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PubMed1980

A disparity analysis of some horopter data.

A form of binocular disparity analysis has been applied to some grid nonius, apparent frontoparallel plane, diplopia limit, and binocular nonius data from studies by Ogle and Ames et al. The results show that all horopter criteria are capable of detecting fixation disparity and indicate that the apparent frontoparallel plane can change shape and position as a result forced vergences. The effect of size lenses, plus lenses, and fixation distance are discussed. A comparison between the disparity analysis of partition data and horopter data is presented.

Data Collection↗

PubMed1989

Craniosynostosis: diagnostic value of three-dimensional CT reconstruction.

Three-dimensional computed tomography (CT) has an important role in determining the presence and extent of congenital and acquired craniofacial deformities. The authors compared the sensitivity and specificity of three-dimensional CT in the detection and characterization of craniosynostosis with that of planar CT and skull radiography. Eighty-two patients with isolated and syndromal synostoses were imaged with CT and three-dimensional CT, and 42 with skull radiography. Three-dimensional CT scan processing was performed by shaded-surface reconstruction, volumetric, and depth-coded methods. Two trained observers read each scan series in a blinded fashion. Diagnostic utility of the images was determined with receiver operating characteristic analysis. The observers ranked three-dimensional shaded images higher than the other types, with three-dimensional volumetric images second and three-dimensional surface images ranked third. Results of this study demonstrate that three-dimensional shaded-surface reconstruction from CT scans is superior to conventional plain radiographs and CT scans in diagnosing craniosynostosis.

Adolescent↗

PubMed2002

A Bayesian approach to the stereo correspondence problem.

I present a probabilistic approach to the stereo correspondence problem. Rather than trying to find a single solution in which each point in the left retina is assigned a partner in the right retina, all possible matches are considered simultaneously and assigned a probability of being correct. This approach is particularly suitable for stimuli where it is inappropriate to seek a unique partner for each retinal position--for instance, where objects occlude each other, as in Panum's limiting case. The probability assigned to each match is based on a Bayesian analysis previously developed to explain psychophysical data (Read, 2002). This provides a convenient way to incorporate constraints that enable the ill-posed correspondence problem to be solved. The resulting model behaves plausibly for a variety of different stimuli.

Bayes Theorem↗

PubMed2005

The stroboscopic Pulfrich effect is not evidence for the joint encoding of motion and depth.

In the Pulfrich effect, an illusion of depth is produced by introducing differences in the times at which a moving object is presented to the two eyes. In the classic form of the illusion, there is a simple explanation for the depth percept: the interocular delay introduces a spatial disparity into the stimulus. However, when the moving object is viewed stroboscopically, this simple explanation no longer holds. In recent years, depth perception in the stroboscopic Pulfrich effect has been explained by invoking neurons that are sensitive both to stereo disparity and to direction of motion. With such joint motion/disparity encoders, interocular delay causes a perception of depth by causing a shift in each neuron's preferred disparity. This model has been implemented by N. Qian and R. A. Andersen (1997). Here we show that this model's predictions for perceived disparity are quantitatively at odds with psychophysical measures. The joint-encoding model predicts that the perceived disparity is the virtual disparity implied by the apparent motion; in fact, the perceived disparity is smaller. We show that the percept can be quantitatively explained on the basis of spatial disparities present in the stimulus, which could be extracted from pure disparity sensors. These results suggest that joint encoding of motion and depth is not the dominant neuronal basis of depth perception in this stimulus.

Computer Simulation↗

PubMed2001

The influence of varied rest interval lengths on depth jump performance.

The purpose of this study was to measure the effects of varied rest interval lengths on the vertical jump heights and ground reaction forces during the execution of a depth jump from a predetermined optimal height. The subjects were 12 men with a mean (SD) age of 25.08 +/- 2.43 years. Each subject's optimal depth jump height was determined by executing depth jumps from 10-80 cm. After determining their optimal depth jump height, the subjects performed 3 sets of 10 depth jumps, each set with a different rest interval duration. The 3 rest intervals between depth jumps were 15, 30, and 60 seconds and were counterbalanced for each subject. Maximal vertical jump height and vertical ground reaction forces were calculated for each depth jump trial. The Peak Performance Motion Measurement System was used to measure vertical jump height and the Kistler force platform was used to measure ground reaction forces. Two-way analyses of variance revealed that rest interval length did not affect (p > 0.05) vertical jump height or vertical ground reaction forces. Therefore, this study demonstrated a 15-second rest interval was sufficient for recovery during the performance of depth jumps.

Adult↗

PubMed1992

Contrast sensitivity and reading through multifocal intraocular lenses.

Multifocal intraocular lenses are intended to increase depth of focus for patients with cataracts, but optical considerations predict reduced retinal-image contrast. We evaluated visual performance through multifocal intraocular lenses by measuring contrast sensitivity functions and reading speed for age-matched groups with multifocal and monofocal intraocular lenses and two normal control groups. Contrast sensitivity functions of the patients with multifocal lenses did not differ significantly for optical distances differing by 2.5 diopters, indicating substantial depth of focus. Normal and monofocal contrast sensitivity functions were nearly identical, and both were about a factor of two higher than multifocal contrast sensitivity functions. Patients with multifocal lenses showed deficits in reading speed only for low-contrast text (less than 30%) and small letters (0.2 degree and 1.0 degree).

Aging↗

PubMed2025

A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.

PURPOSE: The Undiagnosed Diseases Network is a National Institutes of Health funded research study that aims to solve a broad clinical spectrum of challenging rare disease cases. Participants receive care from multiple clinical specialists, who collaborate to perform deep phenotyping and state-of-the-art multiomics analyses. As bioinformatics of short-read sequencing has matured, the discovery of repeat expansion disorders (REDs) is accelerating. REDs comprise approximately 60 characterized disorders, which exhibit a broad spectrum of phenotypes. Thus, a largely unbiased genome-wide approach in a phenotypically diverse sample will add to the diagnostic depth, explore the limits of short-read genome analysis, and establish novel candidate RED loci. METHODS: Here, we present a genome-wide analysis of repeat expansions conducted on 1018 genomes from the Undiagnosed Diseases Network. By leveraging 2 distinct bioinformatics tools, ExpansionHunter Denovo and STRling, we showed that repeat expansions can be accurately detected in short-read genomes. RESULTS: We demonstrated that a genotype-first approach can diagnose atypical cases of known REDs and provide valuable clinical insights. We present clinical details on participants with expansions in ATXN7, DMPK, FMR1, GLS, HTT, RFC1, AFF3, and MARCH6. Importantly, we highlight 2 cases of juvenile Huntington disease that were discovered through our analysis. Finally, we present a list of novel candidate short tandem repeats (TR) that could potentially be pathogenic if expanded. CONCLUSION: Importantly, our approach showcases the bioinformatic advancements in genome analysis for RED detection and highlights its practical applications.

Humans↗

PubMedDate not supplied

A general coverage theory for shotgun DNA sequencing.

The classical theory of shotgun DNA sequencing accounts for neither the placement dependencies that are a fundamental consequence of the forward-reverse sequencing strategy, nor the edge effect that arises for small to moderate-sized genomic targets. These phenomena are relevant to a number of sequencing scenarios, including large-insert BAC and fosmid clones, filtered genomic libraries, and macro-nuclear chromosomes. Here, we report a model that considers these two effects and provides both the expected value of coverage and its variance. Comparison to methyl-filtered maize data shows significant improvement over classical theory. The model is used to analyze coverage performance over a range of small to moderately-sized genomic targets. We find that the read pairing effect and the edge effect interact in a non-trivial fashion. Shorter reads give superior coverage per unit sequence depth relative to longer ones. In principle, end-sequences can be optimized with respect to template insert length; however, optimal performance is unlikely to be realized in most cases because of inherent size variation in any set of targets. Conversely, single-stranded reads exhibit roughly the same coverage attributes as optimized end-reads. Although linking information is lost, single-stranded data should not pose a significant assembly liability if the target represents predominantly low-copy sequence. We also find that random sequencing should be halted at substantially lower redundancies than those now associated with larger projects. Given the enormous amount of data generated per cycle on pyro-sequencing instruments, this observation suggests devising schemes to split each run cycle between twoor more projects. This would prevent over-sequencing and would further leverage the pyrosequencing method.

Computational Biology↗

PubMedDate not supplied

A simple method of producing depth ionization data for electron energy constancy check.

A simple method has been developed to reproduce depth ionization data of electron beams for energy determination. The method utilizes a simple set of equipment, a combination of a specially designed wedge-shaped polystyrene phantom and a linear array of detectors, to collect the necessary data. The wedge-shaped phantom provides varying depths to various detectors in the array. The ionization readings received from the detectors were corrected for off-axis ratio and plotted against corresponding ray-line depths to produce depth ionization curves. The instrument setup was fast and simple. The relevant data, for a high-energy linear accelerator with multiple electron energies, were collected in minutes. The depths of 80% and 50% ionization determined by this method were found to differ by 2 and 3 mm, respectively, at the most, with those determined by a conventional method.

Biophysical Phenomena↗

PubMed1980

Depth-of-focus of the pseudophakic eye.

Pseudophakic patients have been found with the ability to read both 6/6 and N5 without a reading addition. An explanation of this phenomenon is offered in terms of the depth-of-focus of the pseudophakic eye. Results of experiments to measure the depth-of-focus of the pseudophakic eye for Snellen letters are compared with theoretical predictions from earlier work, and implications in terms of visual acuity and refractive error are discussed.

Cataract↗

PubMed1993

The dynamic functions of the act of reading.

This study of 68 avid fiction readers demonstrated that for those who love fiction, deeply personal meanings pervade the act of becoming absorbed in a work and shape the ways that they can use fiction in their lives as a whole. Each respondent had a unique, largely unconscious relationship to the act of reading, a relationship that expressed themes and addressed functions related to self-organisation, real and fantasized relatedness, affect regulation, and the repetition or working through of conflict. To the extent that these inner determinants of the reading experience became rigid and unyielding, readers derived less newness, richness, and depth, though not necessarily less benefit, from engagement in fiction. Greater flexibility allowed reading to take place in what Winnicott called potential space. It enabled readers to involve themselves in fiction without sacrificing either the work's uniqueness or their own inner life, so permitting them to create new experience.

Affect↗

PubMed2026

theBIGbam: compression and interactive exploration of large-scale sequencing alignments with circular mapping support.

SUMMARY: theBIGbam (github.com/bhagavadgitadu22/theBIGbam) is a genome browser and alignment viewer designed for massive metagenomic and metatranscriptomic datasets. The tool takes BAM files containing read alignments, together with genome assemblies in FASTA format or annotated genome sequences in GenBank format. Alternatively, it can start from raw FASTQ reads and generate alignments using a modified mapper that supports circular genomes, enabling seamless read mapping across genome ends. theBIGbam can compress hundreds of gigabytes of input files 10- to 100-fold into dedicated databases while retaining key per-position information, including coverage depth and recurrent mismatches, insertions, and deletions between reads and the reference. These databases can be served to a local web browser, enabling interactive exploration of any contig in any sample using DNAFeaturesViewer for genome maps and Bokeh for mapping-derived features. Contig-sample pairs available for visualization can be filtered using a range of summary metrics calculated per contig, per sample, and per contig-sample pair to guide users toward the most relevant signals. Through its interactive visualization, theBIGbam facilitates the exploration of complex datasets, while its integrated database-combining assembly features, annotated features, and mapping-derived features-provides the information needed to investigate biological hypotheses systematically. Designed to complement existing browsing tools like IGV and Anvi'o, theBIGbam is particularly suited for examining misassemblies, subpopulations, microdiversity, and contig topology in large-scale datasets. AVAILABILITY AND IMPLEMENTATION: theBIGbam is an open-source Rust/Python package that can be installed from Bioconda or PyPI. The source code and documentation are available on GitHub (github.com/bhagavadgitadu22/theBIGbam).

Software↗

PubMed2006

Consumer health information for pet owners.

OBJECTIVE: The author studied health information available for veterinary consumers both in print and online. METHODS: WorldCat was searched using a list of fifty-three Library of Congress subject headings relevant to veterinary consumer health to identify print resources for review. Identified items were then collected and assessed for authority, comprehensiveness of coverage, validity, and other criteria outlined by Rees. An in-depth assessment of the information available for feline lower urinary tract disease (FLUTD) and canine congestive heart failure (CHF) was then conducted to examine the availability and quality of information available for specific diseases and disorders. A reading grade level was assigned for each passage using the Flesch-Kincaid formula in the Readability Statistics feature in Microsoft Word. RESULTS/DISCUSSION: A total of 187 books and 7 Websites were identified and evaluated. More than half of the passages relating to FLUTD and CHF were written above an 11th-grade reading level. A limited quantity of quality, in-depth resources that address specific diseases and disorders and are written at an appropriate reading level for consumers is available. CONCLUSION: The library's role is to facilitate access to the limited number of quality consumer health resources that are available to veterinary consumers.

Abstracting and Indexing↗

PubMed2003

Binocular coordination of saccades at far and at near in children and in adults.

The goal of the study was to test the quality of binocular coordination of saccades in children and adults, and its dependency upon the viewing distance. Fourteen normal children (4.5-12 years old) and 10 normal adults (22-44 years old) participated. Two distances were studied: far (150 cm) and close (20 cm). Horizontal saccades from both eyes were recorded simultaneously by a photoelectric device. The results show (i) poor binocular coordination of saccades in children is distance dependent: coordination is particularly poor at near and could compromise single binocular vision; and (ii) post-saccadic drift analysis indicates that stability of the eyes after the saccade as well as the quality of binocular alignment during fixation are poor in children, regardless of the viewing distance. The results provide a reference for the normal development of binocular motor control and have important implications for reading in young children.

Adult↗

PubMedDate not supplied

Agreement between A-mode and B-mode ultrasonography in the measurement of ocular distances.

It is generally accepted that A-mode ultrasonography is more accurate than B-mode in measuring intraocular dimensions. Consequently, A-mode ultrasonography is the procedure of choice in ocular biometry while B-mode ultrasonography is used principally for diagnostic purposes. In this study, we investigated the agreement between measurement of intraocular distances using A- and B-mode ultrasonography on freshly enucleated camel eyes. Our results suggest that relative to average A-mode values, B-mode overestimates corneal thickness (bias = 0.06 mm) and anterior chamber depth (bias = 0.03 mm), while it underestimates lens thickness (bias = -0.11 mm), vitreous chamber depth (bias = -0.32 mm) and axial length (bias = -0.40 mm). In general, difference between A- and B-mode values is larger for deeper intraocular dimensions. This implies that the two methods are more likely to give different readings for measurements of lens thickness, vitreous chamber depth and axial length.

Animals↗

PubMed2006

The dose-area product, a new parameter for the dosimetry of narrow photon beams.

In the dosimetry of narrow photon fields with side lengths of the order of 1 cm, the traditional parametrisation via the absolute dose on the beam axis and the relative lateral dose distribution has to deal with the difficulty to find sufficiently small detectors and to adjust them accurately on the narrow-beam axis. This can be avoided by reconsidering the parametrisation, using as normalization factor the surface integral of the dose in the plane perpendicular to the beam axis, abbreviated as the "dose-area product" (DAP). We investigated and confirmed the ability of a large-area parallel-plate ionisation chamber, with a sensitive volume shaped as a flat cylinder of 81.6 mm diameter and 2 mm thickness, to perform the integration over the full lateral dose profile of narrow photon beams with side lengths up to 5 cm. The lateral adjustment of this large-area detector relative to a narrow photon beam is not critical. The large-area ionisation chamber was calibrated in terms of the DAP by reference to a 0.3 cm3 ionisation chamber. A field-size dependent "modified output factor" was defined as the ratio of the DAP measured at 5 cm phantom depth for 100 cm SSD, and the monitor reading. A prominent phenomenon of narrow photon fields is the field-size and source-distance independence of the relative axial profile of the DAP as function of the thickness of a pre-absorber or of the depth in a phantom. For narrow-beam treatment planning in IMRT, the DAP is combined with the energy- and field size-dependent relative lateral dose distribution which is represented, for example, by a Gaussian convolution kernel. Another useful feature of the DAP is the possibility of its direct control during patient irradiation by means of an on-line monitor with spatial resolution, arranged in the accessory holder.

Calibration↗

PubMed2001

The effect of reading and near-work on the development of myopia in emmetropic boys: a prospective, controlled, three-year follow-up study.

This study aimed to investigate the effect of reading and near work on myopic development in emmetropic boys in school age. It involved totally 114 children in two groups. Right eyes of 67 randomly selected students (mean age=12.93) with mean 6 h of reading and near work (Group 1) were compared with the right eyes of 47 apprentices (mean age=12.96) working as skilled laborers (Group 2). Cycloplegic refraction, keratometric readings and biometric measurements including anterior chamber depth (ACD), lens thickness (LT), vitreous chamber depth (VCD) and axial length (AL) were performed for 3 years at 18 month intervals. Two analyses were conducted: (1) for subjects in both groups with baseline refractive error from +0.50 to -0.50 D; (2) for all subjects in both groups with baseline refractive error from +1.00 to -1.00 D. For subjects with baseline refractive error of +/-0.50 D, myopic shift was present in 20 of 41 (48.8%) in group 1 and in seven of 37 (18.9%) in group 2 at the end of the study. The magnitude of the myopic shift was 0.56 and 0.07 D in group 1 and 2, respectively. For subjects with a baseline refractive error of +/-1.00 D, myopic progression was present in 40 of 67 (59.7%) in group 1 and in 10 of 47 (21.3%) in group 2 at the last readings. In this larger refractive range, the magnitude of the myopic shift was 0.61 and 0.12 D in group 1 and 2, respectively. The mean ACD, VCD and AL were significantly higher in the last readings after 36 months than in the first readings (for each, P=0.0001) in group 1. There was no statistically significant difference between two measurements of these parameters in group 2. The final keratometric dioptric readings were lower than the first values (for each, P=0.0001) in both groups at the end of the study. This prospective and controlled study suggested that reading and near work, important environmental factors, might cause refractive myopic shifts in emmetropic students. The myopic shift was primarily related to significant increases in ACD, VCD and AL in this young age group.

Anterior Chamber↗

PubMed2006

Neuropsychological deficits and neural dysfunction in familial dyslexia.

We report the neuropsychological profile and the pattern of brain activity during reading tasks in a sample of familial dyslexics. We studied our subjects with an in-depth neuropsychological assessment and with functional neuroimaging (fMRI) during word and pseudoword reading and false font string observations (baseline condition). The neuropsychological assessment revealed that familial dyslexia, in both persistent and compensated forms, is often associated with deficits in verbal short-term memory, phonological awareness and automatization abilities. The functional results showed a lack of activation in the posterior areas of the reading network. This study, together with the previously published VBM study (Brambati, S.M., Termine, C., Ruffino, M., Stella, G., Fazio, F., Cappa, S.F. and Perani, D., Regional reductions of gray matter volume in familial dyslexia, Neurology, 63 (2004) 742-5), provides a multiple modality evaluation of familial dyslexia. The neuropsychological assessment showed cognitive deficits associated with dyslexia that persist also in subjects with compensated reading deficit. Both the anatomical and the functional study point out a deficit in the posterior areas of the reading network.

Adolescent↗