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PubMed1993

Compressive properties of the cartilaginous end-plate of the baboon lumbar spine.

The viscoelastic behavior of the cartilaginous end-plate of the baboon (Papio anubis) was studied in an experiment on compressive creep. Data were analyzed with the biphasic poroviscoelastic constitutive theory to assess the relative contributions of flow-dependent and flow-independent viscoelastic mechanisms to the observed creep behavior. Material coefficients describing the equilibrium compressive behavior (HA) and both flow-independent (c, tau 1, and tau 2) and flow-dependent (k) viscoelastic effects were determined for the end-plate by the curve-fitting of the theoretical solution to the experimental creep data. Biochemical analyses were performed to test for potential relationships between material properties and composition which may give rise to the viscoelastic behavior of the end-plate. The results indicate that the cartilaginous end-plate has a hydraulic permeability of 14.3 x 10(-14) m4/N-s, which is associated with rapid transport and pressurization of the interstitial fluid in response to loading and an increased emphasis on flow-independent viscoelastic effects. Biochemical analyses for water, sulfated glycosaminoglycan content, and hydroxyproline indicate that the end-plate of the baboon is compositionally similar to the cartilaginous end-plate in humans. Interpretation of the mechanical and compositional data suggests that fluid pressurization in the cartilaginous end-plate may be important in the maintenance of a uniform stress distribution across the boundary between vertebral body and intervertebral disc.

Animals↗
PubMed1982

Evaluation of tension and compression forces in the canine femur in vivo.

In order to verify the existence of tension and compression forces from the cortical surface of canine femora, rosette strain gauges and a radio telemetry system were used to observe the animals during normal locomotion. Surface strain measured from the lateral cortical surface was consistently in tension whereas surface strain measured from the medial cortical surface was in compression. This data supported in vitro work which showed that eccentric loading of bone results in the convex side of bone being in tension and the concave side of bone being in compression.

Animals↗
PubMed2002

Internet2-based 3D PET image reconstruction using a PC cluster.

We describe an approach to fast iterative reconstruction from fully three-dimensional (3D) PET data using a network of PentiumIII PCs configured as a Beowulf cluster. To facilitate the use of this system, we have developed a browser-based interface using Java. The system compresses PET data on the user's machine, sends these data over a network, and instructs the PC cluster to reconstruct the image. The cluster implements a parallelized version of our preconditioned conjugate gradient method for fully 3D MAP image reconstruction. We report on the speed-up factors using the Beowulf approach and the impacts of communication latencies in the local cluster network and the network connection between the user's machine and our PC cluster.

Algorithms↗
PubMed2025

CREMSA: compressed indexing of (ultra) large multiple sequence alignments.

MOTIVATION: Recent viral outbreaks motivate the systematic collection of pathogenic genomes in order to accelerate their study and monitor the apparition/spread of variants. Due to their limited length and temporal proximity of their sequencing, viral genomes are usually organized, and analyzed as oversized Multiple Sequence Alignments (MSAs). Such MSAs are largely ungapped, and mostly homogeneous on a column-wise level but not at a sequential level due to local variations, hindering the performances of sequential compression algorithms. RESULTS: In order to enable an efficient handling of MSAs, including subsequent statistical analyses, we introduce CREMSA (Column-wise Run-length Encoding for MSAs), a new index that builds on sparse bitvector representations to compress an existing or streamed MSA, all the while allowing for an expressive set of accelerated requests to query the alignment without prior decompression. Using CREMSA, a 65 GB MSA consisting of 1.9M SARS-CoV 2 genomes could be compressed into 22 MB using less than half a gigabyte of main memory, while executing access requests in the order of 100 ns. Such a speed up enables a comprehensive analysis of covariation over this very large MSA. We further assess the impact of the sequence ordering on the compressibility of MSAs and propose a resorting strategy that, despite the proven NP-hardness of an optimal sort, induces greatly increased compression ratios at a marginal computational cost. AVAILABILITY AND IMPLEMENTATION: CREMSA is freely accessible at https://gitlab.univ-lille.fr/cremsa/cremsa. The Snakemake workflow for the benchmarks is available at: https://gitlab.univ-lille.fr/cremsa/bench. The data used in the paper is on Zenodo at https://zenodo.org/records/14698859 and https://zenodo.org/records/15100011.

SARS-CoV-2↗
PubMed2002

Public health, GIS, and the internet.

Internet access and use of georeferenced public health information for GIS application will be an important and exciting development for the nation's Department of Health and Human Services and other health agencies in this new millennium. Technological progress toward public health geospatial data integration, analysis, and visualization of space-time events using the Web portends eventual robust use of GIS by public health and other sectors of the economy. Increasing Web resources from distributed spatial data portals and global geospatial libraries, and a growing suite of Web integration tools, will provide new opportunities to advance disease surveillance, control, and prevention, and insure public access and community empowerment in public health decision making. Emerging supercomputing, data mining, compression, and transmission technologies will play increasingly critical roles in national emergency, catastrophic planning and response, and risk management. Web-enabled public health GIS will be guided by Federal Geographic Data Committee spatial metadata, OpenGIS Web interoperability, and GML/XML geospatial Web content standards. Public health will become a responsive and integral part of the National Spatial Data Infrastructure.

Geographic Information Systems↗
PubMed1986

Sonographic evaluation of cerebral cortical mantle thickness in the fetus and neonate with hydrocephalus.

Sonographic measurement of the occipital, parietal, and frontal cerebral cortical mantle in ten neonates and ten fetuses with moderate to marked hydrocephalus was performed. In 11 of 14 (78.5 per cent) of the neonatal scans and in 10 of 12 (83 per cent) of the fetal scans, the occipital cortical mantle was less than that of the frontal cortical mantle. This difference varied from 1 to 16 mm. While prognostic data regarding compression of the cerebral mantle from ventricular dilatation exist, they are based upon measurements of the frontal-parietal and not the occipital mantle. Because of the difference observed, if these data are to be used in management, the comparable cerebral cortical mantle should be measured.

Cerebral Cortex↗
PubMed1999

Viability of deformed cells.

Most of the researchers in the field of cryobiology believe that the mechanism of damage during freezing with low cooling rates is chemical and related to the hypertonicity of the extracellular solution. However, there is some evidence to indicate that cells may be destroyed during freezing also by compression between ice crystals. We have developed an experimental procedure to study the effect of cell compression on viability. Using human prostate primary adenoma cancer cells we show that cell viability decreases steeply when cells are compressed to 30% of their original diameter. If uniform expansion of cell membrane is assumed, this corresponds to a 50% increase in the cell membrane surface area. A simple mathematical model shows that the temperature at which the compression effect may cause cell damage is related to the spacing between ice crystals. When the ice crystals are spaced at distances comparable to the cell diameter the model combined with our experimental data predicts compression damage at about -1.8 degrees C. This is consistent with experimental observation on frozen cell destruction in the presence of antifreeze proteins.

Adenocarcinoma↗
PubMed2003

Ultrasonic tissue characterization for prostate diagnostics: spectral parameters vs. texture parameters.

An ultrasonic multi-feature tissue characterizing system for the detection of prostate cancer is presented. The system is based on the processing of radio frequency (RF) ultrasonic echo data. Data from 100 patients was acquired in a clinical study. Parameters are extracted from the RF echo data and classified using two adaptive network-based fuzzy inference systems (FIS) working in parallel as a nonlinear classifier. Next to spectral parameters, conventional texture parameters are calculated using demodulated and log-compressed echo data. In the first approach, the classifier is trained on both, spectral and texture parameters. In the second approach, the classifier is only trained on texture parameters. Classification results of both approaches are compared and it is demonstrated, that only the use of spectral parameters yields satisfying classification results. Results of a minimum distance classifier (MDC) are presented for comparison with the fuzzy inference system. For the final fuzzy inference systems used in this approach, the area under the ROC curve is between 84% and 86% for the combined approach and between 70% and 74% for the approach based on texture parameters only.

Aged↗
PubMed2003

Lossy compression of eye movement and auditory brainstem response signals.

Eye movement and auditory brainstem response signals recorded for balance and hearing investigations were used as a medical test battery for several types of lossy compression techniques. These signals are associated with the function of the ears. The former signals are used to assess the balance problems (especially vertigo) of a subject and the latter his or her hearing problems. New technique is also presented based on successive approximation quantization. The effect of information loss on medical parameters computed from the signals in the course of compression was evaluated for brainstem response signals. It is important to ensure that lossy compression techniques of these biomedical signals do not impair medical parameter values computed from the signals.

Algorithms↗
PubMed2025

Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.

The breadth of life's diversity is unfathomable, but public nucleic acid sequencing data offers a window into the dispersion and evolution of genetic diversity across Earth. However the rapid growth and accumulation of sequence data have outpaced efficient analysis capabilities. The largest collection of freely available sequencing data is the Sequence Read Archive (SRA), comprising 27.3 million datasets or 5 × 1016 basepairs. To realize the potential of the SRA, we constructed Logan, a massive sequence assembly transforming short reads into long contigs and compressing the data over 100-fold, enabling highly efficient petabase-scale analysis. We created Logan-Search, a k-mer index of Logan for free planetary-scale sequence search, returning matches in minutes. We used Logan contigs to identify >200 million plastic-degrading enzyme homologs, and validate novel enzymes with catalytic activities exceeding current reference standards. Further, we vastly expand the known diversity of proteins (30-fold over UniRef50), plasmids (22-fold over PLSDB), P4 satellites (4.5-fold), and the recently described Obelisk RNA elements (3.7-fold). Logan also enables ecological and biomedical data mining, such as global tracking of antimicrobial resistance genes and the characterization of viral reactivation across millions of human BioSamples. By transforming the SRA, Logan democratizes access to the world's public genetic data and opens frontiers in biotechnology, molecular ecology, and global health.

Journal Article↗
PubMed1998

Myoelectric activity of the ileum, cecum, and right ventral colon, and cecal emptying of radiolabeled markers in clinically normal ponies.

OBJECTIVES: To determine normal cecal emptying curves for liquid- and solid-phase radiolabeled markers and to further define myoelectric patterns of the ileum, cecum, and colon in healthy ponies. ANIMALS: 6 adult ponies. PROCEDURE: A cecal cannula and 12 bipolar Ag-AgCl recording electrodes were sutured to the ileum, cecum, and right ventral colon of the ponies. Radioisotopes, indium 111-labeled diethyltriaminepentaacetic acid (111In-DTPA) and technetium 99m (99mTc)-labeled sulfur colloid bound to egg albumen, were introduced through the cannula directly into the cecal body. Movement of these markers from the cecum was monitored by a gamma camera, and power exponential clearance curves were generated. Myoelectric data were collected before and after i.v. administration of isotonic saline (0.9% NaCl) solution, and were analyzed for spike burst (SB) rate, relative activity index, and mean burst duration. Myoelectric complexes were identified from observation of chart recordings or compressed, digitized data. RESULTS: Clearance curves were generated for liquid (111In-DTPA)- and solid (99mTc)-phase markers. Marker types were not different with respect to lag phase, but liquid markers emptied at a slightly faster rate than did solids. Baseline values were calculated after saline solution administration for each of the myoelectric variables investigated. A relation between ileal, cecal, and colonic myoelectric activity was identified. Activity consistent with the previously described colonic migrating myoelectric complex in the pelvic flexure was identified in the right ventral colon. CONCLUSIONS AND CLINICAL RELEVANCE: Baseline data on normal cecal emptying was obtained; this technique could be used to evaluate the effect of postulated motility-modifying treatments used in equine practice.

Animals↗
PubMed2001

Lumbar spine disc height and curvature responses to an axial load generated by a compression device compatible with magnetic resonance imaging.

STUDY DESIGN: Axial load-dependent changes in the lumbar spine of supine healthy volunteers were examined using a compression device compatible with magnetic resonance imaging. OBJECTIVE: To test two hypotheses: Axial loading of 50% body weight from shoulder to feet in supine posture 1) simulates the upright lumbar spine alignment and 2) decreases disc height significantly. SUMMARY OF BACKGROUND DATA: Axial compression on the lumbar spine has significantly narrowed the lumbar dural sac in patients with sciatica, neurogenic claudication or both. METHODS: Using a device compatible with magnetic resonance imaging, the lumbar spine of eight young volunteers, ages 22 to 36 years, was axially compressed with a force equivalent to 50% of body weight, approximating the normal load on the lumbar spine in upright posture. Sagittal lumbar magnetic resonance imaging was performed to measure intervertebral angle and disc height before and during compression. RESULTS: Each intervertebral angle before and during compression was as follows: T12-L1 (-0.8 degrees +/- 2.5 degrees and -1.5 degrees +/- 2.6 degrees ), L1-L2 (0.7 degrees +/- 1.4 degrees and 3.3 degrees +/- 2.9 degrees ), L2-L3 (4.7 degrees +/- 3.5 degrees and 7.3 degrees +/- 6 degrees ), L3-L4 (7.9 degrees +/- 2.4 degrees and 11.1 degrees +/- 4.6 degrees ), L4-L5 (14.3 degrees +/- 3.3 degrees and 14.9 degrees +/- 1.7 degrees ), L5-S1 (25.8 degrees +/- 5.2 degrees and 20.8 degrees +/- 6 degrees ), and L1-S1 (53.4 degrees +/- 11.9 degrees and 57.3 degrees +/- 16.7 degrees ). Negative values reflect kyphosis, and positive values reflect lordosis. A significant difference between values before and during compression was obtained at L3-L4 and L5-S1. There was a significant decrease in disc height only at L4-L5 during compression. CONCLUSIONS: The axial force of 50% body weight in supine posture simulates the upright lumbar spine morphologically. No change in intervertebral angle occurred at L4-L5. However, disc height at L4-L5 decreased significantly during compression.

Adult↗
PubMedDate not supplied

[Normal and pathological compression of the venous system].

A study of 190 female patients was carried out at the level of the solar ring, the crural arch, the left ilio-caval junction and the vena cava ring of the diaphragm, in order to determine whether these represent, per se, critical areas, which may cause compression and hinder the venous return as a result of the narrowing and the poor distention of their structures. Sonotomography alone or associated with the pulsed Doppler were selected for this study. The action of the various components (bone, muscle, tendon, vessels and nodes) on the venous system is each region, was analyzed. The overall results have demonstrated two types of compression: a) intermittent, b) permanent. The former is considered as a hemokinetic mechanism, especially at the level of the solar arch and the vena cava ring of the diaphragm. They represent a major element of the pump and the vis-a front respectively. The permanent compression was considered as pathological, and could be related to a venous displacement occurring as an adaptation mechanism to the extrinsic compression. The data obtained in all four regions, have demonstrated that their various components are in a precarious balance, but they do not constitute a true obstacle to the venous return, even if in some postures or respiratory movements they may cause an intermittent venous compression.

Adult↗
PubMed2001

Ultrasonic characterization of the curing process of hydroxyapatite-modified bone cement.

Ultrasonic parameters such as velocity of sound and broad-band ultrasonic attenuation (BUA) are sensitive to changes in the viscoelastic properties of a material. Bone cement undergoes changes is these properties as it cures. By monitoring the propagation of ultrasonic pulses through a sample of curing bone cement, the curing reaction of polymethylmethacrylate-based (PMMA) bone cement was investigated for hydroxyapatite (HA) concentrations of 0, 10, and 30% (by weight). As the material hardens, the velocity of sound increases by 70%. BUA shows a large peak at the midpoint of the velocity transition. These data are used to compare the cure time and cure duration for PMMA bone cement mixed with hydroxyapatite particles. Measurements of the final sound velocity and BUA were also performed to investigate the mechanical properties of the fully cured cement, and to compare to compression testing data. This is the first time the curing process of bone cement has been investigated as a function of hydroxyapatite concentration. Results indicate that the cure time is not significantly affected by the addition of HA particles, and that both velocity of sound and BUA are sensitive to the curing process.

Bone Cements↗
PubMed2000

Biomechanical evaluation of a new bone cement for use in vertebroplasty.

STUDY DESIGN: Comparative ex vivobiomechanical study. OBJECTIVES: To determine the strength and stiffness of osteoporotic vertebral bodies subjected to compression fractures and subsequently stabilized via bipedicular injection of one of two bone cements: one is a commercially available polymethylmethacrylate (Simplex P) and one is a proprietary glass-ceramic-reinforced BisGMA/BisEMA/TEGDMA matrix composite that is being developed for use in vertebroplasty (Orthocomp). SUMMARY OF BACKGROUND DATA: Osteoporotic compression fractures present diagnostic and therapeutic challenges for the clinician. Vertebroplasty, a new technique for treating such fractures, stabilizes vertebral bodies by injection of cement. Little is known, however, about the biomechanics of this treatment. METHODS: Five vertebral bodies (L1-L5) from each of four fresh spines were harvested from female cadavers (age, 80 +/- 5 years), screened for bone density using DEXA (t = -3.4 to -6.4), disarticulated, and compressed in a materials testing machine to determine initial strength and stiffness. The fractures then were repaired using a transpedicular injection of either Orthocomp or Simplex P and recrushed. RESULTS: For both cement treatments, vertebral body strength after injection of cement was significantly greater than initial strength values. Vertebral bodies augmented with Orthocomp recovered their initial stiffness; however, vertebral bodies augmented with Simplex P were significantly less stiff than they were in their initial condition. CONCLUSIONS: Augmentation with Orthocomp results in similar or greater mechanical properties compared with Simplex P, but these biomechanical results have yet to be substantiated in clinical studies.

Aged↗
PubMed1997

Focal hepatic lesions: effect of three-dimensional wavelet compression on detection at CT.

PURPOSE: To evaluate the effect of three-dimensional, wavelet-based compression on the detection of focal hepatic lesions at computed tomography (CT). MATERIALS AND METHODS: CT images obtained in 69 patients with focal hepatic lesions were studied (35 consecutive cases and 34 cases selected to be difficult on the basis of lesion size or contrast). Image data were compressed by means of a three-dimensional, wavelet-based algorIthm at ratios of 10:1, 15:1, and 20:1. Normal and abnormal sections (on original and compressed images) were reviewed by using an interactive workstation. Four readers rated the presence or absence of a lesion with a five-point scale. RESULTS: At receiver operating characteristic analysis, no statistically significant difference was detected for all cases considered together. Differences approached but did not reach statistical significance for the diagnostic performance of one reader with compressed images (15:1, P = .054; 20:1, P = .051). For the subset of difficult cases, a significant difference was observed with 20:1 compressed images for one reader (P = .026). Diagnostic performance of readers was less certain in normal than in abnormal cases with both original and compressed images (difference was significant for 15:1 [P = .035] and 20:1 [P < .0001] compressed images). CONCLUSION: Three-dimensional wavelet compression is satisfactory at ratios of at least 10:1. Additional studies with a larger sample would help confirm findings with higher ratios.

Cysts↗
PubMed2000

Effect of CT digital image compression on detection of coronary artery calcification.

PURPOSE: To test the effect of digital compression of CT images on the detection of small linear or spotted high attenuation lesions such as coronary artery calcification (CAC). MATERIAL AND METHODS: Fifty cases with and 50 without CAC were randomly selected from a population that had undergone spiral CT of the thorax for screening lung cancer. CT image data were compressed using JPEG (Joint Photographic Experts Group) or wavelet algorithms at ratios of 10:1, 20:1 or 40:1. Five radiologists reviewed the uncompressed and compressed images on a cathode-ray-tube. Observer performance was evaluated with receiver operating characteristic analysis. RESULTS: CT images compressed at a ratio as high as 20:1 were acceptable for primary diagnosis of CAC. There was no significant difference in the detection accuracy for CAC between JPEG and wavelet algorithms at the compression ratios up to 20:1. CT images were more vulnerable to image blurring on the wavelet compression at relatively lower ratios, and "blocking" artifacts occurred on the JPEG compression at relatively higher ratios. CONCLUSION: JPEG and wavelet algorithms allow compression of CT images without compromising their diagnostic value at ratios up to 20:1 in detecting small linear or spotted high attenuation lesions such as CAC, and there was no difference between the two algorithms in diagnostic accuracy.

Adult↗