of all projectors. Our technique is independent of the surfaces' geometry, color and texture, the environment light, as well as of the projectors' position, orientation, luminance, and chrominance.

Algorithms↗
PubMedDate not supplied

Capturing and using clinical outcome data: implications for information systems design.

There is an urgent need to capture and record data related to clinical outcomes, but there are many barriers. The range of problems includes lack of agreement on conceptualization of the term "outcome," inadequate measures of outcomes, and inadequate information systems to capture and manipulate data that would reflect outcomes. This article focuses on information system requirements to capture, store, and utilize clinical outcome data. For greatest accuracy, outcome data should be captured as close to the source as possible, including direct data capture from patients themselves and from their families. To make maximum use of outcome data, systems must be designed to 1) store data in multipurpose databases; 2) share data across different platforms; 3) link outcome data to other data that might influence or explain outcomes; 4) allow querying of the data by authorized personnel; and 5) protect patient confidentiality.

Decision Support Systems, Management↗
PubMed2005

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management.

BACKGROUND: Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. RESULTS: We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. CONCLUSION: MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production.

Computational Biology↗
PubMed2006

Integrative missing value estimation for microarray data.

BACKGROUND: Missing value estimation is an important preprocessing step in microarray analysis. Although several methods have been developed to solve this problem, their performance is unsatisfactory for datasets with high rates of missing data, high measurement noise, or limited numbers of samples. In fact, more than 80% of the time-series datasets in Stanford Microarray Database contain less than eight samples. RESULTS: We present the integrative Missing Value Estimation method (iMISS) by incorporating information from multiple reference microarray datasets to improve missing value estimation. For each gene with missing data, we derive a consistent neighbor-gene list by taking reference data sets into consideration. To determine whether the given reference data sets are sufficiently informative for integration, we use a submatrix imputation approach. Our experiments showed that iMISS can significantly and consistently improve the accuracy of the state-of-the-art Local Least Square (LLS) imputation algorithm by up to 15% improvement in our benchmark tests. CONCLUSION: We demonstrated that the order-statistics-based integrative imputation algorithms can achieve significant improvements over the state-of-the-art missing value estimation approaches such as LLS and is especially good for imputing microarray datasets with a limited number of samples, high rates of missing data, or very noisy measurements. With the rapid accumulation of microarray datasets, the performance of our approach can be further improved by incorporating larger and more appropriate reference datasets.

Algorithms↗
PubMed2006

HotSwap for bioinformatics: a STRAP tutorial.

BACKGROUND: Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique. RESULTS: Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://strapjava.de and http://www.charite.de/bioinf/strap. CONCLUSION: HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.

Algorithms↗
PubMed2005

The tissue microarray data exchange specification: a document type definition to validate and enhance XML data.

BACKGROUND: The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness. RESULTS: A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE). CONCLUSION: ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data.

AIDS-Related Complex↗
PubMed2005

Three-photon induced photobleaching in a three-dimensional memory material.

The photobleaching properties of a 3D memory material based on pyrylium salts are studied. It is shown that under ultrashort pulsed irradiation photobleaching occurs through two diverse mechanisms. One is major and causes fast bleaching, whereas the other is minor and causes slow bleaching. Furthermore, it is proved that both mechanisms are three- or more-photon processes. This fact gives the capability of significantly increasing data storage density.

Computers, Molecular↗
PubMed1997

Numerical proposal for a semiological classification of clinical findings.

The principal goal of this paper is to present a numerical classification of the characteristics of symptoms and signs. This classification begins with the ICD9 code and takes into account the semiological aspects of the already mentioned symptoms an signs, in such a way, that a digit represents, in cases of abdominal pain, site, another: radiating to, and the followings: aggravating, relieving factors, progress, duration and type. This way of representing data, with only a digit for each characteristic facilitates registration and elaboration of data bases, as well as, electronic data interchange.

Classification↗
PubMed1999

Extended SQL for manipulating clinical warehouse data.

Health care institutions are beginning to collect large amounts of clinical data through patient care applications. Clinical data warehouses make these data available for complex analysis across patient records, benefiting administrative reporting, patient care and clinical research. Data gathered for patient care purposes are difficult to manipulate for analytic tasks; the schema presents conceptual difficulties for the analyst, and many queries perform poorly. An extension to SQL is presented that enables the analyst to designate groups of rows. These groups can then be manipulated and aggregated in various ways to solve a number of useful analytic problems. The extended SQL is concise and runs in linear time, while standard SQL requires multiple statements with polynomial performance. The extensions are extremely powerful for performing aggregations on large amounts of data, which is useful in clinical data mining applications.

Clinical Laboratory Techniques↗
PubMed2002

Implementing a document imaging system.

The benefits of a document imaging system are myriad once it's installed--it's the implementation that you need to prepare for. In this article, get a bird's eye view of one facility's implementation and the many lessons learned along the way.

Admitting Department, Hospital↗
PubMed2002

PQL: a declarative query language over dynamic biological schemata.

We introduce the PQL query language (PQL) used in the GeneSeek genetic data integration project. PQL incorporates many features of query languages for semi-structured data. To this we add the ability to express metadata constraints like intended semantics and database curation approach. These constraints guide the dynamic generation of potential query plans. This allows a single query to remain relevant even in the presence of source and mediated schemas that are continually evolving, as is often the case in data integration.

Computational Biology↗
PubMed2006

Soprano Specialty Forms Project--A solution that empowers clinicians in the management of research and audit data.

Throughout the world, clinicians (including nurses) create ad-hoc stand-alone databases in order to meet their individual research and audit requirements. These databases often exist in large numbers within an institution. They meet individual requirements and capture a large quantity of valuable clinical information, but it is not possible to pool or share that information because of a lack of common data structures and coding. The Soprano Specialty Forms solution developed by Orion Health in collaboration with Auckland District Health Board resolves this problem. The solution provides a common data storage and coding infrastructure within which clinicians can create their own forms for data collection, enter data through an integrated portal used as part of their everyday clinical practice, and easily query the data collected regardless of its source.

Databases as Topic↗
PubMed1995

Data capture workstations, scanned forms, and pen-based systems for clinician use.

Data capture is the most difficult aspect of creating an automated medical record. The U.S. Department of Veterans Affairs (V.A.) is developing, testing and evaluating the benefits of a number of data capture technologies, including physician's workstations, scanned forms, and pen-based system as an aid to medical data capture in the outpatient clinic environment. The software being used for physician data entry, which supports a variety of data capture devices, will be demonstrated.

Computer Peripherals↗
PubMed2006

Querying the public databases for sequences using complex keywords contained in the feature lines.

BACKGROUND: High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords. RESULTS: We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use. CONCLUSION: Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs.

Database Management Systems↗