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PubMed2004

Space-conserving optimal DNA-protein alignment.

DNA-protein alignment algorithms can be used to discover coding sequences in a genomic sequence, if the corresponding protein derivatives are known. They can also be used to identify potential coding sequences of a newly sequenced genome, by using proteins from related species. Previously known algorithms either solve a simplified formulation, or sacrifice optimality to achieve practical implementation. In this paper, we present a comprehensive formulation of the DNA-protein alignment problem, and an algorithm to compute the optimal alignment in O(mn) time using only four tables of size (m + 1) x (n + 1), where m and n are the lengths of the DNA and protein sequences, respectively. We also developed a Protein and DNA Alignment program PanDA that implements the proposed solution. Experimental results indicate that our algorithm produces high quality alignments.

Algorithms↗
PubMed1989

Recurrent deep venous thrombosis: limitations of US.

Compression ultrasound (US) has become widely used to diagnose acute deep venous thrombosis (DVT). To determine the appearance of veins with previous DVT, 60 legs (58 patients) in which DVT had been diagnosed 6-31 months earlier (mean, 15.1 months) were reexamined with compression US. At reevaluation there was no indication of acute DVT. Thirty-two extremities had an appearance consistent with clot at the time of this study; 28 demonstrated normal findings. Variables that correlated with findings at follow-up US included age, location of clot, number of previous clots, pain, and augmentation of flow at compression. These preliminary data indicate that compression US may not be reliable as a follow-up study in patients in whom postphlebotic syndrome develops after an acute episode of DVT.

Follow-Up Studies↗
PubMed1997

Clinical and electrophysiologic characteristics of compressed lumbar nerve roots.

STUDY DESIGN: Clinical and electrophysiologic data of compressed nerve roots were evaluated in patients with lumbar disc herniation. OBJECTIVES: To elucidate the characteristics of the nerve root with respect to preoperative neural deficit and to analyze the predictive factors for recovery of leg paralysis after posterior discectomy. SUMMARY OF BACKGROUND DATA: Prolonged paralysis due to disc herniation is reported to be a poor prognostic factor for motor recovery. In addition, an intraoperative somatosensory evoked potential change has been reported to be correlated with clinical outcome. METHODS: Among 64 patients with a lumbar disc herniation, a variety of clinical data, such as age, gender, duration of leg paralysis or leg pain, the angle of the positive straight leg raising test, and time for recovery from paralysis, were investigated. In addition, threshold, amplitude of compound muscle action potentials, and latency for 85 nerve roots were monitored before and after discectomy. Data were analyzed according to the grade of preoperative neural deficits: Grade 1, severe motor and sensory loss; Grade 2, mild motor and sensory loss; Grade 3, sensory loss only; Grade 4, no deficit (leg pain only); and Grade 5, asymptomatic control. RESULTS: The nerve root threshold before discectomy showed an increase in accordance with the severity of neural deficit. Thresholds of Grade 1 and 2 nerve roots were significantly higher than those of normal control subjects. The average amplitudes of compound muscle action potentials before discectomy in Grade 1 and 2 nerve roots were significantly lower than those of asymptomatic control nerve roots. Elongation of latency also showed a correlation with preoperative neurologic abnormality. Patients who complained of leg pain only were significantly younger, and those who showed severe motor disturbance tended to be older and to show a straight leg raising test angle similar to that of control nerve roots. Severe motor weakness for more than 6 months, a negative straight leg raising test, and age were considered to be poor prognostic factors for motor recovery. CONCLUSIONS: Findings of increased threshold, low amplitude of compound muscle action potentials, and elongated latency correlated with degree of motor weakness. Early decompression for compressed nerve root is recommended, especially in older patients with severe motor weakness presenting a negative straight leg raising test.

Action Potentials↗
PubMedDate not supplied

Digital image compression.

The purpose of this paper is to describe the essential elements of digital image compression and its use in digital radiology. Additionally, this article is intended to increase the shared knowledge between radiologic technologists and radiologists, equipment vendors and information technology personnel.

Canada↗
PubMed2005

Contextual encoding in uniform and adaptive mesh-based lossless compression of MR images.

We propose and evaluate a number of novel improvements to the mesh-based coding scheme for 3-D brain magnetic resonance images. This includes: 1) elimination of the clinically irrelevant background leading to meshing of only the brain part of the image; 2) content-based (adaptive) mesh generation using spatial edges and optical flow between two consecutive slices; 3) a simple solution for the aperture problem at the edges, where an accurate estimation of motion vectors is not possible; and 4) context-based entropy coding of the residues after motion compensation using affine transformations. We address only lossless coding of the images, and compare the performance of uniform and adaptive mesh-based schemes. The bit rates achieved (about 2 bits per voxel) by these schemes are comparable to those of the state-of-the-art three-dimensional (3-D) wavelet-based schemes. The mesh-based schemes have been shown to be effective for the compression of 3-D brain computed tomography data also. Adaptive mesh-based schemes perform marginally better than the uniform mesh-based methods, at the expense of increased complexity.

Algorithms↗
PubMed1992

An efficient algorithm for MR image reconstruction and compression.

In magnetic resonance imaging (MRI), the original data are sampled in the spatial frequency domain. The sampled data thus constitute a set of discrete Fourier transform (DFT) coefficients. The image is usually reconstructed by taking inverse DFT. The image data may then be efficiently compressed using the discrete cosine transform (DCT). We present here a method of using DCT to treat the sampled data, which combines two procedures, image reconstruction and data compression. This method may be particularly useful in medical picture archiving and communication systems (PACS) where both image reconstruction and compression are important issues.

Algorithms↗