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At least 109 records · Page 6Linked to original sources
PubMed1988

Imaging system for morphometric assessment of absorption or fluorescence in stained cells.

An image acquisition and processing system has been developed for quantitative microscopy of absorption or fluorescence in stained cells. Three different light transducers are used in the system to exploit the best characteristics of these sensors for different biological measurements. A digital scanner, in the form of a linear array charge-coupled device (CCD), acquires data with high spatial and photometric resolution. A color (RGB) camera is employed when spectral information is required for the segmentation of cellular subcomponents. An image-intensified charged-injection device (CID) camera provides for very low light intensity measurements, primarily for fluorescence-labeled cells. Properties of these transducers, such as contrast transfer function, linearity, and photo-response nonuniformity, have been measured. Two dedicated image processing units were incorporated into the system. The front-end processor, based on a digital signal processor, provides functions such as object detection, raw image calibration, compression, artifact removal, and filtering. The second image processor is associated with the frame memory and includes a histogram processor, a dedicated arithmetic logic unit for image processing functions, and a graphics module for one-bit overlay functions. An interactive program was developed to acquire cell images and to experiment with a range of segmentation algorithms, feature extractions, and other image processing functions. The results of any image operation are displayed on the video monitor. Once a desired processing sequence is determined, the sequence may be stored to become part of a command library and can be executed thereafter as a single instruction.

Algorithms↗
PubMed1986

Experimental determination of the linear biphasic constitutive coefficients of human fetal proximal femoral chondroepiphysis.

The mechanical properties of the cartilaginous regions of the proximal femoral epiphysis are an important factor in load transmission through the hip joint of young children. Cylindrical test specimens excised from the chondroepiphysis of human stillborn femoral heads were subjected to uniaxial loading in peripherally-unconfined compression, using a ramp/plateau input strain history. The corresponding load vs time curves were analyzed in terms of a recent analytical solution for a linear biphasic material (the well-known KLM model), allowing calculation of that model's three fundamental constitutive coefficients (permeability, equilibrium modulus and solid-phase Poisson ratio) for this material. The numerical algorithm developed to evaluate the biphasic solution yielded very precise replication of previously published KLM parametric plots. When fitted to experimental load histories, however, the model provided only a rather loose approximation of specimen behavior, due apparently to a substantial underestimation of the transient response component associated with interstitial fluid transport. Averaged over the series, the best-fit values for permeability (2.51 X 10(-15) m4 Ns-1) and equilibrium modulus (0.699 MPa) were in the range of values accepted for human adult articular cartilage. A consequence of the coarseness of the analytical curve fits was that a solid-phase Poisson ratio of 0.0 was inferred for all specimens. The permeability vs equilibrium modulus exhibited a nearly linear (r = 0.74) inverse relationship similar to that reported for adult articular cartilage.

Femur↗
PubMed1985

Ambulatory management of thermal injuries.

The majority of thermal injuries that occur in this country can be adequately treated on an ambulatory-care basis. The determination regarding ambulatory care can be arrived at using the simple algorithm. The primary concern in outpatient burn care is the management of the burn wound. Aggressive wound cleansing, frequent dressing changes, and appropriate antimicrobials should permit rapid re-epithelialization and prevention of bacterial infection. A nonhealing burn wound should be grafted if it takes more than two to three weeks to heal. Aftercare with splints and elastic compression may be required to obtain maximal functional and cosmetic results.

Age Factors↗
PubMed1985

SEQ-ED: an interactive computer program for editing, analysis and storage of long DNA sequences.

The rapidly growing body of sequenced DNA demands efficient computer programs for its analysis and storage. The program described in this paper, SEQ-ED, has been designed to handle a large number of DNA sequences up to 200 kilobases [kb] long stored in a sequence library. In order to minimize the required storage space, the sequences are stored in a compressed format using three binary digits per base. In the development of this program, special care has been given to make it easy to use for molecular biologists without any previous computer experience.

Algorithms↗
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↗
PubMed1970

Mechanization of library procedures in the medium-sized medical library. X. Uniqueness of compression codes for bibliographic retrieval.

Two-word compression techniques, the University of Chicago experimental search code and a phonetic code similar to the SOUNDEX coding system, were tested as search codes on a data base of 7,464 bibliographic records. These codes were automatically generated and tested for uniqueness. A modified version of the University of Chicago search code produced the best results with a uniqueness factor of 98.83 percent. The algorithms for generating these codes are explained, and implication of the findings for medium-sized libraries are discussed.

Bibliographies as Topic↗
PubMed1992

Treatment options in primary Ewing's sarcoma of the spine: report of seven cases and review of the literature.

Primary Ewing's sarcoma of the spine is reviewed, and seven cases are presented. Ewing's sarcoma of the spine is a rare condition that appears with a clinical triad of local pain, neurological deficit, and a palpable mass. The clinical picture, imaging characteristics, and management are discussed. The definitive management of Ewing's sarcoma of the spine, as in other locations, could include three main modalities: surgery, radiotherapy, and combination chemotherapy. In the presence of acute neurological decompensation, decompressive surgery via an appropriate approach should be performed. Because Ewing's sarcoma is usually sensitive to chemotherapy, initial chemotherapy, in neurologically stable patients, could be attempted first without surgical resection. Further management could then be gauged according to the response.

Adolescent↗
PubMed2025

SKiM: accurately classifying metagenomic ONT reads in limited memory.

MOTIVATION: Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to handle potentially erroneous DNA reads, while ideally inspecting only a few hundred bases of a read. Currently available DNA classifiers leave room for improvement with respect to classification accuracy, memory usage, and the ability to operate in targeted sequencing scenarios. RESULTS: We present SKiM: Short K-mers in Metagenomics, a new lightweight metagenomic classifier designed for ONT reads. Compared to state-of-the-art classifiers, SKiM requires only a fraction of memory to run, and can classify DNA reads with higher accuracy after inspecting only their first few hundred bases. To achieve this, SKiM introduces new data compression techniques to maintain a reference database built from short k-mers, and treats classification as a statistical testing problem. AVAILABILITY AND IMPLEMENTATION: SKiM source code, documentation, and test data are available from: https://gitlab.com/SCoRe-Group/skim.

Metagenomics↗
PubMed1989

[Adjustment of hearing aids using a computer].

There was developed the programme for the fitting of hearing-aids for minicomputer SHARP PC 1500. According to the audiometric investigation the programme enables to choose the SPPL (Saturation Sound Pressure Level), gain, compression and frequency range. The programme was proved in the fitting of hearing-aids to thirty subjects, mostly with sensorineural hearing impairment. The use of the computer is considered as the simplifying of this work to the audiological personal.

Adolescent↗
PubMed1988

Auto-association by multilayer perceptrons and singular value decomposition.

The multilayer perceptron, when working in auto-association mode, is sometimes considered as an interesting candidate to perform data compression or dimensionality reduction of the feature space in information processing applications. The present paper shows that, for auto-association, the nonlinearities of the hidden units are useless and that the optimal parameter values can be derived directly by purely linear techniques relying on singular value decomposition and low rank matrix approximation, similar in spirit to the well-known Karhunen-Loève transform. This approach appears thus as an efficient alternative to the general error back-propagation algorithm commonly used for training multilayer perceptrons. Moreover, it also gives a clear interpretation of the rôle of the different parameters.

Mathematics↗
PubMed1984

Burst fractures of the thoracic and lumbar spine.

A burst fracture may be defined as an unstable compression fracture of the posterior wall of the vertebral body that allows fragments to be retropulsed into the spinal canal. Computerized axial tomography evaluation of these injuries often reveals posterior element fracture heretofore not stressed in the literature. In surgical treatment for these injuries four important considerations must be met; (1) the coronal and sagittal alignment of the spine; (2) patency of the neural canal; (3) the two-column concept of spinal stability; and (4) bony vertebral body reconstitution. An algorithm for treatment may be developed with the aid of these principles. Distraction and the creation of spinal lordosis are necessary for reduction.

Adult↗
PubMed1989

The surface properties of apolipoproteins A-I and A-II at the lipid/water interface.

The monolayer system was employed to investigate the relative affinities of apolipoproteins A-I and A-II for the lipid/water interface. The adsorption of reductively 14C-methylated apolipoproteins to phospholipid monolayers spread at the air/water interface was determined by monitoring the surface pressure of the mixed monolayer and the surface concentration of the apoprotein. ApoA-II has a higher affinity than apoA-I for lipid monolayers; for a given initial surface pressure, apoA-II adsorbs more than apoA-I to monolayers of egg phosphatidylcholine (PC), distearoyl-PC and human high-density lipoprotein (HDL3) surface lipids. Comparison of the molecular packing of apolipoproteins A-I and A-II suggests that apoA-II adopts a more condensed conformation at the lipid/water interface compared to apoA-I. The ability of apoA-II to displace apoA-I from egg PC and HDL3 surface lipid monolayers was studied by following the adsorption and desorption of the reductively 14C-methylated apolipoproteins. At saturating subphase concentrations of the apoproteins (3.10(-5) g/100 ml), two molecules of apoA-II absorbed for each molecule of apoA-I displaced. This displacement was accompanied by an increase in surface pressure. An identical stoichiometry for the displacement of apoA-I from HDL particles by apoA-II has been reported by others. At low subphase concentrations of apoproteins (5.10(-6) g/100 ml), the apoA-I/lipid monolayer was not fully compressed and could accommodate the adsorbing apoA-II molecules without displacement of apoA-I molecules. ApoA-I molecules were unable to displace apoA-II from the lipid/water interface. The average residue hydrophobicity of apoA-II is higher than that of apoA-I; this may contribute to the higher affinity of apoA-II for lipids compared to apoA-I. The probable helical regions in apolipoproteins A-I and A-II were located using a secondary structure prediction algorithm. The analysis suggests that the amphiphilic properties of the alpha-helical regions of apoA-I and apoA-II are probably not significantly different. Further understanding of the differences in surface activity of these apolipoproteins will require more knowledge of their secondary and tertiary structures.

Amino Acid Sequence↗
PubMed1986

Quantitative analysis of intervertebral disc structure.

A reduction in signal intensity from the nucleus can be a feature of intervertebral disc disease. It has been established that T1 and T2 relaxation times of the nucleus decrease with age and that evidence of disc degeneration can be determined before classical clinical features are apparent. A robust multiple point algorithm has been developed which now enables proton density and T1 and T2 values to be computed for each pixel, providing images which are effectively spatial maps of these parameters. Such high resolution maps have provided quantitative data from volunteers, patients and cadavers. These studies have been carried out with specially constructed coils and the cadaveric information compared with cut sections. The spatial maps revealed detailed anatomic structures including the laminae of the annulus and relative levels of hydration. These levels, which are known to be related to the ability of the disc to withstand compressive loads, can now be measured in vivo. Analysis of the proton density and relaxation times in vivo has demonstrated that both water content and the chemical environment in the nucleus change during aging. The results are consistent with changes in the glycosaminoglycan content and fixed charged density measured by other chemical and physical techniques. Such detailed methods can be used to investigate the effects of aging and disease on disc structure and have enabled observations to be made of the effects of stress on the normal disc.

Adolescent↗
PubMedDate not supplied

Brain-stem auditory evoked responses as indicators of early brain insult.

The relationship between cranial ultrasonograms (SONOs) and brain-stem auditory evoked responses (BAERs) was evaluated in 2 independent samples of newborn infants at risk for brain injury (n = 113 and 203). Features of the BAER wave forms subjected to stepwise linear discriminant analysis formed the basis of an algorithm used to detect and follow early brain injury. Using this algorithm, information derived from BAERs reliably predicted SONO abnormalities at least 82.3% of the time in the initial study which was replicated with the second sample (77.3%). The wave I component latency (CL) and the wave III-V inter-peak latency interval (IPL) were independent of each other, and both contributed to a prediction of SONO abnormality. Possible mechanisms for these BAER results include compromise to the cochlear membrane or to the auditory nerve itself as well as prolongation of transmission in the brain-stem due to brain-stem hemorrhage, edema, or compression. Normative BAER values and non-linear regression functions for the wave I, III and V CLs, and the I-III, III-V, and I-V IPLs were calculated across age using data from 109 infants who demonstrated normal BAER patterns and had no history of SONO abnormalities. Our analyses indicate BAER techniques, where a single higher intensity is used to produce the BAER wave form, are both valid and efficient for use in the evaluation of early brain injury.

Brain Injuries↗
PubMed1989

Treatment of recurrent metatarsalgia by neuroma resection and muscle implantation: case report and proposed algorithm of management for Morton's "neuroma".

This report describes the theoretical basis for an approach to treating a recurrent Morton's "neuroma." The recurrence, being a true, classic neuroma, is treated by a technique validated in the treatment of the upper extremity painful neuroma: neuroma resection and muscle implantation. A plantar approach, implanting into the deep layer of intrinsics, was used. The three year success of this technique in a long-distance runner is reported.

Adolescent↗
PubMed1991

Thoracic gas volume at functional residual capacity measured with an integrated-flow plethysmograph in infants and young children.

Thoracic gas volume (TGV) was measured with an integrated flow plethysmograph in 15 infants aged 2-34 months. End-expiratory (TGVe) and end-inspiratory (TGVi) airway occlusions were compared, after correction of TGV for the occluded volume above functional residual capacity (FRC). The relationship between pressure at the airway opening (Pao) and volume displaced from the box during airway occlusion (Vg) was studied numerically by: 1) an algorithm including a correction for the drift of Vg and linear regression analysis (LR); and 2) Fourier analysis of the signals (FFT). TGVe was significantly higher than TGVi (256 vs 237 ml, 20.4 (square root of residual variance; p less than 0.002). The correlation coefficient of the Pao-Vg relationship was slightly but significantly higher for TGVi than for TGVe: 0.9968 (0.9937-0.9995) vs 0.9947 (0.9840-0.9990) (means and range). No difference was observed between LR and FFT, although the intra-individual coefficient of variation was lower for LR than FFT: 5.2% (1.6-11.3) vs 7.9% (1.9-21.0) (means and range). Model simulations suggested that the difference between TGVe and TGVi could be mainly attributed to gas compression in the instrumental deadspace and upper airway wall motion and/or to uneven distribution of alveolar and pleural pressure associated with chest wall distortion.

Airway Resistance↗
PubMed1990

Speech enhancement by filtering in the loudness domain.

Several attempts that employed dynamic compression to compensate for cochlear impairment in combination with recruitment have failed to improve speech intelligibility. One reason is the attenuation of dynamic intensity modulations in the range of 1 to 50 Hz which contribute significantly to speech discrimination. In the approach presented here, these modulations were enhanced rather than attenuated by an envelope highpass filter operating in the loudness domain as follows: the output of a filterbank was lowpass filtered to extract the envelope, converted to loudness in accordance with normal hearing, highpass-filtered and converted back to the 'desired' envelope by the loudness characteristic of each individual hearing-impaired subject. The output signal was finally obtained by summing the outputs of the filterbank channels after correcting their amplitudes. The algorithm was implemented by a computer to simulate a digital hearing aid fitted to the loudness-scaling function of each individual. Loudness scaling and speech-discrimination data in quiet and in noisy conditions are presented for 2 impaired subjects with and without highpass filtering in the loudness domain. The results indicate that loudness compensation without highpass filtering improves speech intelligibility for a wide range of input levels by achieving an optimum gain characteristic at all input levels. The highpass filter applied to the envelope has no noticeable effect on speech discrimination either in quiet or in noise.

Algorithms↗
PubMed1989

Spontaneous rates, thresholds and tuning of auditory-nerve fibers in the gerbil: comparisons to cat data.

Characteristics of 245 auditory nerve fibers in eleven Mongolian gerbils are described in terms of spontaneous rates, thresholds, and tuning curves. The animals were reared in a low-noise environment and had similar hearing thresholds across frequency. Tuning curves were obtained with an algorithm developed to characterize the tuning of auditory fibers in cat, thereby allowing direct comparisons to published data from cat. The results demonstrate that basic similarities exist between gerbil and cat data, although some minor differences are also apparent. Tuning curve bandwidths, as measured 10 and 40 dB above the thresholds at the characteristic frequency (CF), follow trends found in cat data. Like cat, auditory nerve fibers in the gerbil have a range of spontaneous rates. In individual gerbils, fibers associated with low spontaneous rates have higher thresholds than do fibers of similar CF with high rates. Five of the eleven gerbils showed profiles of spontaneous rate across frequency reminiscent of those obtained from quiet-raised young cats. The profiles of the remaining gerbils tended to be compressed to a smaller range of spontaneous rates for characteristic frequencies above about five kHz, much like older cats with unknown noise histories. The cause of the spontaneous compression is not obvious. The correspondence between cat and gerbil with regard to spontaneous rate and CF threshold implies the presence of fundamental mechanisms that are common to mammalian auditory systems.

Action Potentials↗