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At least 919 records · Page 51Linked to original sources
PubMed2003

Implementing a MIRC query interface for a database driven teaching file.

This paper describes the authors' experience with integrating an existing database-driven teaching file with the RSNA (Radiological Society of North America) Medical Imaging Resource Center (MIRC). MIRC is the product of an RSNA-sponsored initiative to enable medical institutions to share their electronic medical content (images, text, and multimedia) by creating a distributed repository accessible from the Internet. An existing database-driven teaching file, developed by the authors and used extensively by the University of California San Francisco (UCSF) Department of Radiology since 1998, was retrofitted to include an interface for handling broadcast queries initiated by a MIRC query service. These queries take place through the exchange of XML documents via HTTP. After all the storage services have responded, the results are collated by the query service and presented to the user. The teaching file and MIRC interface were developed using the 4th Dimension Relational Database Management System (RDBMS). The integration process primarily involved mapping the "MIRCdocument" schema to the teaching file's schema, translating the actual MIRC query into the internal query language of the database and extending the access control mechanisms of the teaching file to allow public access. A working implementation of the interface required only 3 days of development time, with refinements taking place over several months. Interface development was greatly aided by MIRC's use of well-established Internet standards. This project has demonstrated the feasibility of implementing a MIRC interface on an existing teaching file server.

Computer-Assisted Instruction↗
PubMed2004

Medical Image Resource Center--making electronic teaching files from PACS.

A picture archive and communications system (PACS) is a rich source of images and data suitable for creating electronic teaching files (ETF). However, the potential for PACS to support nonclinical applications has not been fully realized: at present there is no mechanism for PACS to identify and store teaching files; neither is there a standardized method for sharing such teaching images. The Medical Image Resource Center (MIRC) is a new central image repository that defines standards for data exchange among different centers. We developed an ETF server that retrieves digital imaging and communication in medicine (DICOM) images from PACS, and enables users to create teaching files that conform to the new MIRC schema. We test-populated our ETF server with illustrative images from the clinical case load of the National Neuroscience Institute, Singapore. Together, PACS and MIRC have the potential to benefit radiology teaching and research.

Computer Communication Networks↗
PubMed2004

Multivariate statistical model for 3D image segmentation with application to medical images.

In this article we describe a statistical model that was developed to segment brain magnetic resonance images. The statistical segmentation algorithm was applied after a pre-processing stage involving the use of a 3D anisotropic filter along with histogram equalization techniques. The segmentation algorithm makes use of prior knowledge and a probability-based multivariate model designed to semi-automate the process of segmentation. The algorithm was applied to images obtained from the Center for Morphometric Analysis at Massachusetts General Hospital as part of the Internet Brain Segmentation Repository (IBSR). The developed algorithm showed improved accuracy over the k-means, adaptive Maximum Apriori Probability (MAP), biased MAP, and other algorithms. Experimental results showing the segmentation and the results of comparisons with other algorithms are provided. Results are based on an overlap criterion against expertly segmented images from the IBSR. The algorithm produced average results of approximately 80% overlap with the expertly segmented images (compared with 85% for manual segmentation and 55% for other algorithms).

Algorithms↗
PubMed2006

Megaplasmids encode differing combinations of lantibiotics in Streptococcus salivarius.

Streptococcus salivarius strains commonly produce bacteriocins as putative anti-competitor or signalling molecules. Here we report that bacteriocin production by the oral probiotic strain S. salivarius K12 is encoded by a large (ca. 190 kb) plasmid. Oral cavity transmission of the plasmid from strain K12 to a plasmid-negative variant of this bacterium was demonstrated in two subjects. Tests of additional S. salivarius strains showed large (up to ca. 220 kb) plasmids present in bacteriocin-producing isolates. Various combinations (up to 3 per plasmid) of loci encoding the known streptococcal lantibiotics salivaricin A, salivaricin B, streptin and SA-FF22 were localised to these plasmids. Since all bacteriocin-producing strains of S. salivarius tested to date appear to harbour plasmids, it appears that they may function as mobile repositories for bacteriocin loci, especially those of the lantibiotic class.

Bacterial Proteins↗
PubMed2004

Comparison of established cell lines at different passages by karyotype and comparative genomic hybridization.

Two established cancer cell lines, MCF-7 and Ishikawa, were both obtained directly from a cell repository and through another laboratory. The karyotypes from the two MCF-7 cell lines had up to 83 chromosomes and similarities for chromosomal gain and structural abnormalities. The two Ishikawa cell lines had up to 60 chromosomes with only a missing X as the common chromosome abnormality. CGH studies were performed by co-hybridizing the two Ishikawa or MCF-7 cell lines to normal metaphases. The differences seen between the two MCF-7 cell cultures reflect changes due to passage number and culture conditions. For Ishikawa, DNA polymorphic data and mutation studies suggest that the two cell lines are not derived from the same established tumor cell line. Our study shows the utilization of CGH in comparing cell lines originating from the same specimen. Our study also demonstrates the necessity for periodically evaluating cell lines to confirm their origin.

Base Sequence↗
PubMedDate not supplied

A bioinformatics perspective on proteomics: data storage, analysis, and integration.

The field of proteomics is advancing rapidly as a result of powerful new technologies and proteomics experiments yield a vast and increasing amount of information. Data regarding protein occurrence, abundance, identity, sequence, structure, properties, and interactions need to be stored. Currently, a common standard has not yet been established and open access to results is needed for further development of robust analysis algorithms. Databases for proteomics will evolve from pure storage into knowledge resources, providing a repository for information (meta-data) which is mainly not stored in simple flat files. This review will shed light on recent steps towards the generation of a common standard in proteomics data storage and integration, but is not meant to be a comprehensive overview of all available databases and tools in the proteomics community.

Computational Biology↗
PubMed2006

The expression of neurokinin-1 and preprotachykinin-1 in breast cancer cells depends on the relative degree of invasive and metastatic potential.

Breast cancer has a predilection for metastasis to the bone marrow. The preprotachykinin-I (PPT-I) gene has a central role in the early migration of breast cancer cells into the bone marrow, making this organ a latent repository of the cancer cells. This study investigated whether the invasive and metastatic potential of breast cancer cells correlate with the expression of the PPT-I gene and the receptors for its peptides, neurokinin-1 (NK-1) and NK-2. The studies compared cells that are non-tumorigenic (MCF12A), low metastatic and invasive potential (MCF7), and sublines of MCF with increased invasive and metastatic potential (LCC1 and LCC2). LCC2, but not LCC1 is tamoxifen resistant. Quantitative RT-PCR showed increased expression of PPT-I, NK-1 and NK-2 mRNA LCC1 and LCC2. MCF7 required stimulation by phorbol ester for NK-1 induction. The levels of NK-2 mRNA were significantly increased in LCC2. Clonogenic assays with specific receptor antagonists showed a predominant role for NK-2 in the proliferation of both LCC1 and LCC2. While the growth rate of LCC1 and LCC2 were similar, the latter showed increased migration. Use of a nude mouse model confirmed higher metastatic potential of LCC2, including increased migration to regions of the endosteum. Overall, these studies show a correlation between three neuroendocrine-related genes: PPT-I, NK-1 and NK-2 and the metastatic potential of specific breast cancer cells. These cells provide a model for future studies on bone marrow metastasis.

Breast Neoplasms↗
PubMed2006

The biobank of the Norwegian Mother and Child Cohort Study: a resource for the next 100 years.

INTRODUCTION: Long-term storage of biological materials is a critical component of any epidemiological study. In designing specimen repositories, efforts need to balance future needs for samples with logistical constraints necessary to process and store samples in a timely fashion. OBJECTIVES: In the Norwegian Mother and Child Cohort Study (MoBa), the Biobank was charged with long-term storage of more than 380,000 biological samples from pregnant women, their partners and their children for up to 100 years. METHODS: Biological specimens include whole blood, plasma, DNA and urine; samples are collected at 50 hospitals in Norway. All samples are sent via ordinary mail to the Biobank in Oslo where the samples are registered, aliquoted and DNA extracted. DNA is stored at -20 degrees C while whole blood, urine and plasma are stored at -80 degrees C. RESULTS: As of July 2006, over 227,000 sample sets have been collected, processed and stored at the Biobank. Currently 250-300 sets are received daily. An important part of the Biobank is the quality control program. CONCLUSION: With the unique combination of biological specimens and questionnaire data, the MoBa Study will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental factors on pregnancy outcome and on human morbidity, mortality and health in general.

Adult↗
PubMed2005

Development of a quality-assessed agrichemical database for monitoring anthropogenic impacts on ground-water quality.

The Quality-Assessed Agrichemical Contaminant Database for Nebraska Ground Water is a unique repository of nitrate and pesticide data collected by federal, state, and local agencies. Each contaminant concentration in the database has been evaluated based upon well-defined criteria that address completeness of the well-attribute data, analytical method and field and laboratory quality control practices and assigned to one of five quality levels. The quality assessment level always accompanies the contaminant concentration so that the end-user knows the quality assurance effort expended in the acquisition of the data, can select comparable data, and choose data whose quality assurance effort is commensurate with project objectives. The database can be viewed and queried on-line; downloaded in its entirety; or imported to a spreadsheet or a geographic information system. Setting criteria for data quality and assessing the level of quality have resulted in significant increases in the percentages of high quality (Levels 3-5) nitrate and pesticide data. These high quality data presently constitute 52% of the nitrate and 55% of the pesticide data.

Agrochemicals↗
PubMed2004

The Mouse Phenome Project.

The laboratory mouse is the organism of choice for many studies in biology and medicine. Reliable phenotypic data are essential for the full utility of genotypic information emerging from efforts to sequence human and mouse genomes. The Mouse Phenome Project has been organized to help accomplish this task by establishing a collection of baseline phenotypic data on commonly used and genetically diverse inbred mouse strains and making this information publicly available through a web-accessible database. The Mouse Phenome Database (MPD) is being developed to manage these data and to provide researchers with tools for exploring both raw phenotypic data and comparative summary analyses. The MPD serves as a repository for detailed protocols and raw data. This resource enables investigators to identify appropriate strains for (1) physiological testing, (2) drug discovery, (3) toxicology studies, (4) mutagenesis, (5) modeling human diseases, (6) QTL analyses and identification of new genes and (7) unraveling the influence of environment on genotype.

Animals↗
PubMed2026

Ethical Governance of Open Data Across Biomedical Research, Healthcare, and Public Health: Privacy, Equity, Trust, and Controlled Access.

Open data has become central to biomedical research and public health, but health information is uniquely sensitive and difficult to share responsibly. In this narrative review, open data is considered as a spectrum of health-data sharing arrangements, ranging from public aggregate datasets to controlled-access repositories, federated analysis, and synthetic data. This narrative review synthesizes the scientific and societal rationale for greater openness with the ethical, legal, and governance constraints that shape what "open" can realistically mean in healthcare. We examine how data sharing supports reproducibility, machine learning, and more efficient research, while also enabling public health surveillance and learning health systems. Against these benefits, we analyze privacy and re-identification risks, consent challenges in large-scale secondary use, inequities including data colonialism, and tensions introduced by commercialization. We integrate lessons from prominent case examples spanning pandemic data sharing, genomic initiatives, population registries, patient-led rare disease infrastructures, and regional data spaces. Across these domains, experience suggests that durable progress depends less on unrestricted openness than on calibrated access, privacy-preserving architectures, clear accountability, and sustained public engagement. We conclude by proposing a pragmatic ethical orientation for healthcare open data: treat openness as a spectrum of controlled sharing arrangements, embed equity and reciprocity into governance, and institutionalize trust-building measures that can persist beyond emergencies and political cycles.

Data colonialism↗
PubMed2006

Modeling activated states of GPCRs: the rhodopsin template.

Activation of G Protein-Coupled Receptors (GPCRs) is an allosteric mechanism triggered by ligand binding and resulting in conformational changes transduced by the transmembrane domain. Models of the activated forms of GPCRs have become increasingly necessary for the development of a clear understanding of signal propagation into the cell. Experimental evidence points to a multiplicity of conformations related to the activation of the receptor, rendered important physiologically by the suggestion that different conformations may be responsible for coupling to different signaling pathways. In contrast to the inactive state of rhodopsin (RHO) for which several high quality X-ray structures are available, the structure-related information for the active states of rhodopsin and all other GPCRs is indirect. We have collected and stored such information in a repository we maintain for activation-specific structural data available for rhodopsin-like GPCRs, http://www.physiology.med.cornell.edu/GPCRactivation/gpcrindex.html . Using these data as structural constraints, we have applied Simulated Annealing Molecular Dynamics to construct a number of different active state models of RHO starting from the known inactive structure. The common features of the models indicate that TM3 and TM5 play an important role in activation, in addition to the well-established rearrangement of TM6. Some of the structural changes observed in these models occur in regions that were not involved in the constraints, and have not been previously tested experimentally; they emerge as interesting candidates for further experimental exploration of the conformational space of activated GPCRs. We show that none of the normal modes calculated from the inactive structure has a dominant contribution along the path of conformational rearrangement from inactive to the active forms of RHO in the models. This result may differentiate rhodopsin from other GPCRs, and the reasons for this difference are discussed in the context of the structural properties and the physiological function of the protein.

Models, Molecular↗
PubMed2006

Milestones in electron crystallography.

Electron crystallography determines the structure of membrane embedded proteins in the two-dimensionally crystallized state by cryo-transmission electron microscopy imaging and computer structure reconstruction. Milestones on the path to the structure are high-level expression, purification of functional protein, reconstitution into two-dimensional lipid membrane crystals, high-resolution imaging, and structure determination by computer image processing. Here we review the current state of these methods. We also created an Internet information exchange platform for electron crystallography, where guidelines for imaging and data processing method are maintained. The server (http://2dx.org) provides the electron crystallography community with a central information exchange platform, which is structured in blog and Wiki form, allowing visitors to add comments or discussions. It currently offers a detailed step-by-step introduction to image processing with the MRC software program. The server is also a repository for the 2dx software package, a user-friendly image processing system for 2D membrane protein crystals.

Cryoelectron Microscopy↗
PubMed2005

The fate of Lyngbya majuscula toxins in three potential consumers.

Blooms of Lyngbya majuscula have been reported with increasing frequency and severity in the last decade in Moreton Bay, Australia. A number of grazers have been observed feeding upon this toxic cyanobacterium. Differences in sequestration of toxic compounds from L. majuscula were investigated in two anaspideans, Stylocheilus striatus, Bursatella leachii, and the cephalaspidean Diniatys dentifer. Species fed a monospecific diet of L. majuscula had different toxin distribution in their tissues and excretions. A high concentration of lyngbyatoxin-a was observed in the body of S. striatus (3.94 mg/kg(-1)) compared to bodily secretions (ink 0.12 mg/kg(-1); fecal matter 0.56 mg/kg(-1); eggs 0.05 mg/kg(-1)). In contrast, B. leachii secreted greater concentrations of lyngbyatoxin-a (ink 5.41 mg/kg(-1); fecal matter 6.71 mg/kg(-1)) than that stored in the body (2.24 mg/kg(-1)). The major internal repository of lyngbyatoxin-a and debromoaplysiatoxin was the digestive gland for both S. striatus (6.31 +/- 0.31 mg/kg(-1)) and B. leachii (156.39 +/- 46.92 mg/kg(-1)). D. dentifer showed high variability in the distribution of sequestered compounds. Lyngbyatoxin-a was detected in the digestive gland (3.56 +/- 3.56 mg/kg(-1)) but not in the head and foot, while debromoaplysiatoxin was detected in the head and foot (133.73 +/- 129.82 mg/kg(-1)) but not in the digestive gland. The concentrations of sequestered secondary metabolites in these animals did not correspond to the concentrations found in L. majuscula used as food for these experiments, suggesting it may have been from previous dietary exposure. Trophic transfer of debromoaplysiatoxin from L. majuscula into S. striatus is well established; however, a lack of knowledge exists for other grazers. The high levels of secondary metabolites observed in both the anaspidean and the cephalapsidean species suggest that these toxins may bioaccumulate through marine food chains.

Animals↗
PubMed2005

Transductive machine learning for reliable medical diagnostics.

In the past decades Machine Learning tools have been successfully used in several medical diagnostic problems. While they often significantly outperform expert physicians (in terms of diagnostic accuracy, sensitivity, and specificity), they are mostly not being used in practice. One reason for this is that it is difficult to obtain an unbiased estimation of diagnose's reliability. We discuss how reliability of diagnoses is assessed in medical decision making and propose a general framework for reliability estimation in Machine Learning, based on transductive inference. We compare our approach with a usual (Machine Learning) probabilistic approach as well as with classical stepwise diagnostic process where reliability of diagnose is presented as its posttest probability. The proposed transductive approach is evaluated on several medical data sets from the UCI (University of California, Irvine) repository as well as on a practical problem of clinical diagnosis of the coronary artery disease. In all cases significant improvements over existing techniques are achieved.

Adult↗
PubMed2006

Increasing access to program information: a strategy for improving adolescent health.

OBJECTIVES: To identify existing programs serving 11- to 15-year-olds that aim to improve adolescent health in the areas of Health & Well-being, Fitness, Family & Peer Relationships, School Environment, Smoking, Alcohol Use, and Violence and to assess the utility of readily available resources in providing detailed program information. METHODS: In Phase 1, publicly available program databases were searched to identify potential programs serving the target population. In Phase 2, an in-depth search of a limited sample of programs meeting the content and age criteria was performed to identify program descriptors. RESULTS: Over 1,000 program names were identified in Phase 1. Information regarding programs is becoming more readily available through the internet; however, the program information that was publicly available only begins to draw the picture. Phase 2 revealed that a broad array of efforts are underway in all seven content areas, but found information on the program descriptors to be limited. CONCLUSIONS: Investment in programming is not enough; an upfront investment in communication and information sharing is critical in order to maximize the resources dedicated to the improvement of adolescent health. A well-publicized centralized program repository offered in conjunction with technical assistance would provide an efficient mechanism for this information sharing. We further suggest that the inherent gap between research and practice can be lessened by building a new body of practice knowledge. This would require improved program data collection by programs, the incorporation of program participation information in national surveys and enhanced evaluation efforts.

Adolescent↗
PubMed2005

Functionality of cross-linked polyvinylpyrrolidone as a spheronization aid: a promising alternative to microcrystalline cellulose.

PURPOSE: This work seeks to explore and demonstrate the functionality of cross-linked polyvinylpyrrolidone (crospovidone) as a spheronization aid and a promising alternative to microcrystalline cellulose (MCC). METHODS: Pellets were prepared with various grades of crospovidone using both small- and large-scale extrusion-spheronization. A Box-Behnken experimental design was employed to elucidate the effects of operating variables on the quality of the pellets. Size and shape analyses of these pellets were conducted and compared to those prepared using MCC. RESULTS: Crospovidone was believed to behave like a liquid repository in its interaction with water during extrusion-spheronization, although its binding ability was weaker than that of MCC. Spherical pellets of narrow size distribution could be made from the finer crospovidone grades with different lactose grades. However, crospovidone-based formulations required higher water levels than weight-equivalent MCC-based formulations. Crospovidone pellets were of equivalent quality to those prepared with MCC, especially in the shape, size, and yield. CONCLUSIONS: Crospovidone can be successfully employed as a spheronization aid to produce good pellets without the need of a binder, unlike most of the previously proposed materials. This study exemplified the enormous potential of crospovidone to serve as a competent alternative to MCC in the production of pellets by extrusion-spheronization.

Cellulose↗
PubMed2002

Rheumatic Fever and Long-term Sequelae in Children.

Rheumatic fever and rheumatic heart disease continue unabated, affecting young individuals in most of the developing nations. Focal outbreaks of smaller magnitude have also been reported since the mid-1980s from industrialized western nations, where this disease had almost disappeared. The introduction of penicillin in the mid-1940s has markedly changed the natural history of rheumatic fever, although the incidence of rheumatic fever declined in developed nations even before that, mainly due to better living conditions. Treatment of rheumatic fever chiefly involves the use of antibiotics (penicillin) and anti-inflammatory drugs, like salicylates or corticosteroids, to eradicate Streptococci. Patients with severe carditis, congestive heart failure, or pericarditis are best treated with corticosteroids because these are more potent anti-inflammatory agents than salicylates. Salicylates may be sufficient for cases with mild or no carditis. The treatment must be continued for 12 weeks. Several studies have shown that valvular regurgitation, and not myocarditis, is the cause of congestive heart failure in active rheumatic carditis. Therefore, surgery with mitral valve replacement or repair is indicated in cases with intractable hemodynamics due to mitral regurgitation. The development of chronic valvular lesion after an episode of rheumatic fever is dependent upon the presence or absence of carditis in the previous attack and compliance with secondary prophylaxis. Recurrences due to inadequate penicillin prophylaxis are responsible for hemodynamically significant chronic valvular lesions requiring surgery. Primary prevention of rheumatic fever is fraught with difficulties and may not be feasible in most of the countries where the disease is rampant. Secondary prevention, ie, preventing recurrence of rheumatic fever, is the appropriate strategy with proven efficacy. A repository form of penicillin, benzathine penicillin G, given as an intramuscular injection at 3 weekly intervals in the dose of 1,200,000 U, remains the treatment of choice for secondary prevention of rheumatic fever. Alternative antibiotics may be used in those allergic to penicillin. An effective and safe vaccine against rheumatic fever is not yet available.

Journal Article↗