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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↗
PubMed1987

Mechanism of penile erection in the dog. Pressure-flow study combined with morphological observation of vascular casts.

A pressure-flow study of the corpus cavernosum penis in the dog was performed during the flaccid, tumescent, erect and rigid stages. Perfusion was selectively made into the penile deep artery. The erect stage was induced with the local administration of papaverine hydrochloride, and the rigid stage by electrostimulation of the ischiocavernous muscle during the erect stage. Concurrently, vascular casts of the penis at each stage of erection were observed under a scanning electron microscope for the anatomical analysis of the mechanisms controlling cavernous pressure. In the pressure-flow study, it was demonstrated that a combination of decreased arterial resistance and restricted venous outflow was essential to both cause and maintain the erect state. The rigid stage was generated by contraction of the ischiocavernous muscle tightly compressing the crus penis. In the rigid stage, the cavernous pressure was elevated as high as five times the perfusion pressure; nevertheless, no backflow from the cavernous sinus to the deep artery was recognized. By use of the casts, it was confirmed that venous outflow restriction in the erect and rigid stages was due to compression of the postcavernous venules and penetrating veins in the tunica albuginea. The deep artery was occluded in the tunica albuginea in the casts made during the rigid stage, suggesting that the backflow from the corpus cavernosum penis to the deep artery was prevented by this occlusion. Therefore, in the rigid stage, the arterial and venous occlusion isolated the cavernous sinus from the systemic circulation; this mechanism seems to account for the maintenance of the extremely high cavernous pressure.

Algorithms↗
PubMed1986

A Doppler flowmeter for use in theatre.

We have developed a Doppler flowmeter based on a 10 MHz pencil probe and mean frequency estimator which overcomes many of the limitations of existing electromagnetic and ultrasonic flowmeters. The output of the flowmeter, which is proportional to the first moment of the Doppler power spectrum and hence mean blood velocity is linear from 1.3 to over 50 cm s-1 for pulsatile flow. Variation in vessel diameter and angle of insonation, which are the common sources of error in Doppler flowmetry, are minimised by constraining the vessel in a plastic cuff which fixes the probe angle at 50 degrees. A simple gauge is used to compress the vessel flat, before the cuff is applied, to measure the wall thickness to within 0.25 mm. The vessel internal diameter and hence blood flow can then be calculated using an experimentally determined calibration factor to compensate for non-even insonation. A range of sterilizable cuffs from 3-12 mm diameter have been built and the flowmeter is now being used routinely during all arterial reconstructive surgery. The accuracy and reproducibility of the system was tested for range of different sized silastic tubes on a hydraulic model and found to be less than 12% for vessels greater than 2 mm internal diameter. Satisfactory signals were easily obtained from all prosthetic materials with the exception of PTFE. The instantaneous output was compared to an electromagnetic flowmeter using a fast Fourier transform algorithm; the moduli of the harmonics were virtually identical but the Doppler system produced a smaller phase shift with increasing harmonics.(ABSTRACT TRUNCATED AT 250 WORDS)

Humans↗
PubMed2026

A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.

The rapid growth of genomic sequencing demands fast, accurate, and scalable analysis methods. In viral genomic classification, expanding labeled reference collections can make supervised models costly to update and dependent on fixed label sets, motivating retrieval-based genomic classification as a simpler, more flexible alternative. We present a unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification across three viral classification tasks: hepatitis C virus (HCV) genotyping, COVID-19 discrimination, and human papillomavirus (HPV) genotyping. We compare standard sequence encodings (one-hot, k-mers, FCGR) with dense embeddings (dna2vec, DNABERT). For each representation, we evaluate supervised classifiers (Random Forest, Decision Tree, XGBoost) and retrieval-based classification, where sequence vectors are indexed with FAISS and labels are assigned via similarity-weighted k-NN. Furthermore, we benchmark multiple FAISS index types (Flat, IVF, HNSW, IVFPQ, OPQ) to characterize accuracy-speed-memory trade-offs at scale. The results show that XGBoost and retrieval using Flat or IVF indexes achieve strong classification performance under different computational profiles. Compressed indexes such as IVFPQ and OPQ substantially reduce memory usage, although their accuracy loss depends on the dataset and representation. Overall, supervised XGBoost provides a favorable accuracy-size trade-off, while retrieval-based classification remains competitive and allows labeled reference sequences to be incorporated without retraining a global classifier. This benchmark provides practical guidance for selecting sequence representations, classifiers, and vector-search indexes under different accuracy, memory, and update requirements.

Genome, Viral↗
PubMed1992

Pneumothorax as a complication of recompression therapy for cerebral arterial gas embolism.

The danger from pneumothorax in patients who undergo compression chamber treatment for cerebral arterial gas embolism (CAGE) following pulmonary barotrauma is frequently emphasized. Two cases of CAGE treated by recompression after submarine escape tank training (SETT) accidents are described. Both were complicated by bilateral pneumothoraces but the first case, treated on an air table, required thoracentesis in the chamber, whereas the second case, treated on an oxygen table, escaped the need for in-chamber thoracentesis despite large pneumothoraces. Review of similar Royal Navy and United States Navy SETT accidents suggests that the danger from pneumothorax during recompression treatment of CAGE victims may be overstated. Modern management on oxygen-based therapeutic recompression tables may significantly reduce the risk. Thoracentesis while under pressure should be reserved for cases developing symptoms or signs of tension pneumothorax. Treatment options for these cases are discussed and a decision algorithm is proposed.

Atmosphere Exposure Chambers↗
PubMed1985

The Pennsylvania Plan II: an algorithm for the management of lumbar degenerative disc disease.

We have thus presented a series of decision-making processes that are easy to follow, clearly defined, and cost effective. We have found that with the use of this decision-making algorithm our patients receive the therapeutic measures most helpful at the optimal time and are neither denied helpful surgery nor submitted to operations that are useless surgical exercises. With the use of this protocol, we believe that our efficiency as surgeons, physicians, and advisors will increase and the specter of fear found in the general population regarding low back pain will diminish.

Adult↗
PubMed1989

[To what extent are oscillometric data of a simple resistor-volume model physically recordable?].

To obtain data on the volume-dependence of the oscillatory parameters of the Siregnost FD 5, we investigated the course of iso-volume and iso-resistance lines in a simple mechanical resistor-volume model in the different coordinate systems, initially in the absence of additional superimposed stationary flow. While the P-psi diagram reveals no uniform course, and no preferential relationship of changes in resistance to P or Ros, or of changes in volume to psi, such a relationship develops on transformation to the Rre-phi and the Rre-X diagram. Rre proves to contain not only the purely resistor component, but also a reactance-proportional or inversely volume-proportional component, which is apparently due to internal friction resulting from volume compression. On the other hand, reactance is almost totally derivable from volume compression. With reference to the theoretical Franken model and others (1981), we discussed the influence of various physical factors on the impedance of a tube segment, and the different volume-dependence of impedance of closed- and open-ended cylindrical tubes. Further work on the theoretical consideration of the forced oscillation technique will examine the influence of additional superimposed stationary flow, which has a considerable effect on the resistor-volume model. Furthermore, the critical value of Reynold's number may be expected to be exceed in the FD 5 reference tube already at low respiratory flow.

Airway Resistance↗
PubMed2026

RSHash: a fast and space-efficient hash table for k-mers.

SUMMARY: Large genomic data collections can be viewed as a continuous string of DNA characters. The essential operations for data structures indexing the k-mer content of such a string are lookup and locate. Lookup determines whether a query k-mer q exists in the string and locate returns all locations in the string where q is present. High-throughput DNA sequencing generates very many k-mer sets of size exceeding billions of characters. In such scenarios, memory consumption and query efficiency pose significant challenges to a data structure supporting the above mentioned queries. To address this problem, we describe a simple, compressed, static data structure for k-mers that answers lookup and can be extended for supporting locate. The general scheme follows the use of minimizers like the state-of-the art SSHash. However, instead of using minimum perfect hash functions our solution (RSHash for Rank-Select Hash) relies on bitvectors with rank and select support, a multiple layered minimizer scheme, and a clever buffering strategy. We can show that RSHash is on average 40% and in some cases up to two times faster than SSHash while having the same memory requirements. Indeed we can go as low as 8 bits per canonical 31-mer on a human dataset. AVAILABILITY: https://github.com/jonsmcode/rshash.

Sequence Analysis, DNA↗
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↗
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↗
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↗
PubMed1989

Indexes to the reassociation and stability of solution DNA hybrids.

The computation, assumptions, and properties of DNA-hybrid stability and reassociation indexes were reviewed. Different methods of computing the same index typically yielded similar values. However, because dissociation curves change from asymmetric to symmetric as increasingly divergent DNAs are compared, adequate determination of mode required fitting a complex function. Delta Tm, delta mode, and delta T50H correlated well up to ca. 12, and all were found to be useful indexes of genomic similarity in that range. They also exhibited similar levels of error, even though T50H comprises a percent reassociation component with relatively large variance. At greater distances, the delta Tm scale became markedly compressed because of the boundary imposed by the temperature of hybrid formation (incubation temperature). Though not compressed or technically limited by it, delta mode and delta T50H could not be extrapolated with certainty below the incubation temperature. Among theoretical problems discussed: Tm and mode index an increasingly small percentage of the genome as the extent of reassociation decreases, and they may compare different genomic segments as DNAs become highly diverged. T50H relies upon the assumptions that all sequences evolve at a constant rate and that reassociation behavior is the same among all sequences regardless of their extent of divergence. Tm and T50H may be biased by self-hybridization of repetitive elements or cross-hybridization of paralogous sequences. Delta mode is free of such biases as long as the genomes under comparison are not too diverged. No index was found to be best in all circumstances.

Algorithms↗
PubMed1991

Classification of vertebral fractures.

Although it is a cardinal feature of involutional osteoporosis, there is often disagreement on what constitutes a vertebral fracture. We measured vertebrae T4-L5 in 52 healthy women to develop a normal range (mean +/- 3 SD) for vertebral shape and used these data to assess the prevalence of vertebral fractures. We classified vertebral fractures by type of deformity (wedge, biconcavity, or compression) and further by the degree of deformity (grades 1 and 2). In 195 postmenopausal women who were an age-stratified random sample of the Rochester population (ages 47-94), 40 (21%) had vertebral fractures (mean, 2 per person). There was a similar number of compression and wedge fractures, and grade 2 fractures were as common as grade 1. In a referral sample of 74 women with suspected osteoporosis, 62 (84%) had vertebral fractures (mean, 3.3 per person). Wedge fractures were most common, and grade 2 fractures were more common than grade 1. The distribution of type and grade of fractures differed between the two patient groups (P less than 0.01). Bone mineral density of the lumbar spine was related to mean fracture grade (r = -0.33, P less than 0.05) and to fracture number (r = -0.57, P less than 0.001) but not to fracture type. We conclude that a comprehensive approach is required in describing vertebral fractures. Using this approach we found distortion in the fracture characteristics of women referred to an osteoporosis clinic compared to women in the community.

Aged↗
PubMed1988

Data compression: 8-dimensional flow cytometric data processing with 28K addressable computer memory.

A method of data analysis for flow cytometry is presented which enables up to eight-dimensional data to be handled by a microcomputer with 28K addressable plus a further 32K non-addressable memory. The multi-parameter coordinates are coded into single numbers using a minimal modification of the array vector mapping equation. These code numbers, each of which corresponds to a given set of coordinates, and then ranked in ascending order according to magnitude and the frequency of each code number is found. Following this step the code is then decoded by integer arithmetic into its original coordinates which are then packed, together with the frequency, into two, three or four 16-bit words depending on the dimensionality of the data set. A five-dimensional data set is used as the illustration. Three regions were set on one two-dimensional data space and the five mono-dimensional histograms, plus a different bivariate distribution, were extracted in a single pass through the processed data file. In addition to considerable space saving the technique has two further attributes, namely, increased speed with which the user can appreciate multiparameter data and the ability to analyse such data sets with a microcomputer.

Algorithms↗
PubMed1992

Treatment of iatrogenic femoral artery injuries with ultrasound-guided compression.

Iatrogenic injuries of the groin are becoming more common after increasingly sophisticated vascular intervention. These injuries are accurately detected by duplex and color Doppler ultrasonography. Recent treatment of these lesions by ultrasound-guided compression repair (UGCR) has been described. During a 1-year period we identified 18 femoral artery injuries, including 17 pseudoaneurysms and one arteriovenous fistula. Three of the pseudoaneurysms thrombosed spontaneously before attempted treatment. The remaining 15 lesions underwent a trial of UGCR. Successful closure was accomplished in 10 patients (56%). Seven of these lesions were successfully treated during the initial session, and thrombosis was accomplished after repeat compression in three additional lesions. Three patients who were given anticoagulants had a failed UGCR, but their pseudoaneurysms thrombosed after administration of anticoagulants was discontinued. Two patients had failed UGCR and required operation. Seven (88%) of eight patients who were not given anticoagulants were successfully treated. In contrast only two (29%) of seven patients given therapeutic doses of anticoagulant medication were successfully treated by the technique. There was no statistical difference between mean pseudoaneurysm diameter, mean width and length of pseudoaneurysm neck, or depth of pseudoaneurysm neck from skin surface in patients in whom successful initial closure was achieved when compared with those patients in whom the initial attempt failed. UGCR is a safe, simple, noninvasive technique that can be used to treat many femoral artery injuries that traditionally were treated with surgery. The technique can be applied by any laboratory that has the necessary ultrasonography equipment and is currently the method of choice for treating uncomplicated iatrogenic femoral artery injuries at our institution.

Adult↗
PubMed1991

Review of arterial thoracic outlet syndrome with a report of five new instances.

Arterial damage, causing ischemia of the limb, occurs in less than 5 per cent of all instances of thoracic outlet syndrome. Arterial complications are usually associated with cervical ribs or rudimentary first ribs, but 12 per cent have occurred in patients with no osseous abnormality. The physiopathologic factors begin with compression of the subclavian artery which, in most patients, produces stenosis, poststenotic dilatation, formation of aneurysms and mural thrombosis. In other patients, aneurysms do not form, but the compression still causes stenosis, intimal injury and mural thrombosis. With either scenario, distal embolization can occur and produce signs and symptoms of ischemia that can limb-threatening. In this study, more than 200 patients reported previously and five additional sides in four patients were reviewed. Treatment depends upon the condition of the patient at presentation. Those with osseous abnormalities and no aneurysm or symptoms are not treated, while those with poststenotic dilatation or small aneurysms undergo rib resection only. Aneurysms more than twice the arterial diameter, intimal injury or mural thrombus are indications to resect, replace or bypass the subclavian artery. Patients who have had distal embolization and severe ischemic symptoms require, in addition to the aforementioned, distal thromboembolectomy, dorsal sympathectomy or both. Good results from treatment have been reported in 84 per cent of the 137 patients reported since 1970; 3 per cent required amputation and 3 per cent had cerebral emboli. Because the severe arterial complications were primarily the result of delayed therapy, they can best be avoided by early recognition, diagnosis and treatment.

Adult↗
PubMed1988

Modelling the phase equilibria in two-component membranes of phospholipids with different acyl-chain lengths.

A phenomenological model is proposed to describe the membrane phase equilibria in binary mixtures of saturated phospholipids with different acyl-chain lengths. The model is formulated in terms of thermodynamic and thermomechanic properties of the pure lipid bilayers, specifically the chain-melting transition temperature and enthalpy, the hydrophobic bilayer thickness, and the lateral area compressibility modulus. The model is studied using a regular solution theory made up of a set of interaction parameters which directly identify that part of the lipid-lipid interaction which is due to hydrophobic mismatch of saturated chains of different lengths. It is then found that there is effectively a single universal interaction parameter which, in the full composition range, describes the phase equilibria in mixtures of DMPC/DPPC, DPPC/DSPC, DMPC/DSPC, and DLPC/DSPC, in excellent agreement with experimental measurements. The model is used to predict the variation with temperature and composition of the specific heat, as well as of the average membrane thickness and area in each of the phases. Given the value of the universal interaction parameter, the model is then used to predict the phase diagrams of binary mixtures of phospholipids with different polar head groups, e.g., DPPC/DPPE, DMPC/DPPE and DMPE/DSPC. By comparison with experimental results for these mixtures, it is shown that difference in acyl-chain lengths gives the major contribution to deviation from ideal mixing. Application of the model to mixtures with non-saturated lipids is also discussed.

Algorithms↗