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PubMed2000

Enhanced 3D PET OSEM reconstruction using inter-update Metz filtering.

We present an enhancement of the OSEM (ordered set expectation maximization) algorithm for 3D PET reconstruction, which we call the inter-update Metz filtered OSEM (IMF-OSEM). The IMF-OSEM algorithm incorporates filtering action into the image updating process in order to improve the quality of the reconstruction. With this technique, the multiplicative correction image--ordinarily used to update image estimates in plain OSEM--is applied to a Metz-filtered version of the image estimate at certain intervals. In addition, we present a software implementation that employs several high-speed features to accelerate reconstruction. These features include, firstly, forward and back projection functions which make full use of symmetry as well as a fast incremental computation technique. Secondly, the software has the capability of running in parallel mode on several processors. The parallelization approach employed yields a significant speed-up, which is nearly independent of the amount of data. Together, these features lead to reasonable reconstruction times even when using large image arrays and non-axially compressed projection data. The performance of IMF-OSEM was tested on phantom data acquired on the GE Advance scanner. Our results demonstrate that an appropriate choice of Metz filter parameters can improve the contrast-noise balance of certain regions of interest relative to both plain and post-filtered OSEM, and to the GE commercial reprojection algorithm software.

Algorithms↗

PubMed1991

Trends in future urodynamics: computer support-data base-digitized imaging.

The use of computers in urodynamics must be based preferably on the structure of the urodynamic investigation itself. This enables implementation of computerized systems in the urodynamic laboratory in the most natural way and provides transparency of urodynamic software for the investigators. Additionally, the algorithms of the urodynamic software then can provide for a urodynamic investigation following a logical path based on the patient's history and clinical data and (automatically interpreted) results from earlier steps in the urodynamics. As an extension of this structured logical reasoning, the computer use in urodynamics can be extended to include validation and decision rules, comprising measurement data and rules for interpretation and combination of history, clinical and measurement data. Conclusions will be presented then in the form of a preliminary differential diagnosis, including the odds for each of the possible diagnoses. These kinds of computerized interpretation systems will be validated by comparison with the classical clinical diagnoses and are generally known as expert systems. These systems rely on logical branching-as opposed to systems that are statistical in nature and use large data bases to classify individual data into known groups. Data bases will remain for the purpose of documentation, based on individual patients and comprising all patient data-comparable to the existing patient files in the hospital's archives. The computer files have to include also the original data from functional studies like urodynamics-and not just the abstracted conclusions-and from imaging techniques. Intelligent compression of data prevents the data bases from exploding. Digital imaging techniques combined with computerized urodynamic investigations open possibilities for dynamic analysis of morphologic data and combination thereof with urodynamic measurement data.

Databases, Factual↗

PubMed1999

Adaptation of bulk constitutive equations to insoluble monolayer collapse at the air-water interface.

A constitutive equation based on stress-strain models of bulk solids was adapted to relate the surface pressure, compression rate, and temperature of an insoluble monolayer of monodendrons during collapse at the air-water interface. A power law relation between compression rate and surface pressure and an Arrhenius temperature dependence of the steady-state creep rate were observed in data from compression rate and creep experiments in the collapse region. These relations were combined into a single constitutive equation to calculate the temperature dependence of the collapse pressure with a maximum error of 5 percent for temperatures ranging from 10 degrees to 25 degrees C.

Air↗

PubMed1988

Saccular aneurysm of the transverse thoracic aorta detected by transesophageal echocardiography.

A patient with a saccular aneurysm of the thoracic aortic arch presented with severe right ventricular failure due to pulmonary artery compression. Contradictory data were derived from computed tomography, pulmonary isotope perfusion scan and cardiac catheterization. Transesophageal echocardiography revealed a saccular aneurysm which compressed the main pulmonary artery and gave access to a fistulous connection to the left pulmonary artery. Surgery confirmed these findings.

Aorta, Thoracic↗

PubMed2000

Load-carrying capacity of the human cervical spine in compression is increased under a follower load.

STUDY DESIGN: An experimental approach was used to test human cadaveric cervical spine specimens. OBJECTIVE: To assess the response of the cervical spine to a compressive follower load applied along a path that approximates the tangent to the curve of the cervical spine. SUMMARY OF BACKGROUND DATA: The compressive load on the human cervical spine is estimated to range from 120 to 1200 N during activities of daily living. Ex vivo experiments show it buckles at approximately 10 N. Differences between the estimated in vivo loads and the ex vivo load-carrying capacity have not been satisfactorily explained. METHODS: A new experimental technique was developed for applying a compressive follower load of physiologic magnitudes up to 250 N. The experimental technique applied loads that minimized the internal shear forces and bending moments, loading the specimen in nearly pure compression. RESULTS: A compressive vertical load applied in the neutral and forward-flexed postures caused large changes in cervical lordosis at small load magnitudes. The specimen collapsed in extension or flexion at a load of less than 40 N. In sharp contrast, the cervical spine supported a load of up to 250 N without damage or instability in both the sagittal and frontal planes when the load path was tangential to the spinal curve. The cervical spine was significantly less flexible under a compressive follower load compared with the hypermobility demonstrated under a compressive vertical load (P < 0.05). CONCLUSION: The load-carrying capacity of the ligamentous cervical spine sharply increased under a compressive follower load. This experiment explains how a whole cervical spine can be lordotic and yet withstand the large compressive loads estimated in vivo without damage or instability.

Cadaver↗

PubMed1988

Measurements of bone strain in foals with altered foot balance.

Two to 7 days after birth, 9 foals were anesthetized, and strain gauges were applied to lateral and medial aspects of the third metacarpal bone of the left forelimb. In 5 of these foals, strain gauges also were applied to the radius of the left forelimb. Four to 6 days later, foals were walked (5 sets of 10 to 20 strides), and compressive and tensile strains in the bone beneath strain gauges were recorded on paper and diskette. After recording base-line data, a wedge was fitted to the hoof of the limb with the strain gauges, in such a way that the lateral bearing surface was raised, and strains were recorded again. The wedge was left in place, and further recordings were made every 2 to 3 days for 10 days. At the normal walk (base-line data), the compressive strain was higher than the tensile strain in the third metacarpal bone, on the medial side of which the mean principal compressive strain was approximately twice that on the lateral surface. Immediately after application of the wedge, strain values from the medial surface of the third metacarpal bone decreased by 40%, and the lateral surface compressive strain increased by 100%. These changes gradually decreased over 10 days, at which time there was no significant difference from base-line values (P less than 0.05). Similar but much less obvious trends were observed in the radius. Abnormal hoof balance apparently had no lasting effect on compressive forces running through the limb, and the natural situation of higher compressive strain medially was restored quickly.

Animals↗

PubMedDate not supplied

Video on the Internet: An introduction to the digital encoding, compression, and transmission of moving image data.

In this paper, we seek to provide an introduction to the fast-moving field of digital video on the Internet, from the viewpoint of the biological microscopist who might wish to store or access videos, for instance in image databases such as the BioImage Database (http://www.bioimage.org). We describe and evaluate the principal methods used for encoding and compressing moving image data for digital storage and transmission over the Internet, which involve compromises between compression efficiency and retention of image fidelity, and describe the existing alternate software technologies for downloading or streaming compressed digitized videos using a Web browser. We report the results of experiments on video microscopy recordings and three-dimensional confocal animations of biological specimens to evaluate the compression efficiencies of the principal video compression-decompression algorithms (codecs) and to document the artefacts associated with each of them. Because MPEG-1 gives very high compression while yet retaining reasonable image quality, these studies lead us to recommend that video databases should store both a high-resolution original version of each video, ideally either uncompressed or losslessly compressed, and a separate edited and highly compressed MPEG-1 preview version that can be rapidly downloaded for interactive viewing by the database user.

Algorithms↗

PubMed1989

Edema formation in spinal nerve roots induced by experimental, graded compression. An experimental study on the pig cauda equina with special reference to differences in effects between rapid and slow onset of compression.

Edema formation in spinal nerve roots of the pig cauda equina was studied following experimental compression at various pressure levels, durations, and rates of onset, using a fluorescence microscopic technique. The time-pressure thresholds for the occurrence of edema in the nerve roots were: following rapid onset of compression (0.05-0.1 seconds), 2 minutes at both 50 mm Hg and 200 mm Hg, and following slow onset of compression (the pressure was slowly increased during 15-20 seconds), 2 hours at 50 mm Hg and 2 minutes at 200 mm Hg. Generally, the edema formation was more pronounced after rapid than after slow onset of compression. The data in this study also indicate that intraneural edema might be more easily formed in nerve roots than in peripheral nerves after compression injury.

Animals↗

PubMed1994

[The compression of numerical radiological images].

A digital radiological image is made by a number of pixels, each of them characterized by a definite numerical value obtained by quantization which represents the luminance in that specific image unit. Spatial resolution and dynamic range are the main factors in determining the quality of a digital radiological image. The product of the two above factors defines the global dimensions of the image and is expressed in bits. In conventional radiographic images the global dimension of the image is expressed in MBytes, because of its high spatial and contrast resolution. To reduce the visualization and storage requirements as well as the transmission time of large image data sets, compression algorithms have been recently introduced. These algorithms are based on the fact that often in a digital image parts of the binary data are "redundant", that is they are not necessary for correct image representation. Therefore, compression methods are aimed at reducing both statistical and perceptive redundancy. Statistical redundancy is reduced by means of lossless coding which does not allow to compress images with a ratio higher than 4-5:1 and that--by definition--allows to recover the original image quality. On the other hand "lossy" compression algorithms, which eliminate the perceptive redundancy, are based on the reduction of spatial resolution and dynamic range and on transform-based methods. In particular, the latter have usually been more successful in terms of efficient compression, even when applied to conventional radiographic images. The basic transform procedure can be modified at various levels. JPEG is one of these methods, originally developed for photographic images, which can be usefully applied to radiological images as well. Lossy procedures allow to reach higher compression ratios than lossless methods, but the decrease in information content must be prevented from reducing diagnostic accuracy. In order to assess the diagnostic efficiency of the images compressed with lossy methods, semi-objective analyses are usually performed and ROC curves are produced and evaluated. A model ROC analysis is presented.

Algorithms↗

PubMed2001

A linear relation between the compressibility and density of blood.

By considering the blood as a mixture of ultrafiltrate and protein concentrate, the additive nature of compressibility and density from the components is utilized to deduce a linear relation between the compressibility and density for blood. This deduction also indicates that the intercept and slope of the linear relation are independent of the hematocrit, plasma protein concentration, and hemoglobin concentration of red blood cells. To verify experimentally this linear relation, saline and plasma dilutions on porcine or canine blood flowing in an extracorporeal circuit were carried out. The hematocrit of the experiments ranges from 0% to 55% and the plasma protein concentration ranges from 10 to 90 g/l. A resonance device in the circuit measured the density rhob of blood at 37 degrees C and an ultrasound system measured the sound velocity cb. The range of density is from 1,010 to 1,060 g/l and that of sound velocity is from 1,530 to 1,580 m/s. The linear relation that best fits the data of compressibility [computed as (rhob cb(2))-1] and density has a correlation coefficient of 0.9978. The linear relation is found to fit well the dependence of compressibility on density derived from the sound velocity data of human, horse, and porcine blood in the literature.

Animals↗

PubMed1999

Wavelet image compression--the quadtree coding approach.

Perfect reconstruction, quality scalability, and region-of-interest coding are basic features needed for the image compression schemes used in telemedicine applications. This paper proposes a new wavelet-based embedded compression technique that efficiently exploits the intraband dependencies and uses a quadtree-based approach to encode the significance maps. The algorithm produces a losslessly compressed embedded data stream, supports quality scalability, and permits region-of-interest coding. Moreover, experimental results obtained on various images show that the proposed algorithm provides competitive lossless/lossy compression results. The proposed technique is well suited for telemedicine applications that require fast interactive handling of large image sets, over networks with limited and/or variable bandwidth.

Algorithms↗

PubMedDate not supplied

External pneumatic intermittent compression for treatment of dependent pregnancy edema.

A portable external pneumatic intermittent compression (EPIC) device has been successful in reducing peripheral edema. This study explored the effectiveness of EPIC for treating dependent pregnancy edema. In the study, 42 healthy pregnant women received EPIC for 30 minutes at 40 torr while in the left lateral recumbent position: Group One with mid-thigh boots, and Group Two with below-knee boots. Prior to compression, descriptive data were gathered, leg circumference measurements made, and surface skin temperatures recorded for three sites per leg. Vital signs were taken and pedal edema subjectively indexed. Following compression, circumferences, skin temperatures, vital signs, and edema indices were rerecorded. Three volumes were calculated for each leg using a mathematical model of leg segments as conical frustum units. Mean volume reductions for each leg were significant. The mid-thigh-length boots produced greater mean volume decreases. The volume decrease for calf, lower leg, and foot frustum units were significant. EPIC holds promise as a useful treatment for dependent pregnancy edema.

Adolescent↗

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↗

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↗

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↗

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↗