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Abstract Background Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI), funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace) recovered using methylation filtration technology and providing annotation and analysis of the sequence data. Description CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS) isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs) knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource), and UniProtKB-TrEMBL). Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from Arabidopsis thaliana, Oryza sativa, Medicago truncatula, and Populus trichocarpa. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the potential domains on annotated GSS were analyzed using the HMMER package against the Pfam database. The annotated GSS were also assigned with Gene Ontology annotation terms and integrated with 228 curated plant metabolic pathways from the Arabidopsis Information Resource (TAIR) knowledge base. The UniProtKB-Swiss-Prot ENZYME database was used to assign putative enzymatic function to each GSS. Each GSS was also analyzed with the Tandem Repeat Finder (TRF) program in order to identify potential SSRs for molecular marker discovery. The raw sequence data, processed annotation, and SSR results were stored in relational tables designed in key-value pair fashion using a PostgreSQL relational database management system. The biological knowledge derived from the sequence data and processed results are represented as views or materialized views in the relational database management system. All materialized views are indexed for quick data access and retrieval. Data processing and analysis pipelines were implemented using the Perl programming language. The web interface was implemented in JavaScript and Perl CGI running on an Apache web server. The CPU intensive data processing and analysis pipelines were run on a computer cluster of more than 30 dual-processor Apple XServes. A job management system called Vela was created as a robust way to submit large numbers of jobs to the Portable Batch System (PBS). Conclusion CGKB is an integrated and annotated resource for cowpea GSS with features of homology-based and HMM-based annotations, enzyme and pathway annotations, GO term annotation, toolkits, and a large number of other facilities to perform complex queries. The cowpea GSS, chloroplast sequences, mitochondrial sequences, retroelements, and SSR sequences are available as FASTA formatted files and downloadable at CGKB. This database and web interface are publicly accessible at http://cowpeagenomics.med.virginia.edu/CGKB/.

We describe the methodology and impact of merging detailed statewide mortality data into the master patient index tables of the clinical data repository (CDR) of the University of Virginia Health System (UVAHS). We employ three broadly inclusive linkage passes (designed to result in large numbers of false positives) to match the patients in the CDR to those in the statewide files using the following criteria: a) Social Security Number; b) Patient Last Name and Birth Date; c) Patient Last Name and Patient First Name. The results from these initial matches are refined by calculation and assignment of a total score comprised of partial scores depending on the quality of matching between the various identifiers. In order to validate our scoring algorithm, we used those patients known to have died at UVAHS over the eight year period as an internal control. We conclude that we are able to update our CDR with 97% of the deaths from the state source using this scheme. We illustrate the potential of the resulting system to assist caregivers in identification of at-risk patient groups by description of those patients in the CDR who were found to have committed suicide. We suggest that our approach represents an efficient and inexpensive way to enrich hospital data with important outcomes information.

Objective: Patients with polydipsia and intermittent hyponatremia have greater ventricle-brain ratios (VBRs) than matched patients without polydipsia and intermittent hyponatremia and normal subjects. Unlike previous studies, this study controlled for the impact of water loading when examining the volume of intracranial structures., Method: Under controlled conditions, eight male schizophrenic patients with polydipsia and intermittent hyponatremia were first assigned to either normal fluid intake or oral water loading and then the alternative condition the following day. Magnetic resonance imaging (MRI) volumetric measurements were made with the use of a standardized protocol., Results: During water loading, total VBR and lateral ventricle volume significantly decreased by 13.1% and 12.6%, respectively. A strong association between change in serum sodium concentration and change in VBR was noted across conditions., Conclusions: These findings indicate that 1) water loading does not account for the diminished brain volume observed in patients with polydipsia and intermittent hyponatremia in previous studies, and 2) hyponatremia can significantly alter brain morphology on MRI.

Despite clear anthropomorphic differences, gender differences in human skeletal muscle protein and carbohydrate metabolism have not been carefully examined. We compared postabsorptive forearm glucose, oxygen, and lactate balances and forearm protein kinetics between 40 male and 36 female subjects. Forearm composition was measured in a subset of 17 subjects (8 males and 9 females) using multislice magnetic resonance imaging. Oxygen uptake, net phenylalanine release, and estimated rates of forearm protein synthesis and degradation were greater in male than in female subjects when expressed as the rate per 100 mL forearm volume (P < 0.05). In males, however, muscle accounted for 58% of forearm volume, compared with 46% in females (P < 0.001). When phenylalanine balance, protein degradation and synthesis, and glucose and oxygen uptake were expressed per 100 mL forearm muscle, there were no significant differences across gender. Likewise, the extraction fractions for oxygen, glucose, phenylalanine, and labeled phenylalanine were comparable in males and females. We conclude that cross-gender comparisons of metabolic variables must accommodate differences in tissue composition. These data indicate that in the postabsorptive state, skeletal muscle metabolism of glucose, protein, and oxygen do not differ by gender in healthy young humans.

The authors represent a cooperative group of 15 institutions that examined the feasibility of using metabolic features observed in vivo with 1H-magnetic resonance (MR) spectroscopy to characterize brain tumors of the glial type. The institutions provided blinded, centralized MR spectroscopy data processing long with independent central review of MR spectroscopy voxel placement, composition and contamination by brain, histopathological typing using current World Health Organization criteria, and clinical data. Proton 1H-MR spectroscopy was performed using a spin-echo technique to obtain spectra from 8-cc voxels in the tumor and when feasible in the contralateral brain. Eighty-six cases were assessable, 41 of which had contralateral brain spectra. Glial tumors had significantly elevated intensities of choline signals, decreased intensities of creatine signals, and decreased intensities of N-acetylaspartate compared to brain. Choline signal intensities were highest in astrocytomas and anaplastic astrocytomas, and creatine signal intensities were lowest in glioblastomas. However, whether expressed relative to brain or as intratumoral ratios, these metabolic characteristics exhibited large variations within each subtype of glial tumor. The resulting overlaps precluded diagnostic accuracy in the distinction of low-and high-grade tumors. Although the extent of contamination of the 1H-MR spectroscopy voxel by brain had a marked effect on metabolite concentrations and ratios, selection of cases with minimal contamination did not reduce these overlaps. Thus, each type and grade of tumor is a metabolically hetero-geneous group. Lactate occurred infrequently and in all grades. Mobile lipids, on the other hand, occurred in 41% of high-grade tumors with higher mean amounts found in glioblastomas. This result, coupled with the recent demonstration that intratumoral mobile lipids correlate with microscopic tumor cell necrosis, leads to the hypothesis that mobile lipids observed in vivo in 1H-MR spectroscopy may correlate independently with prognosis of individual patients.

Keyhole imaging is a scheme introduced to improve temporal resolution in dynamic contrast-enhanced MRI by a factor of four or more. A "full" acquisition before contrast administration is followed by truncated acquisitions sensitive primarily to changes in image contrast. Simulations of the point-spread functions that obtain, and their effect on contrast and spatial resolution, reveal significant degradation only for the smallest objects. Our simulations also address the feasibility of three-dimensional keyhold imaging, and demonstrate a potential 16-fold increase in temporal resolution. This suggests roles for keyhole imaging in conventional (nondynamic) precontrast and postcontrast studies and other applications.

Rationale and Objectives: Existing retrieval models for radiology film libraries have not incorporated the influence of previous retrievals. A Markov chain model for the retrieval rates from an analog film library is proposed as a means of considering this effect., Methods: A Markov chain model was developed for the retrieval rates of an analog film library. The Markov chain model required identification of the states of the Markov chain, the required one-step transition probabilities between states, and the initial state probabilities., Results and Conclusions: The results from the Markov chain model compared favorably with the 30-day measurements (25,775 retrievals), but a large enough sample to determine a statistical confidence level was not considered.

ECG-triggered cinematographic studies of the cardiovascular system are hampered by several technical restrictions such as the inability to image end-diastole, ghosting, varying signal intensity, and phase contributions from eddy currents. Retrospective gating may solve these problems, but involves signal manipulation such as interpolating raw data from a time window. In this study, the performance of the two gating strategies was compared in quantitative MR velocity mapping on the abdominal aorta in eight healthy volunteers and on a pulsatile flow phantom. The results were compared to a one-dimensional velocity mapping technique and Doppler ultrasound. Finally, the consequence of decreasing the time window in the raw data interpolation used for retrospective gating was also examined. With retrospective gating, a low-pass filtering was seen, causing significantly prolonged duration and decreased amplitude of flow pulses. However, by reducing the time window retrospectively gated flow measurements were in good agreement with those that are ECG triggered. When fulfilling the demand of a narrow time window for interpolation, retrospective gating offers several advantages in MR velocity mapping.

A new "wireless" method of cardiac imaging is introduced, which, unlike ECG triggering, allows imaging the heart at end-diastole, and greatly reduces smearing artifacts in the phase-encoding direction. It is an improvement over ECG-driven retrospective gating, in that patients with poor ECGs can be imaged. This method extends the applicability of cardiac imaging, and since it requires no physiological monitoring hardware, can be implemented easily on any MR imager. The images produced by this method are superior to those from ECG triggering, especially when viewed in a "cine" loop. The technique described herein is, furthermore, extendable to any area where periodic or quasi-periodic motion is a problem.

A semiautomated computerized method of in vivo morphometric analysis that is based upon high-resolution three-dimensional magnetic resonance imaging has been developed. This morphometric method is efficient and is of greater analytical precision than any other morphometric method currently applied to living human tissue. Including error inherent in image data acquisition, the aggregate error of the methodology, as estimated by the phantom studies, ranges from 4.5 to 9.6%, with incremental error above 4.5% a function of magnetic resonance slice thickness. This method was applied to magnetic resonance scans of 7 normal volunteers. The derived volumes of whole brain and of individual substructures were closely concordant with previously published volumes of normal fresh (unfixed) brains obtained post mortem. This morphometric methodology is potentially applicable to any structure or lesion that can be visualized by magnetic resonance imaging.

Nonspectroscopic magnetic resonance (MR) imaging often shows that a slice is composed of several compartments, each of which can be assumed to have a spatially homogeneous magnetic resonance spectrum, e.g., a limb composed of fat, muscle, bone marrow, and tumor. We show how to use structural information from such a nonspectroscopic image in order to increase the efficiency of subsequent localized spectroscopic measurements. Specifically, knowledge of the boundaries of N compartments makes it possible to reconstruct compartmental spectra from spectroscopic signals from an entire cross section with N or more different degrees of phase encoding. Experimental studies of a two-compartment phantom show that this method (SLIM) can be used to derive regional hydrogen spectra of a single slice from signals with as few as 2 phase-encoding steps, although Fourier transform chemical-shift imaging requires 64 steps to achieve a result of comparable accuracy. SLIM required only 16 phase-encoding steps to obtain accurate regional single slice spectra in a human limb with three compartments. Spectra of similar quality, obtained by Fourier transform chemical-shift imaging, required 256 to 1024 steps.