Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mapping glaucoma patients' 30-2 and 10-2 visual fields reveals clusters of test points damaged in the 10-2 grid that are not sampled in the sparse 30-2 grid.

ABSTRACT:

Purpose

To cluster test points in glaucoma patients' 30-2 and 10-2 visual field (VF) (Humphrey Field Analyzer: HFA, Carl Zeiss Meditec, Dublin, CA) in order to map the different regions damaged by the disease.

Method

This retrospective study included 128 eyes from 128 patients. 142 total deviation (TD) values (74 from the 30-2 VF and 68 from the 10-2 VF) were clustered using the 'Hierarchical Ordered Partitioning And Collapsing Hybrid-Partitioning Around Medoids' algorithm. The stability of the identified clusters was evaluated using bootstrapping.

Results

65 sectors were identified in total: 38 sectors were located outside the 10-2 VF whereas 29 sectors were located inside the 10-2 VF (two sectors overlap in both grids). The mapping of many sectors appeared to follow the distribution of retinal nerve fiber bundles. The results of bootstrapping suggested clusters were stable whether they were outside or inside the 10-2 VF.

Conclusion

A considerable number of sectors were identified in the 10-2 VF area, despite the fact that clustering was carried out on all points in both the 30-2 VF and 10-2 VF simultaneously. These findings suggest that glaucomatous central VF deterioration cannot be picked up by the 30-2 test grid alone, because of poor spatial sampling; denser estimation of the central ten degrees, than offered by the 30-2 test grid alone, is needed. It may be beneficial to develop a new VF test grid that combines test points from 30-2 and 10-2 VFs--the results of this study could help to devise this test grid.

SUBMITTER: Asaoka R

PROVIDER: S-EPMC4064971 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

24-2 Visual Fields Miss Central Defects Shown on 10-2 Tests in Glaucoma Suspects, Ocular Hypertensives, and Early Glaucoma.

Project description:PURPOSE:To investigate the prevalence of visual field defects in glaucomatous eyes, glaucoma suspects, and ocular hypertensives with 24-2 and 10-2 visual fields. DESIGN:Prospective, cross-sectional study. PARTICIPANTS:Patients with or suspected glaucoma tested with 24-2 and 10-2. Patients were classified into 3 groups on the basis of the presence of glaucomatous optic neuropathy (GON) and 24-2 visual field abnormalities: early glaucoma (GON and abnormal visual field, mean deviation >-6 decibels [dB]), glaucoma suspects (GON and normal visual field), and ocular hypertensives (normal disc, normal visual field, and intraocular pressure >22 mmHg). For the classification of visual field abnormalities, 24-2 and 10-2 tests performed on the same visit were analyzed. MAIN OUTCOME MEASURES:Comparison of the prevalence of abnormal 24-2 versus 10-2 visual field results based on cluster criteria in each diagnostic group. RESULTS:A total of 775 eyes (497 patients) were evaluated. A total of 364 eyes had early glaucoma, 303 eyes were glaucoma suspects, and 108 eyes were ocular hypertensives. In the glaucoma group, 16 of the 26 eyes (61.5%) classified as normal based on cluster criteria on 24-2 tests were classified as abnormal on 10-2 visual fields. In eyes with suspected glaucoma, 79 of the 200 eyes (39.5%) classified as normal on the 24-2 test were classified as abnormal on 10-2 visual fields. In ocular hypertensive eyes, 28 of the 79 eyes (35.4%) classified as normal on the 24-2 were classified as abnormal on the 10-2. Patients of African descent were more likely to have an abnormal 10-2 result (67.3 vs. 56.8%, P = 0.009). CONCLUSIONS:Central visual field damage seen on the 10-2 test is often missed with the 24-2 strategy in all groups. This finding has implications for the diagnosis of glaucoma and classification of severity.

| S-EPMC5610609 | biostudies-literature

Grid cell co-activity patterns during sleep reflect spatial overlap of grid fields during active behaviors.

Project description:Continuous-attractor network models of grid formation posit that recurrent connectivity between grid cells controls their patterns of co-activation. Grid cells from a common module exhibit stable offsets in their periodic spatial tuning curves across environments, and this may reflect recurrent connectivity or correlated sensory inputs. Here we explore whether cell-cell relationships predicted by attractor models persist during sleep states in which spatially informative sensory inputs are absent. We recorded ensembles of grid cells in superficial layers of medial entorhinal cortex during active exploratory behaviors and overnight sleep. Per grid cell pair and collectively, and across waking, rapid eye movement sleep and non-rapid eye movement sleep, we found preserved patterns of spike-time correlations that reflected the spatial tuning offsets between these grid cells during active exploration. The preservation of cell-cell relationships across waking and sleep states was not explained by theta oscillations or activity in hippocampal subregion CA1. These results indicate that recurrent connectivity within the grid cell network drives grid cell activity across behavioral states.

| S-EPMC7412059 | biostudies-literature

Linear reinforcement learning in planning, grid fields, and cognitive control.

Project description:It is thought that the brain's judicious reuse of previous computation underlies our ability to plan flexibly, but also that inappropriate reuse gives rise to inflexibilities like habits and compulsion. Yet we lack a complete, realistic account of either. Building on control engineering, here we introduce a model for decision making in the brain that reuses a temporally abstracted map of future events to enable biologically-realistic, flexible choice at the expense of specific, quantifiable biases. It replaces the classic nonlinear, model-based optimization with a linear approximation that softly maximizes around (and is weakly biased toward) a default policy. This solution demonstrates connections between seemingly disparate phenomena across behavioral neuroscience, notably flexible replanning with biases and cognitive control. It also provides insight into how the brain can represent maps of long-distance contingencies stably and componentially, as in entorhinal response fields, and exploit them to guide choice even under changing goals.

| S-EPMC8368103 | biostudies-literature

Amsler grid test for detection of advanced glaucoma in Ethiopia.

Project description:OBJECTIVE:This study was done to determine the validity of amsler grid test black on white (BOW), as well as white on black (WOB) for identifying central visual field (VF) defects in patients with advanced glaucoma. DESIGN:Prospective study. PARTICIPANTS:We prospectively included 100 consecutive eyes of 88 adult patients with advanced glaucoma and 100 eyes of 100 normal individuals. We used a lottery method to choose the side of the eye for the control groups. METHODS:All participants had reliable Humphrey 10-2 Swedish Interactive Threshold Algorithm (SITA) standard VF. Both the BOW and WOB amsler grid tests were done for each group. Sensitivity, specificity, and positive and negative predictive values of the amsler grid scotoma area were calculated with the 10-2 VF as the reference standard. RESULTS:The mean ± standard deviation (SD) of age and the 10-2 VF mean deviation (MD) of advanced glaucoma eyes were 59.8 ± 11.8 (range 34-84) years and -19.94 ± 9.8(range -34.98--0.52) respectively. Among 108 eyes with normal 10-2 VF test, 103 had a normal BOW amsler grid test and 5 had an abnormal BOW test. Among 92 eyes with an abnormal 10-2 VF test, 74 had an abnormal and 18 had normal BOW amsler grid test. Sensitivity, specificity, and positive and negative predictive values of the BOW amsler grid test were 80.4%, 95.4%, 93% and 85.1% respectively whereas that of the WOB amsler grid test were 71.7%, 95.4%, 93% and 72.8% respectively. CONCLUSION:The sensitivity and specificity of both BOW and WOB amsler grid tests were high in detecting VF defects in advanced glaucoma.

| S-EPMC7064174 | biostudies-literature

Inferring circuit mechanisms from sparse neural recording and global perturbation in grid cells.

Project description:A goal of systems neuroscience is to discover the circuit mechanisms underlying brain function. Despite experimental advances that enable circuit-wide neural recording, the problem remains open in part because solving the 'inverse problem' of inferring circuity and mechanism by merely observing activity is hard. In the grid cell system, we show through modeling that a technique based on global circuit perturbation and examination of a novel theoretical object called the distribution of relative phase shifts (DRPS) could reveal the mechanisms of a cortical circuit at unprecedented detail using extremely sparse neural recordings. We establish feasibility, showing that the method can discriminate between recurrent versus feedforward mechanisms and amongst various recurrent mechanisms using recordings from a handful of cells. The proposed strategy demonstrates that sparse recording coupled with simple perturbation can reveal more about circuit mechanism than can full knowledge of network activity or the synaptic connectivity matrix.

| S-EPMC6078497 | biostudies-literature

Comparing 10-2 and 24-2 Visual Fields for Detecting Progressive Central Visual Loss in Glaucoma Eyes with Early Central Abnormalities.

Project description:PurposeTo compare the ability of 10-2 visual field tests and central 12 locations of the 24-2 tests (C24-2) to detect central visual field progression in glaucoma eyes with early central visual field abnormalities.DesignObservational cohort study.ParticipantsThree-hundred eyes of 180 participants with glaucoma or ocular hypertension.MethodsParticipants with both 10-2 and 24-2 tests performed on ≥3 visits over ≥1-year period were included to estimate the longitudinal variability of 10-2 and C24-2 visual field mean deviation (MD). The variability estimates were then used to reconstruct real-world visual field results by computer simulations, in a scenario where eyes had a baseline 10-2 and C24-2 MD was -2 dB and exhibited various rates of change (-0.25, -0.50, -0.75 and -1.00 dB/year), and the time to detect these changes were evaluated using trend-based analyses.Main outcome measuresTime required to detect progression.ResultsOverall, the time to detect central visual field progression was reduced by 7-9% using the 10-2 compared to C24-2 MD values, equivalent to a total reduction of 0.1-0.3 dB lost. For example, 90% of eyes with a central 10-2 or C24-2 MD loss of -0.50 dB/year would be detected after 5.0 and 5.5 years of semi-annual testing respectively, or after 3.4 and 3.7 years respectively for eyes with a -1.00 dB/year loss.ConclusionsTrend-based analyses using 10-2 MD resulted in a mild reduction (7-9%) in the time to detect central visual field progression compared to C24-2 MD in glaucoma eyes with early central visual field abnormalities. Further studies are needed to determine whether other progression analyses can better exploit the increased sampling of 10-2 tests. These findings provide evidence-based guidance on the potential value-add of 10-2 testing in the clinical management of glaucoma patients.

| S-EPMC6860370 | biostudies-literature

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.

Project description:Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem-loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowledge the most complete RNA structure ensembles reported to date for these systems, we remove the coupling between force field errors and errors due to incomplete sampling, providing a comprehensive comparison between current top-performing MD force fields for RNA. Of the RNA force fields tested in this study, none demonstrate the ability to correctly identify the most thermodynamically stable structure for all three systems. We discuss the deficiencies present in each potential function and suggest areas where improvements can be made. The results imply that although "short" (nsec-μsec timescale) simulations may stay close to their respective experimental structures and may well reproduce experimental observables, inevitably the current force fields will populate alternative incorrect structures that are more stable than those observed via experiment.

| S-EPMC4536319 | biostudies-literature

Off-Grid DOA Estimation Using Sparse Bayesian Learning for MIMO Radar under Impulsive Noise.

Project description:Direction of arrival (DOA) estimation is an essential and fundamental part of array signal processing, which has been widely used in radio monitoring, autonomous driving of vehicles, intelligent navigation, etc. However, it remains a challenge to accurately estimate DOA for multiple-input multiple-output (MIMO) radar in impulsive noise environments. To address this problem, an off-grid DOA estimation method for monostatic MIMO radar is proposed to deal with non-circular signals under impulsive noise. In the proposed method, firstly, based on the property of non-circular signal and array structure, a virtual array output was built and a real-valued sparse representation for the signal model was constructed. Then, an off-grid sparse Bayesian learning (SBL) framework is proposed and further applied to the virtual array to construct novel off-grid sparse model. Finally, off-grid DOA estimation was realized through the solution of the sparse reconstruction with high accuracy even in impulsive noise. Numerous simulations were performed to compare the algorithm with existing methods. Simulation results verify that the proposed off-grid DOA method enables evident performance improvement in terms of accuracy and robustness compared with other works on impulsive noise.

| S-EPMC9416458 | biostudies-literature

Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data.

Project description:Implementation of a new algorithm, SMILE, is described for reconstruction of non-uniformly sampled two-, three- and four-dimensional NMR data, which takes advantage of the known phases of the NMR spectrum and the exponential decay of underlying time domain signals. The method is very robust with respect to the chosen sampling protocol and, in its default mode, also extends the truncated time domain signals by a modest amount of non-sampled zeros. SMILE can likewise be used to extend conventional uniformly sampled data, as an effective multidimensional alternative to linear prediction. The program is provided as a plug-in to the widely used NMRPipe software suite, and can be used with default parameters for mainstream application, or with user control over the iterative process to possibly further improve reconstruction quality and to lower the demand on computational resources. For large data sets, the method is robust and demonstrated for sparsities down to ca 1%, and final all-real spectral sizes as large as 300 Gb. Comparison between fully sampled, conventionally processed spectra and randomly selected NUS subsets of this data shows that the reconstruction quality approaches the theoretical limit in terms of peak position fidelity and intensity. SMILE essentially removes the noise-like appearance associated with the point-spread function of signals that are a default of five-fold above the noise level, but impacts the actual thermal noise in the NMR spectra only minimally. Therefore, the appearance and interpretation of SMILE-reconstructed spectra is very similar to that of fully sampled spectra generated by Fourier transformation.

| S-EPMC5438302 | biostudies-literature

Sparse codes for speech predict spectrotemporal receptive fields in the inferior colliculus.

Project description:We have developed a sparse mathematical representation of speech that minimizes the number of active model neurons needed to represent typical speech sounds. The model learns several well-known acoustic features of speech such as harmonic stacks, formants, onsets and terminations, but we also find more exotic structures in the spectrogram representation of sound such as localized checkerboard patterns and frequency-modulated excitatory subregions flanked by suppressive sidebands. Moreover, several of these novel features resemble neuronal receptive fields reported in the Inferior Colliculus (IC), as well as auditory thalamus and cortex, and our model neurons exhibit the same tradeoff in spectrotemporal resolution as has been observed in IC. To our knowledge, this is the first demonstration that receptive fields of neurons in the ascending mammalian auditory pathway beyond the auditory nerve can be predicted based on coding principles and the statistical properties of recorded sounds.

| S-EPMC3395612 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data