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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↗

PubMed1997

Near-infrared spectroscopy for monitoring of tissue oxygenation of exercising skeletal muscle in a chronic compartment syndrome model.

Variations in the levels of muscle hemoglobin and of myoglobin oxygen saturation can be detected non-invasively with near-infrared spectroscopy. This technique could be applied to the diagnosis of chronic compartment syndrome, in which invasive testing has shown increased intramuscular pressure associated with ischemia and pain during exercise. We simulated chronic compartment syndrome in ten healthy subjects (seven men and three women) by applying external compression, through a wide inflatable cuff, to increase the intramuscular pressure in the anterior compartment of the leg. The tissue oxygenation of the tibialis anterior muscle was measured with near-infrared spectroscopy during gradual inflation of the cuff to a pressure of forty millimeters of mercury (5.33 kilopascals) during fourteen minutes of cyclic isokinetic dorsiflexion and plantar flexion of the ankle. The subjects exercised with and without external compression. The data on tissue oxygenation for each subject then were normalized to a scale of 100 per cent (the baseline value, or the value at rest) to 0 per cent (the physiological minimum, or the level of oxygenation achieved by exercise to exhaustion during arterial occlusion of the lower extremity). With external compression, tissue oxygenation declined at a rate of 1.4 +/- 0.3 per cent per minute (mean and standard error) during exercise. After an initial decrease at the onset, tissue oxygenation did not decline during exercise without compression. The recovery of tissue oxygenation after exercise was twice as slow with compression (2.5 +/- 0.6 minutes) than it was without the use of compression (1.3 +/- 0.2 minutes).

Adolescent↗

PubMed2026

Optimizing sparse and skew hashing: faster k-mer dictionaries.

MOTIVATION: Representing a set of k-mers-strings of length k-in small space under fast lookup queries is a fundamental requirement for several applications in Bioinformatics. A data structure based on sparse and skew hashing (SSHash) was recently proposed for this purpose (Pibiri 2022): it combines good space effectiveness with fast lookup and streaming queries. It is also order-preserving, i.e. consecutive k-mers (sharing a prefix-suffix overlap of length k-1) are assigned consecutive hash codes which helps compressing satellite data typically associated with k-mers, like abundances and color sets in colored De Bruijn graphs. RESULTS: We study the problem of accelerating queries under the sparse and skew hashing indexing paradigm, without compromising its space effectiveness. We propose a refined data structure with less complex lookups and fewer cache misses. We give a simpler and faster algorithm for streaming lookup queries. The refined architecture translates to substantial performance gains, outperforming the original version of SSHash in both index construction speed and query efficiency. Compared to indexes with similar capabilities and based on the Burrows-Wheeler transform, like SBWT and FMSI, SSHash is significantly faster to build and query. SSHash is competitive in space with the fast (and default) modality of SBWT when both k-mer strands are indexed. While larger than FMSI, it is also more than one order of magnitude faster to query. AVAILABILITY AND IMPLEMENTATION: The SSHash software is available at https://github.com/jermp/sshash, and also distributed via Bioconda. A benchmark of data structures for k-mer sets is available at https://github.com/jermp/kmer_sets_benchmark. The datasets used in this article are described and available at https://zenodo.org/records/17582116.

Algorithms↗

PubMed1999

Extraspinal bone and soft-tissue tumors as a cause of sciatica. Clinical diagnosis and recommendations: analysis of 32 cases.

STUDY DESIGN: Between 1982 and 1997, the authors treated 32 patients with sciatica who subsequently were found to have a tumor along the extraspinal course of the sciatic nerve. SUMMARY OF BACKGROUND DATA: Extraspinal compression of the sciatic nerve by a tumor is a rare cause of sciatica. Signs and symptoms overlap those of the more common causes of sciatica (i.e., herniated disc and spinal stenosis). OBJECTIVE: To characterize the unique clinical presentation of these patients and to formulate guidelines that may lead to early diagnosis. METHODS: All pertinent clinical data and studies were reviewed retrospectively, and standard demographic data were collected for analysis. RESULTS: These patients typically sought treatment for an insidious onset of sciatic pain that was constant, progressive, and unresponsive to change in position or bed rest. The mean time to final diagnosis was 11.9 months (median, 6 months). Seventeen patients were able to locate their pain to a specific point along the extraspinal course of the sciatic pain, and a mass was noted in 13 patients. Eighteen of these tumors were in the pelvis, 10 in the thigh, and 4 in the popliteal fossa and calf. CONCLUSIONS: A high index of clinical suspicion is the key to early diagnosis of bone or soft-tissue tumors as a cause of sciatica; special attention should be given to pain pattern, physical examination of the entire course of the sciatic nerve, and selection of proper imaging studies. Routine anteroposterior plain radiography of the pelvis as part of the initial imaging screening process is recommended.

Bone Neoplasms↗

PubMed2002

Linear modes of gene expression determined by independent component analysis.

MOTIVATION: The expression of genes is controlled by specific combinations of cellular variables. We applied Independent Component Analysis (ICA) to gene expression data, deriving a linear model based on hidden variables, which we term 'expression modes'. The expression of each gene is a linear function of the expression modes, where, according to the ICA model, the linear influences of different modes show a minimal statistical dependence, and their distributions deviate sharply from the normal distribution. RESULTS: Studying cell cycle-related gene expression in yeast, we found that the dominant expression modes could be related to distinct biological functions, such as phases of the cell cycle or the mating response. Analysis of human lymphocytes revealed modes that were related to characteristic differences between cell types. With both data sets, the linear influences of the dominant modes showed distributions with large tails, indicating the existence of specifically up- and downregulated target genes. The expression modes and their influences can be used to visualize the samples and genes in low-dimensional spaces. A projection to expression modes helps to highlight particular biological functions, to reduce noise, and to compress the data in a biologically sensible way.

Algorithms↗

PubMed1999

Movement-related variation in forces under compression stockings.

OBJECTIVES: Compression therapy is widely used in the treatment of venous leg ulcers, but the efficacy of this treatment is variable. Assessment of variation in compression forces associated with movement may help to elucidate the mechanism of action of compression therapy. The aim of this study was to develop and apply a system to investigate forces under compression stockings during movement. METHOD: Three sensors were placed on the medial aspect of the left leg on six healthy volunteers to monitor forces under class 2 (Continental European classification) compression stockings. Data were recorded during dorsiflexion and plantar flexion of the left foot and also during short periods of walking. RESULTS: Changes in pressure were observed, associated with dorsiflexion and plantar flexion of the foot. These changes were dependent on sensor position. Changes in pressure during walking were also position-dependent and of variable duration. CONCLUSIONS: The system enables forces associated with compression therapy to be examined during movement and may thus be of value in further understanding its mechanism of action. Foot movement can be associated with clear changes in pressure under compression stockings and rapid changes in pressure may occur during walking.

Adult↗

PubMed1988

The pathogenesis of spinal epidural abscess: microangiographic studies in an experimental model.

An experimental model of spinal epidural abscess was developed in rabbits by injecting Staphylococcus aureus into the posterior thoracolumbar epidural space. This model has been shown to reproduce the neurological, bacteriological, and radiological aspects of the human disease. In this study, the effect of the infectious epidural mass on the vasculature of the spinal cord in paraplegic rabbits was studied using microangiographic techniques. The normal vascular anatomy of the rabbit spinal cord was defined in control experiments. Vascular proliferation was demonstrated in the epidural space surrounding the abscesses. Anterior and paired posterior spinal arteries remained patent in paraplegic rabbits with mild or moderate spinal cord compression and in some cases of severe compression. In animals with severe compression, the anterior epidural venous plexus remained patent, but the dorsal spinal vein was occluded. Occlusion of perforating arteries occurred only with extreme spinal cord compression. These data indicate that the initial neurological deficit associated with experimental spinal epidural abscess is not due to vascular thrombosis.

Abscess↗

PubMed2000

Wavelet compression on detection of brain lesions with magnetic resonance imaging.

The purpose of this report is to assess clinically acceptable compression ratios on the detection of brain lesions at magnetic resonance imaging (MRI). Four consecutive T2-weighted and the corresponding T1-weighted images obtained in 20 patients were studied for 109 anatomic sites including 50 with lesions and 59 without lesions. The images were obtained on a 1.5-T MR unit with a pixel size of 0.9 to 1.2 x 0.47 mm and a section thickness of 5 mm. The image data were compressed by wavelet-based algorithm at ratios of 20:1, 40:1, and 60:1. Three radiologists reviewed these images on an interactive workstation and rated the presence or absence of a lesion with a 50 point scale for each anatomic site. The authors also evaluated the influence of pixel size on the quality of image compression. At receiver operating characteristic (ROC) analysis, no statistically significant difference was detected at a compression ratio of 20:1. A significant difference was observed with 40:1 compressed images for one reader (P = .023), and with 60:1 for all readers (P = .001 to .012). A root mean squared error (RMSE) was higher in 0.94- x 0.94-mm pixel size images than in 0.94- x 0.47-mm pixel size images at any compression ratio, indicating compression tolerance is lower for the larger pixel size images. The RMSE, subjective image quality, and error images of 10:1 compressed 0.94- x 0.94-mm pixel size images were comparable with those of 20:1 compressed 0.94- x 0.47-mm pixel size images. Wavelet compression can be acceptable clinically at ratios as high as 20:1 for brain MR images when a pixel size at image acquisition is around 1.0 x 0.5 mm, and as high as 10:1 for those with a pixel size around 1.0 x 1.0 mm.

Algorithms↗

PubMed2026

FFC: a scalable FASTA compressor.

SUMMARY: FASTA is a widely used text-based format for storing nucleotide and protein sequences. The existing FASTA compressors usually focus on (slightly) improving the compression ratio, not on practical performance. We present FFC, a scalable FASTA compressor that achieves average compression speeds 4.7× and 11.4× higher than two high-performance compressors, zstd and NAF, respectively, across a benchmark set of seven single genomes. It also delivers average decompression speeds 3.5× and 2.7× higher than zstd and NAF, respectively. Although a chunk-based zstd variant with parallel decompression, pzstd, almost matches FFC speed, its compression ratio is on average by 23% worse than FFC's. For the experiment, a 14-core workstation and a RAM disk (to reduce the impact of I/O) were used. AVAILABILITY AND IMPLEMENTATION: FFC is freely available at github.com/kowallus/ffc and also as a Zenodo repository at 10.5281/zenodo.18892353, and the used datasets at 10.5281/zenodo.18873744.

Data Compression↗

PubMed1989

Efficient storage of urodynamic signals by computer: application of FAN adaptive sampling.

Digital storage of urodynamic signals such as detrusor pressure and flowrate at a sufficiently high sampling rate (10 samples per second) to allow subsequent analysis requires considerable computer memory. A procedure for compressing these data by deleting redundant samples (the fan method of adaptive sampling) was tested. The method allows a flexible adaptation to specific hardware and a compromise between storage requirements and accuracy. In this study the number of samples required for adequate reconstruction of the detrusor pressure signal could be varied from 80% to 4% of the original number of samples by varying the average difference between reconstructed and original signal from 0.01 to 2 cm H2O. Fast components of the measurements (for example cough peaks) which were lost if a lower sampling rate or averaging was used to obtain equally low storage requirements were unaffected by this compression technique.

Algorithms↗

PubMed1991

Influence of different sources on the processing and biopharmaceutical properties of high-dose ibuprofen formulations.

It is known that depending on the manufacturing and synthetic processes, drugs may exist as different forms. As a result, physicochemical properties, compression characteristics, intrinsic dissolution and bioavailability may vary substantially. The purpose of this study was to investigate the effect of different sources of ibuprofen on the processing of tablets and on their properties. Another emphasis of this work was to rationalize one or several key characteristics of the raw material as directly related to wet granulation parameters and to the behavior of final tablets. Commercially available ibuprofen was obtained from different manufacturers and a preformulation program, including X-ray crystallography, differential scanning calorimetry, scanning electron microscopy, determination of particle size distribution and flowability, was performed to characterize the raw material. Granules were prepared with a planetary mixer and liquid requirements for the end point were obtained by monitoring power consumption. Tablets were manufactured on Stokes rotary and single punch instrumented presses. Data acquisition interfaces produced compression data for each formulation. Granules and final tablets were analyzed for hardness, dissolution profiles and content uniformity. Statistical evaluations using analysis of variance and multiple comparison procedures were performed on the results to determine the significance of the variability between independent parameters. The ibuprofen tested was found to be a unique polymorphic form with some differences in the external crystallinity. The particle size characteristics of the material also allowed a differentiation between sources and although there was no differences in dissolution patterns or content uniformity, particle size was found to account for 50% of the variability in tablet hardness. Two sources of ibuprofen with lower mean particle size showed significant variations in end point liquid requirements resulting in variable tablet crushing strength.

Biopharmaceutics↗