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PubMed2000

Cholangiographic features in the diagnosis and management of obstructive icteric type hepatocellular carcinoma.

In 11 years and 3 months, 2,037 patients with HCC were seen and 48 patients (2.4%) were diagnosed to have obstructive icteric type HCC. Five patients were terminally ill and were not investigated further. Forty three patients were initially investigated by endoscopic retrograde cholangiography (ERC) or percutaneous transhepatic cholangiogram (PTC) and classified as having obstructive icteric type 1, 2, or 3 HCC based on the cholangiographic findings. The obstruction in type 1 HCC was due to intraluminal tumour casts and/or tumour fragments obstructing the hepatic ductal confluence or common bile duct, while intraluminal blood clots, from haemobilia, filling the biliary tree was the cause in type 2 HCC. The pathology in type 3 HCC was extraluminal obstruction by extensive tumour encasement of the intra-hepatic biliary ductal system and/or extrinsic compression of the hepatic and common bile ducts by tumour(s) and/or malignant lymph nodes. At the initial ERC/PTC, 10 patients (5 resected, 50%) had obstructive icteric type 1 and 23 patients (0 resected) had obstructive icteric type 3 HCC. Of the 10 patients initially classified according to cholangiography to have obstructive icteric type 2 HCC, subsequent investigations revealed that 6 patients had type 1 HCC (4 resectable,67%) and 4 patients had type 3 HCC (0 resectable). The classification of the obstructive icteric type HCC into types 1, 2, and 3, based on the initial cholangiographic appearances has simplified and rationalized our management strategy for this condition.

Algorithms↗
PubMed2001

Photocrosslinkable polysaccharides for in situ hydrogel formation.

In situ photopolymerization is an exciting new technique for tissue engineering. Two photocrosslinkable polysaccharides composed of alginate and hyaluronan are described that upon photolysis form soft, flexible, and viscoelastic hydrogels. The degree of methacrylate modification and thus covalent affects mechanical properties such as swelling, compression, and creep compliance. Significant swelling is observed in aqueous solution; these hydrogels can swell up to 14 times their dry weight. Both hydrogels exhibit low phase angles and (G*) values indicative of viscoelastic materials. The hyaluronan based hydrogel is stronger and more resilient than the corresponding alginate gel. SEM and AFM studies on both hydrogels show smooth and uniform surfaces at the macroscopic level with salient features observed only on the nanometer scale. Rapid polymerization by an optical trigger allows for controlled in situ photopolymerization in a minimally invasive manner, indicating that these hydrogels are relevant for biomedical applications such as sealing wounds and reconstructing soft tissues.

Algorithms↗
PubMed2003

A novel image quality index using Moran I statistics.

Measurement of image quality is very important for various applications such as image compression, restoration and enhancement. Conventional methods (e.g., mean squared error; MSE) use error summation to measure quality change pixel by pixel and do not correlate well with subjective quality measurement. This is due to the fact that human eyes extract structural information from the viewing field. In this study a new quality index using a Moran I statistics is proposed. The Moran statistic that measures the sharpness from a local area is a good index of quality as most image processing techniques alter the smoothness of the image. Preliminary results show that the new quality index outperforms the MSE significantly under various types of image distortions.

Algorithms↗
PubMed2006

Volumetric breast density estimation from full-field digital mammograms.

A method is presented for estimation of dense breast tissue volume from mammograms obtained with full-field digital mammography (FFDM). The thickness of dense tissue mapping to a pixel is determined by using a physical model of image acquisition. This model is based on the assumption that the breast is composed of two types of tissue, fat and parenchyma. Effective linear attenuation coefficients of these tissues are derived from empirical data as a function of tube voltage (kVp), anode material, filtration, and compressed breast thickness. By employing these, tissue composition at a given pixel is computed after performing breast thickness compensation, using a reference value for fatty tissue determined by the maximum pixel value in the breast tissue projection. Validation has been performed using 22 FFDM cases acquired with a GE Senographe 2000D by comparing the volume estimates with volumes obtained by semi-automatic segmentation of breast magnetic resonance imaging (MRI) data. The correlation between MRI and mammography volumes was 0.94 on a per image basis and 0.97 on a per patient basis. Using the dense tissue volumes from MRI data as the gold standard, the average relative error of the volume estimates was 13.6%.

Adult↗
PubMed2003

Electrophoretic signal comparison applied to mRNA differential display analysis.

Gene expression analysis by electrophoretic methods is currently limited by the labor-intensive visual evaluation of the electrophoretic signal profiles. For this purpose, we present a flexible approach to computer-assisted comparison of quantitative electrophoretic patterns between multiple expression signals. Gaussian curves are first fitted to the complex peak mixtures, and the resulting approximate signals are then aligned and compared on a peak-by-peak basis with respect to specific patterns defined by the investigator. The rationale of the method is to produce a compressed list of exceptional expression patterns quantified by a set of associated numeric features. A score value is attached to each pattern in such a way that large values identify the most potential findings to be focused on in visual analysis instead of the vast amount of original electrophoretic results. The validity of the method is demonstrated by analyzing a large set of electrophoretic data from mRNA differential display experiments monitoring changes in gene expression patterns in human colonic carcinoma. The automated identification of variously defined gene expression patterns agrees well with the visual evaluation of the same electropherograms. The general comparison approach may also be found useful with other gene expression profiling instruments.

Adenocarcinoma↗
PubMed1999

Virtual endoscopic environments in modern neurosurgical practice.

Modern radiographic techniques have allowed the creation of high-definition planar images that can provide important anatomical as well as physiological data. Planar imaging sets can be reformatted into three-dimensional (3-D) data sets that can then be manipulated to demonstrate important anatomical or gross pathological features. Three-dimensional data sets have been used with success in modern image-guided or frameless stereotactic surgery. Another potential application is so-called "virtual endoscopy" or "scopeless endoscopy," in which a 3-D anatomical data set is reformatted into a volume-rendered image that can then be viewed. By reformatting images in this way, a "surgeon's-eye" view can be obtained, which can aid in presurgical planning and diagnosis. The use of virtual endoscopy has the potential to increase our understanding of the appropriate anatomy and the anatomical relationships most apparent during neurosurgical approaches. In so doing, virtual endoscopy may serve as an important means of planning for therapeutic interventions. On the other hand, one must always be cognizant of the technical limitations of these studies regardless of the quality of the reconstructed images. Prospective, correlative, clinical studies in which the anatomical advantages of virtual-based endoscopy are evaluated in large cadaver or patient series must be performed. Until then, the only potential ways to compensate for errors that exist in the algorithms and reconstructions of 3-D endoscopic images are based on the surgeon's understanding of the clinical state of the patient and prior experience with the anatomy in the region of question.

Journal Article↗
PubMed2000

Effect of some physical parameters on the sustained drug-release properties of substituted amylose matrices.

Substituted amylose (SA) matrix drug tablets prepared by direct compression show sustained drug-release properties. The influence of compression force (CF) and tablet weight (TW) on release properties was studied. CF ranging from 0.5 to 5.0 tons/cm(2) has no significant effect on the release properties of SA,G (glycidol) polymers, with a degree of substitution (DS) greater than 1.5. For a low DS, an augmentation of CF increases the release time of acetaminophen, used as a model drug, until a certain limit is reached. On the other hand, TW has a major effect on the release time of acetaminophen. Release time is directly proportional to TW. The effect of the nature of the active material, its solubility and its concentration in the formulation on the release properties of SA, G polymers was also evaluated, demonstrating the versatility of the system.

Acetaminophen↗
PubMed2005

Euler vector for search and retrieval of gray-tone images.

A new combinatorial characterization of a gray-tone image called Euler Vector is proposed. The Euler number of a binary image is a well-known topological feature, which remains invariant under translation, rotation, scaling, and rubber-sheet transformation of the image. The Euler vector comprises a 4-tuple, where each element is an integer representing the Euler number of the partial binary image formed by the gray-code representation of the four most significant bit planes of the gray-tone image. Computation of Euler vector requires only integer and Boolean operations. The Euler vector is experimentally observed to be robust against noise and compression. For efficient image indexing, storage and retrieval from an image database using this vector, a bucket searching technique based on a simple modification of Kd-tree, is employed successfully. The Euler vector can also be used to perform an efficient four-dimensional range query. The set of retrieved images are finally ranked on the basis of Mahalanobis distance measure. Experiments are performed on the COIL database and results are reported. The retrieval success can be improved significantly by augmentiong the Euler vector by a few additional simple shape features. Since Euler vector can be computed very fast, the proposed technique is likely to find many applications to content-based image retrieval.

Algorithms↗
PubMed2003

In vivo real-time freehand palpation imaging.

Previous experience with laboratory fixtures and off-line processing of elasticity data showed that problems occurring in data acquisition often resulted in poor elasticity image quality. A system for real-time estimation and display of tissue elastic properties using a clinical ultrasonic imaging system has been developed. A brief description of that system and the initial clinical tests of that system are reported. Experience with real-time freehand elasticity imaging shows that images with high contrast-to-noise ratios are consistently obtained. Images of breast lesions were acquired with freehand palpation using standard linear-array ultrasound (US) transducers. Results in volunteer patients show that high-quality elasticity images are easily obtained from in vivo breast studies. The key element to successful scanning is real-time visual feedback of B-mode and strain images that guide the patient positioning and compression direction. Results show that individual images of axial strain in tissues can be quite misleading, and that a "movie loop" of side-by-side B-mode and strain images provides significantly more information. Our preliminary data suggest that the strain image sequences for various breast pathologies are unique. For example, strain images of fibroadenomas lose contrast with increasing precompression, but those of invasive ductal carcinoma have high negative contrast (dark relative to "normal" tissue) for a wide range of precompression. In addition, a comparison of the lesion area measured in B-mode vs. strain images, for a representative image from the sequence, appears to be a sensitive criterion for separating invasive ductal carcinoma from cyst and fibroadenoma.

Algorithms↗
PubMed2005

Spinal epidural abscess: early clinical outcome in patients treated medically.

Treatment of spinal epidural abscess has been based on surgical debridement. Medical treatment with antibiotics has been proposed as an alternative, but data on its efficacy are limited. The purpose of this study was to determine the early clinical outcome of medical treatment. This is a retrospective review of 52 patients with a spinal epidural abscess who were treated at our institution. Medical treatment was selected if no systemic sepsis was present and the neurologic examination was normal or stable (radiculopathy or signs of partial cord compression present for more than 72 hours before admission without deterioration). Twenty-nine patients had medical treatment and 23 patients were treated surgically. Medical treatment resulted in good or excellent early neurologic outcome in 24 of 29 patients (83%) at a median followup of 2 months. Three patients (11%) had failed medical treatment and required surgery and one patient (3%) who had severe comorbidities died. Staphylococcus aureus was the most common infectious pathogen, isolated in 28 of 36 positive cultures (78%). Medical treatment is a viable alternative to surgery for selected patients with a spinal epidural abscess. However, close clinical followup is essential and surgical decompression should be done when neurologic deterioration or development of systemic sepsis is observed.

Adult↗
PubMed2025

Columba: fast approximate pattern matching with optimized search schemes.

MOTIVATION: Aligning sequencing reads to reference genomes is a fundamental task in bioinformatics. Aligners can be classified as lossy or lossless: lossy aligners prioritize speed by reporting only one or a few high-scoring alignments, whereas lossless aligners output all optimal alignments, ensuring completeness and sensitivity. RESULTS: This paper introduces Columba, a high-performance lossless aligner tailored for Illumina sequencing data. Columba processes single or paired-end reads in FASTQ format and outputs alignments in SAM format. By utilizing advanced search schemes and bit-parallel alignment techniques, Columba achieves exceptional speed. Columba is available in two variants. The first, based on the bidirectional FM-index, prioritizes speed. The second, Columba RLC, uses run-length compression using a bidirectional move structure, significantly reducing memory usage for large, repetitive datasets like pan-genomes. Benchmarks on the human genome, as well as bacterial and human pan-genome datasets, demonstrate that Columba is much faster than existing lossless aligners and even competitive with lossy tools. We integrated Columba into the OptiType HLA genotyping pipeline, where it substantially reduced computational time while maintaining accuracy. These results position Columba as a versatile, state-of-the-art tool for high-sensitivity genomic analyses. AVAILABILITY AND IMPLEMENTATION: The source code of Columba is available at https://github.com/biointec/columba under AGPL license. Scripts to reproduce the benchmarks and analyses are available at https://doi.org/10.5281/zenodo.15849246.

Software↗
PubMed1998

A comparison of threshold-based fitting strategies for nonlinear hearing aids.

OBJECTIVE: In recent years, wide dynamic range compression (WDRC) has been used with increasing success. To optimize the fit with this type of hearing aid circuitry, subjective measures of loudness growth often are used. Unfortunately, these type of measures cannot be performed with infants, young children, and some elderly individuals. The primary purpose of this study was to compare the fitting recommendations of two recently described threshold-based procedures for fitting nonlinear hearing aids (DSL 4.0 and FIG6) to the use gain settings of satisfied adult hearing aid users for whom the fitting was based on subjective measures of loudness growth. Because it cannot be assumed that the use settings for adults will be appropriate for young children, a secondary goal was to quantify the audibility of speech at the use settings derived from loudness growth measures. DESIGN: Forty-nine adult hearing aid users with mild to severe sensorineural hearing loss participated in this study. For all subjects, loudness growth measures were used to optimize the fit of a 2-channel WDRC hearing aid. The use gain at 50 and 80 dB SPL was compared with the gain recommended by DSL, FIG6, and the manufacturer's threshold-based fitting algorithm. RESULTS: In general, both DSL and FIG6 prescribed more gain than actually was used by these hearing aid wearers. These discrepancies increased as a function of frequency, and differences in excess of 20 dB were observed in some cases. The manufacturer's algorithm provided a closer approximation to the use gain than either DSL or FIG6. Utilizing these use gain values, an Aided Audibility Index (AAI) was calculated for soft, average, and loud speech across four degrees of hearing loss, ranging from mild to severe (12 conditions). Transfer functions for continuous discourse and nonsense syllables were applied to yield estimated intelligibility scores. For the higher context speech materials, estimated intelligibility was > or = 85% for nine of the 12 conditions. For low-context speech materials, estimated intelligibility was > or = 85% for only three of the 12 conditions. CONCLUSIONS: Results suggest that the gain recommendations provided by both DSL and FIG6 exceeded the gain actually used by the adult hearing-impaired subjects in this study. Gain recommendations from the manufacturer's algorithm provided a closer approximation to the use gain values of these subjects. These findings suggest that, for adult hearing aid users who cannot perform loudness judgments reliably, the manufacturer's algorithm would be expected to provide a closer approximation to loudness-based use gain values than either DSL or FIG6. However, AAI calculations revealed that the gain recommendations from this algorithm produce adequate audibility of speech only if one assumes linguistic competence. When AAI values are transformed to predict the intelligibility of low-context speech materials, it appears that the degree of audibility may not be appropriate for prelingually hearing-impaired children with more than a moderate hearing loss.

Aged↗
PubMed2004

Evaluation of painful hydronephrosis in pregnancy: magnetic resonance urographic patterns in physiological dilatation versus calculous obstruction.

PURPOSE: We evaluated magnetic resonance urography (MRU) appearances in symptomatic hydronephrosis in pregnancy and compared urographic patterns in physiological and calculous disease. MATERIALS AND METHODS: A total of 24 consecutive pregnant women with symptomatic hydronephrosis underwent MRU, comprising an overview fast T2-weighted examination of the abdomen and pelvis, and thick slab, heavily T2-weighted MRU images, followed by focused, high resolution T2-weighted sequences obtained in an axial and coronal oblique plane through the level of ureteral caliber change. RESULTS: Of these 24 pregnant women 15 were found to have physiological hydronephrosis, 7 had calculous disease and 2 had preexisting urinary anomalies. MRU findings in physiological hydronephrosis cases were extrinsic compression of the middle third of the ureter, no filling defect and a collapsed ureter below it. Obstruction by ureteral calculi was seen at points of ureteral narrowing in the ureter, that is at the vesicoureteral junction in 2 cases, in the compressed mid ureter in 3 and at the pelviureteral junction in 1. Nonobstructive renal calculi were seen in another patient. Calculi presented throughout pregnancy but physiological hydronephrosis presented only in the late second and third trimesters. With distal calculi the MRU appearance was the double kink sign with constriction at the pelvic brim and the vesicoureteral junction with a standing column of urine in the pelvic ureter. There was renal edema and perirenal extravasation. Small calculi were only identified using high resolution T2-weighted magnetic resonance imaging. CONCLUSIONS: MRU is a valuable and well tolerated investigation for evaluating painful hydronephrosis in pregnancy. There are characteristic and differing urographic appearances in physiological and calculous obstruction.

Adolescent↗
PubMed2002

Relaxation modulus of denture base resin reinforced with woven glass fibers.

This study examined the reinforcing effect of woven glass fibers on the relaxation modulus by three-point loading of denture base resin. Three sandwich-type flexure test specimens polymerized by heating were used, all 3 mm thick: glass fibers in compression (U type); glass fibers in the center (C type); and glass fibers in tension (L type). Unreinforced specimens (ACR) were produced as a control. The relaxation modulus after 8 sec from the start of stress (Er(8)) was calculated from stress relaxation curves. In the glassy state, the Er(8)s of the U and L types were greater than those of the ACR and C types. In the rubbery state (plateau region), the Er(8)s of the U and L types were greater than those of the ACR and C types. The woven glass fibers added to the U and L type specimens increased the relaxation modulus of PMMA near the oral temperature; moreover, they inhibited stress relaxation when the temperature increased.

Algorithms↗
PubMed1996

Mechanical stability of the in vivo lumbar spine: implications for injury and chronic low back pain.

One important mechanical function of the lumbar spine is to support the upper body by transmitting compressive and shearing forces to the lower body during the performance of everyday activities. To enable the successful transmission of these forces, mechanical stability of the spinal system must be assured. The purpose of this study was to develop a method and to quantify the mechanical stability of the lumbar spine in vivo during various three-dimensional dynamic tasks. A lumbar spine model, one that is sensitive to the various ways that individuals utilize their muscles and ligaments, was used to estimate the lumbar spine stability index three times per second throughout the duration of each trial. Anatomically, this model included a rigid pelvis, ribcage, five vertebrae, 90 muscle fascicles and lumped parameter discs, ligaments and facets. The method consisted of three sub-models: a cross-bridge bond distribution-moment muscle model for estimating muscle force and stiffness from the electromyogram, a rigid link segment body model for estimating external forces and moments acting on the lumbar vertebrae, and an 18 degrees of freedom lumbar spine model for estimating moments produced by 90 muscle fascicles and lumped passive tissues. Individual muscle forces and their associated stiffness estimated from the EMG-assisted optimization algorithm, along with external forces were used for calculating the relative stability index of the lumbar spine for three subjects. It appears that there is an ample stability safety margin during tasks that demand a high muscular effort. However, lighter tasks present a potential hazard of spine buckling, especially if some reduction in passive joint stiffness is present. Several hypotheses on the mechanism of injury associated with low loads and aetiology of chronic back pain are presented in the context of lumbar spine stability.

Journal Article↗
PubMed2026

Movi 2: fast and space-efficient queries on pangenomes.

SUMMARY: Space-efficient compressed indexing methods are critical for pangenomics and for avoiding reference bias. In the Movi study, we implemented the move-structure index, highlighting its locality-of-reference and speed. However, Movi had a high memory footprint compared to other compressed indexes. Here, we introduce Movi 2 and describe new methods that greatly reduce size and memory footprint of move structure-based indexes. The most compressed version of Movi 2 reduces the Movi index's space footprint more than five-fold. We also introduce sampling approaches that enable trade-offs between query and space efficiency. To demonstrate, we show that Movi 2 achieves advantageous time and space tradeoffs when applied to large pangenome collections, including both the first and second releases of the Human Pangenome Reference Consortium (HPRC) collection, the latter of which spans over 460 human haplotypes. We show that Movi 2 dominates prior methods on both speed and memory footprint, including both r-index-based and our previous move-structure-based method. AVAILABILITY AND IMPLEMENTATION: The methods we developed for Movi 2 are publicly available at https://github.com/mohsenzakeri/Movi.

Humans↗
PubMed1999

Venous ulcer reappraisal: insights from an international task force. Veines International Task Force.

UNLABELLED: An international task force made up of a panel of 16 experts was mandated to review and objectively evaluate all aspects of chronic venous disease of the leg. All available publications on chronic venous disease of the leg from 1983 to 1997 were identified through computerized search. Three different screenings were then performed in order to select only relevant papers providing moderate to strong scientific evidence. Final conclusions and further therapeutic recommendations were made based on these publications. Compression, medications, local therapies, sclerotherapy and surgery are the existing therapeutic options for which the following recommendations can be made. Compression: Properly applied bandages both fixed and stretched have been shown to be effective. Compression stockings may be used. Compression needs to be in excess of 35 mm Hg. Medications: Although preliminary results have shown a beneficial effect of several vasodilators and oral micronized purified flavonoid fraction, the evidence for the efficacy of medications on venous ulcer healing is still limited and further studies are required before recommendations can be made. There is no evidence to routinely administer antibiotics. Local therapies have an as yet unproven adjunctive role. Sclerotherapy is unlikely to be effective unless there is superficial venous insufficiency, in which it may have an as yet unproven role. SURGERY: Patients with active venous ulcer and sapheno-femoral or sapheno-popliteal junction incompetence benefit from surgical treatment. In the absence of reflux or following deep vein thrombosis, there is no evidence to support surgical treatment.

Algorithms↗
PubMed2005

Illumination-tolerant face verification of low-bit-rate JPEG2000 wavelet images with advanced correlation filters for handheld devices.

Face recognition on mobile devices, such as personal digital assistants and cell phones, is a big challenge owing to the limited computational resources available to run verifications on the devices themselves. One approach is to transmit the captured face images by use of the cell-phone connection and to run the verification on a remote station. However, owing to limitations in communication bandwidth, it may be necessary to transmit a compressed version of the image. We propose using the image compression standard JPEG2000, which is a wavelet-based compression engine used to compress the face images to low bit rates suitable for transmission over low-bandwidth communication channels. At the receiver end, the face images are reconstructed with a JPEG2000 decoder and are fed into the verification engine. We explore how advanced correlation filters, such as the minimum average correlation energy filter [Appl. Opt. 26, 3633 (1987)] and its variants, perform by using face images captured under different illumination conditions and encoded with different bit rates under the JPEG2000 wavelet-encoding standard. We evaluate the performance of these filters by using illumination variations from the Carnegie Mellon University's Pose, Illumination, and Expression (PIE) face database. We also demonstrate the tolerance of these filters to noisy versions of images with illumination variations.

Algorithms↗