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PubMed1997

Compression guidelines for diagnostic telepathology.

As the healthcare community has begun to rely increasingly upon digital technologies for acquisition, storage, and transmission of pictorial data, image compression has become an indispensable tool. We have investigated the feasibility of lossy compression in a well-defined task domain, the clinical assessment of digitized images of chromatic microscopic pathology specimens. The effect of compression was measured under two distinct perceptual criteria, just noticeable difference (j.n.d.) and largest tolerable distortion (l.t.d.), differing in the involvement required from subjects, who were experts in pathology. For standard JPEG compressed images it was found that when the experiment is performed under the l.t.d. criterion, a significantly larger compression ratio is reported as satisfactory. It is concluded that lossy compression holds promise for diagnostic telepathology.

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PubMed1998

Compression-induced degeneration of the intervertebral disc: an in vivo mouse model and finite-element study.

STUDY DESIGN: An in vivo study of the biologic and biomechanical consequences of static compressive loading on the mouse tail intervertebral disc. OBJECTIVES: To determine whether static compression in vivo alters the biologic activity of the disc and leads to diminished biomechanical performance. SUMMARY OF BACKGROUND DATA: Static compressive stress that exceeds the disc's swelling pressure is known to change hydration and the intradiscal stress distribution. Alterations in hydration and stress have been associated with changes in disc cell activity in vitro and in other collagenous tissues in vivo. METHODS: Mouse tail discs were loaded in vivo with an external compression device. After 1 week at one of three different stress levels, the discs were analyzed for their biomechanical performance, morphology, cell activity, and cell viability. A second group of mice were allowed to recuperate for 1 month after the 1-week loading protocol to assess the disc's ability to recover. As an aid to interpreting the histologic and biologic data, finite-element analysis was used to predict region-specific changes in tissue stress caused by the static loading regimen. RESULTS: With increasing compressive stress, the inner and middle anulus became progressively more disorganized, and the percentage of cells undergoing apoptosis increased. The expression of Type II collagen was suppressed at all levels of stress, whereas the expression of aggrecan decreased at the highest stress levels in apparent proportion to the decreased nuclear cellularity. Compression for 1 week did not affect the disc bending stiffness or strength but did increase the neutral zone by 33%. As suggested by the finite-element model, during sustained compression, tension is maintained in the outer anulus and lost in the inner and middle regions where the hydrostatic stress was predicted to increased nearly 10-fold. Discs loaded at the lowest stress recovered anular architecture but not cellularity after 1 month of recuperation. Discs loaded at the highest stress did not recover anular architecture, displaying islands of cartilage cells in the middle anulus at sites previously populated by fibroblasts. CONCLUSIONS: The results of the current project demonstrate that static compressive loading initiates a number of harmful responses in a dose-dependent way: disorganization of the anulus fibrosus; an increase in apoptosis and associated loss of cellularity; and down regulation of collagen II and aggrecan gene expression. The finite element model used in this study predicts loss of collagen fiber tension and increased matrix hydrostatic stress in those anular regions observed to undergo programmed cell death after 1 week of loading and ultimately become populated by chondrocytes after one month of recuperation. This correspondence conforms with the suggestions of others that the cellular phenotype in collagenous tissues is sensitive to the dominant type of tissue stress. Although the specific mechanisms by which alterations in tissue stress lead to apoptosis and variation in cell phenotype remain to be identified, our results suggest that maintenance of appropriate stress within the disc may be an important basis for strategies to mitigate disc degeneration and initiate disc repair.

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PubMed2026

RSHash: a fast and space-efficient hash table for k-mers.

SUMMARY: Large genomic data collections can be viewed as a continuous string of DNA characters. The essential operations for data structures indexing the k-mer content of such a string are lookup and locate. Lookup determines whether a query k-mer q exists in the string and locate returns all locations in the string where q is present. High-throughput DNA sequencing generates very many k-mer sets of size exceeding billions of characters. In such scenarios, memory consumption and query efficiency pose significant challenges to a data structure supporting the above mentioned queries. To address this problem, we describe a simple, compressed, static data structure for k-mers that answers lookup and can be extended for supporting locate. The general scheme follows the use of minimizers like the state-of-the art SSHash. However, instead of using minimum perfect hash functions our solution (RSHash for Rank-Select Hash) relies on bitvectors with rank and select support, a multiple layered minimizer scheme, and a clever buffering strategy. We can show that RSHash is on average 40% and in some cases up to two times faster than SSHash while having the same memory requirements. Indeed we can go as low as 8 bits per canonical 31-mer on a human dataset. AVAILABILITY: https://github.com/jonsmcode/rshash.

Sequence Analysis, DNA↗
PubMed2005

Using sequence compression to speedup probabilistic profile matching.

MOTIVATION: Matching a biological sequence against a probabilistic pattern (or profile) is a common task in computational biology. A probabilistic profile, represented as a scoring matrix, is more suitable than a deterministic pattern to retain the peculiarities of a given segment of a family of biological sequences. Brute-force algorithms take O(NP) to match a sequence of N characters against a profile of length P << N. RESULTS: In this work, we exploit string compression techniques to speedup brute-force profile matching. We present two algorithms, based on run-length and LZ78 encodings, that reduce computational complexity by the compression factor of the encoding.

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PubMed2001

Characteristics of velocity-controlled knee movement in patients with cervical compression myelopathy: what is the optimal rehabilitation exercise for spastic gait?

STUDY DESIGN: The isokinetic strength of knee extensors and flexors was measured at various controlled velocities in patients with spastic paraparesis caused by cervical compression myelopathy. OBJECTIVE: To evaluate leg function objectively in patients with myelopathy. SUMMARY OF BACKGROUND DATA: Cervical compression myelopathy causes varying degrees of spastic paresis in the legs and affects the activities of patients. However, the leg function characteristics of the patients have not been fully elucidated. METHODS: Velocity-controlled voluntary knee movements were studied in 39 patients (25 men and 14 women) with compression myelopathy. Their mean age was 60.2 years (range, 44-77 years). The patients were divided into Group A (ambulation without aid, n = 22) and Group AA (ambulation with aid, n = 17). Isometric peak torque values were measured in knee flexor and extensor muscles at 60 degrees of knee flexion, and isokinetic peak torque values were determined in maximal voluntary concentric movements of these muscles at constant angle velocities of 40 degrees, 80 degrees, 120 degrees, 160 degrees, and 180 degrees per second. The relative strength (percentage of isometric peak torque value) of the isokinetic motion was calculated at each velocity. RESULTS: In both groups, the relative strength decreased as the velocity increased, and the degree of reduced strength in the flexors at the high velocities of 160 degrees and 180 degrees per second was significantly greater in Group AA than in Group A (P < 0.05), whereas no significant difference was found in the extensors between the groups. CONCLUSIONS: The results indicate that isokinetic strength at a high velocity may reflect the severity of spastic paresis in the legs resulting from compression myelopathy.

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