Search PubMedSearch

SEARCH · Search PubMed

Results for “Measuring algorithm”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

Computer rejection of EEG artifact. II. Contamination by drowsiness.

As part of an effort to automatically measure a background EEG baseline against which changes due to therapy or experimental manipulations may be measured, algorithms to detect EEG patterns associated with drowsiness have been developed and objectively evaluated. The decision of drowsiness is tentatively based upon changes in simple signal features, including increased ratios of both delta-band to alpha-band and theta-band to alpha-band spectral intensity as compared to thresholds automatically determined from a waking calibration period. Several heuristic criteria are then required to reach a final decision. Thirty-one normal and abnormal, 3-minute, 8-channel clinical EEG recordings containing drowsiness were scored by 5 expert scorers. Out of a total of 106 events labeled drowsy by at least one judge, 85 were found by a consensus of 3 or more of the 5 experts. On the 20 recordings not used for training the decision thresholds (testing data set), the system found 84% for the 85 episodes found by the consensus, and 89% of the 62 episodes found by all 5 scorers. Only one event was found by the system which was not found by any scorer, or which did not border on a consensus-defined episode of drowsiness. This performance is adequate to justify inclusion of these algorithms into a previously described real time EEG analysis system, ADI-EEG, allowing integration of the decisions of the separate subsystems for detection of artifact, sharp transients and drowsiness.

Computers

Measuring Cell Dimensions in Fission Yeast Using Machine Learning.

In fission yeast (Schizosaccharomyces pombe), cell length is a crucial indicator of cell cycle progression. Microscopy screens that examine the effect of agents or genotypes suspected of altering genomic or metabolic stability and thus cell size are crucial for studying disruptions to cell cycle dynamics. This method is based on using an automated cell segmentation algorithm to measure S. pombe cells imaged by brightfield (BF) microscopy methods. PhotoPhenosizer (PP) is a machine learning-based tool designed for automated cell measuring and dimensional analysis of morphology frequency distributions. Integration of this method into large-scale pipelines for tracking cell dimension change streamlines morphological measurements, which facilitates the examination of cellular responses to genomic and metabolic stresses. In this protocol, we use PP to observe the effect of genomic instability on cell size dynamics over a 12-day chronological lifespan assay. Our results show that relative to wild-type cells, a replication stress mutant shows larger cells during chronological aging in excess glucose media. Our results are consistent with activation of checkpoints that regulate cell morphology in response to DNA damage. This method's application highlights the relevance of its incorporation in experimental routines that require large-scale image processing and its adoption by users with routine needs in S. pombe molecular research projects.

Schizosaccharomyces

Signal-processing techniques in a computerized hearing aid test system.

General background is given to describe the factors leading up to the implementation of a computerized hearing aid test system in a production environment. The digital measurement methods for determination of the required acoustal components such as fundamental, rms, distortion, etc., in the presence of noise are discussed. The use of the concept of the average cycle for repetitive signals is described with its advantages in a Fourier type system. An algorithm for measuring rms for nonrepetitive signals that trades off resolution for memory size is described. Features and advantages of computerized testing of hearing aids are listed.

Acoustics

Application of information theory to the assessment of computed tomography.

The imaging process has two fundamental stages: detection and display. The detection stage can be quantified rigourously using Shannon's information theory. This requires the contrast scale (CS), modulation transfer function (MTF), and noise power spectrum [N(f)] to be combined into a signal-to-noise ratio (SNR). This results in two fundamental summary figures of merit: the density of noise equivalent quanta (NEQ) in the image and the information bandwidth integral (IBWI). These algorithm-independent measures are used to quantify the recording stage. The display stage is less well understood since it couples to an external observer. Several types of decision makers are treated. Examples are drawn from first and second generation CT, demonstrating that thye are nearly quantum limited for large signals, indicating how their algorithms are matched or mismatched to the geometry, and calculating the contrast-detail diagrams for those decision makers.

Data Display

Error measures for objective assessment of scene segmentation algorithms.

Scene segmentation is an important element in pattern recognition problems. Previous efforts to evaluate and compare scene segmentation procedures have been largely subjective. Quantitative error measures would facilitate objective comparison of scene segmentation algorithms. A theoretical discussion leading to a new generalized quantitative error measure, G2, based on comparison of both pixel class proportions and spatial distributions of "true" and test segmentations, is presented. This error measure was tested on 14 manual segmentations and 40 gynecologic cytology specimens segmented with five different scene segmentation techniques. Results indicate that G2 seems to have the desirable properties of correlation with human observation, categorization of error allowing for weighting, invariance with picture size and ease of computation necessary for a useful scene segmentation error measure.

Autoanalysis

Clinical measurement of renal clearance.

The importance of renal clearance in uronephrology has motivated the continuous reassessment of well-established methods and the relentless search for better techniques. Concerning radionuclide methods, data in the current literature confirm the validity of the simplified one-compartment model or the empirical single-sample method for renal clearance measurement, and new algorithms have been described to broaden the application of the techniques to the pediatric population. Based on the same principles, accurate measurement of renal clearance can also be obtained using contrast agents. Using the technique for determination of the glomerular filtration rate during radiographic contrast examination is recommendable. However, potential adverse effects of the contrast substances should be compared with those of other methods before using this technique for measuring renal clearance without scheduled contrast roentgenographic examination. Controversy remains concerning the validity of predicting glomerular filtration rate from plasma creatinine. Although the predicted clearance is correlated with reference clearance, analysis of individual results reveals that important differences of up to 50 mL/min frequently occur.

Algorithms

Ellipse test for the reduction of false positive signals in automated cytology.

One of the major problems in automated cytology is the elimination of false positive 'abnormal cell' alarms caused by objects such as overlapping cell pairs, leukocyte clusters, etc. The paper describes an algorithm for the separation of images of abnormal cell nuclei and non=nuclear objects in computer image analysis systems for automated cytology. The algorithm involves the measurement of the agreement between the object outline and a computer ellipse of equal area, aspect ratio and orientation. Results obtained with the CERVISCAN experimental computer image analysis system show that the algorithm gives good discrimination between abnormal cell nuclei and typical non-nuclear objects found in cervical scrape specimens prepared specially for automated analysis.

Cell Nucleus

Utilization of cross-plane rays for three-dimensional reconstruction by filtered back-projection.

Present popular computed tomography (CT) algorithms reconstruct an object from the ray measurements lying on a set of parallel planes. This paper presents an algorithm that can also utilize "cross-plane" rays (i.e., rays that cross through many planes) to reconstruct the object. In this reconstruction algorithm, the ray measurements are grouped into two-dimensional projections, filtered, and stored. The filtered projections can then be back-projected onto a three-dimensional matrix or any plane through the three-dimensional volume. General theoretical aspects are presented and then applied to the special case in which ray measurements have been made in all directions. The algorithm is tested using computer-generated data. Expressions for the noise power spectrum and the variance in the reconstruction are derived. It is shown that the noise-to-signal ratio per detected photon for this reconstruction method is close to a theoretical limit, as it also is for normal CT. The ability to use ray measurements that cross many planes is especially useful in emission CT, where order-of-magnitude improvements in image quality per unit dose can be achieved.

Computers

Linking cortical structure and delirium in the elderly: insights from cohort study and shared genetic risk analysis.

BACKGROUND: This study aimed to assess the association between regional cortical changes measured via baseline magnetic resonance imaging (MRI) and the incidence of delirium. METHODS: Observational associations were assessed using a prospective cohort from the UK Biobank and an independent clinical cohort. The population-based study included participants aged 60 years or older who had undergone structural brain MRI since 2014. Regional cortical volume, mean thickness, and surface area were extracted based on the Desikan-Killiany cortical atlas. Delirium was defined using ICD-10 diagnostic codes. Additionally, preoperative brain MRI images from participants in another cohort were collected and automatically segmented using deep learning algorithms to obtain cortical measurements. Logistic analysis was performed to investigate the associations between cerebral cortical structure and delirium risk. Lastly, genome-wide association study data derived from the ENIGMA Consortium and FinnGen Biobank were utilized to conduct conditional/conjunctional false discovery rate (cond/conjFDR) analyses to identify shared genetic loci associated with cortical structures and delirium. RESULTS: This observational analysis included 31,890 participants from the UK Biobank and 152 participants from an independent cohort. In the UK Biobank cohort, decreased cortical thickness in the 17 regions was associated with a significantly increased risk of delirium. Similarly, a preoperative reduction in cortical volume in 7 regions was associated with an increased risk of delirium in the independent cohort. Besides, 100 single-nucleotide polymorphisms (SNPs) were identified as significantly associated with cortical structures when conditioned on delirium. Finally, colocalization analysis demonstrated that these pleiotropic risk loci modulated the expression of NT5C2, RGP1, CCDC25, TPM2, EEF1AKMT2, IQANK1 and LHPP in blood and brain tissues. CONCLUSION: Regional cortical atrophy is associated with an increased risk of delirium in the elderly. Brain MRI examinations may be beneficial for preoperative delirium risk assessment in elderly individuals undergoing elective surgery.

Humans

Discovery and validation of novel plasma protein biomarkers for severe tuberculosis patients.

OBJECTIVE: Severe tuberculosis (STB) imposes a substantial disease burden, yet reliable biomarkers for distinguishing STB from mild/moderate tuberculosis (MTB) remain scarce. This study aimed to identify and independently validate plasma protein biomarkers associated with tuberculosis severity. METHODS: In this multicenter prospective study, 298 adults with confirmed pulmonary tuberculosis were enrolled into screening (n = 128) and independent validation (n = 170) cohorts. Plasma samples were analysed using data-independent acquisition proteomics. Differentially expressed proteins were screened via Limma and four machine-learning algorithms, with candidate proteins measured by enzyme-linked immunosorbent assays. Receiver operating characteristic analysis assessed individual and combined diagnostic performance. RESULTS: STB patients were older and presented with lymphopenia, hypoalbuminemia, neutrophilia, and elevated lactate dehydrogenase. Among 166 differentially expressed proteins, HSPA5, HSP90B1, EEF1D, and SULT1A1 were selected for validation. In STB patients, HSPA5, HSP90B1, and EEF1D were upregulated, whereas SULT1A1 was downregulated. The four-protein panel achieved an AUC of 0.908 (95% CI 0.864-0.952), with 87.5% sensitivity and 83.8% specificity, modestly outperforming HSPA5 alone (AUC = 0.894). Functional enrichment implicated cholesterol metabolism, immune-inflammatory pathways, and endoplasmic reticulum stress. CONCLUSIONS: The four-protein panel effectively discriminated STB from MTB; however, its marginal improvement over HSPA5 alone suggests that an HSPA5-based assay may offer a simpler, more practical, and potentially cost-effective strategy for severity stratification.

Humans

PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks.

Phylogenetic diversity (PD) plays an important role in biodiversity, conservation, and evolutionary studies by measuring the diversity of a set of taxa based on their phylogenetic relationships. In phylogenetic trees, a subset of k taxa with maximum PD can be found by a simple and efficient greedy algorithm. However, this algorithmic tractability is lost when considering phylogenetic networks, which incorporate reticulate evolutionary events such as hybridization and horizontal gene transfer. To address this challenge, we introduce PaNDA (Phylogenetic Network Diversity Algorithms), the first software package and interactive graphical user-interface for exploring, visualizing, and maximizing diversity in phylogenetic networks. PaNDA includes a novel algorithm to find a subset of k taxa with maximum diversity, running in polynomial time for networks of bounded scanwidth, a measure of tree-likeness of a network that grows slower than the well-known level measure. This algorithm considers the variant of PD on networks in which the branch lengths of all paths from the root to the selected taxa contribute towards their diversity. We demonstrate the scalability of this algorithm on simulated networks, successfully analyzing level-15 networks with up to 200 taxa in seconds. We also provide a proof-of-concept analysis using a phylogenetic network on Xiphophorus species, illustrating how the tool can support diversity studies based on real genomic data. The software is easily installable and freely available at https://github.com/nholtgrefe/panda. Additionally, we extend the definition of PD to semi-directed phylogenetic networks, which are mixed graphs increasingly used in phylogenetic analysis to model uncertainty of the root location. We prove that finding a subset of k taxa with maximum diversity remains NP-hard on semi-directed networks, but do present a polynomial-time algorithm for networks with bounded level.

network

Methods for defining equity-stratifying variables: a systematic review of validation studies.

BACKGROUND AND OBJECTIVE: Disease burden is often disproportionally higher among those who are socially disadvantaged by factors defined in the PROGRESS-Plus framework (ie, Place of residence, Race/ethnicity/culture/language, Occupation, Gender/sex, Religion, Education, Socioeconomic status, and Social capital, with "Plus" covering features like age and disability). The accuracy and applicability of case definitions to identify these variables from administrative and clinical health data are unknown. We conducted a systematic review to explore how equity-stratifying variables, as categorized by the PROGRESS-Plus framework, have been defined and validated in epidemiologic studies using administrative health, population-level, or electronic health record (EHR) data. METHODS: Medline, EMBASE, CINAHL, Web of Science, and Google Scholar were searched from the inception of the databases to 2024 for validation studies of equity-stratifying variables in adults using administrative health datasets, health registries, or EHR data. Titles and abstracts, followed by relevant full-text articles, were screened in duplicate by two reviewers for eligibility. The data sources utilized, algorithms employed, and their associated performance measures were extracted and synthesized from included studies. Given substantial heterogeneity in study design, equity-stratifying variable definition, and performance metrics, meta-analysis was not possible. RESULTS: Of the 9099 unique citations screened, 188 full texts were reviewed and 116 were included in this review. Most studies were published between 2019 and 2024 (n = 64, 55%) and were validation studies of race/ethnicity definitions that used race/ethnicity codes or surname list algorithms (n = 66, 57%). No studies examined religion. Regarding the reported performance measure estimates, the race/ethnicity/culture/language equity-stratifying variables category had the largest variability across sensitivity, positive predictive value (PPV), and Cohen's Kappa. Occupation validation studies had the lowest variation in sensitivity and PPV. CONCLUSION: Despite an increasing number of publications reporting on the validation of equity-stratifying variables relevant to the PROGRESS-Plus framework, performance measures varied widely across studies. The significant heterogeneity in equity-stratifying variable definitions and methods used to validate them support the need for further rigorous validation of equity-stratifying variables in administrative and clinical health data. PLAIN LANGUAGE SUMMARY: Disease burden is often higher in people who experience financial hardships, lower level of education, discrimination due to race/ethnicity, and unstable housing. These social factors can be considered health equity factors and are important for understanding health inequalities. Health researchers often use large datasets, such as hospital or electronic health records (EHRs), to study these health equity factors. However, it is not clear how accurately these data sources capture information about people's social circumstances and how these factors are defined. In this study, we reviewed existing research to understand how health equity factors have been defined across health data sources and how accurate they are at measuring aspects of health equity and social disadvantage. Of the more than 9000 studies we identified, we included 116 that met our criteria for this systematic review. Most included studies focused on identifying race and ethnicity, often using codes or surname-based methods. We found that the accuracy of these methods varied widely across studies, meaning results may not always be reliable or comparable. Overall, our findings show that there are inconsistencies in how social factors are defined and measured in health data. This makes it difficult to fully understand and address health inequalities using routinely collected health data. More work is needed to develop and validate better quality and more consistent methods for capturing these important social factors.

Humans

Failure of total calcium corrected for protein, albumin, and pH to correctly assess free calcium status.

The clinical effectiveness of published algorithms in correcting serum total calcium (CaT) for the effects of protein, albumin, and pH was tested. Corrected calcium (CaC) values obtained by 13 of these methods were compared with values of measured free calcium (CaF) in 55 samples from normal controls and 404 samples from patients with various disorders of calcium metabolism. Three criteria were used to compare either CaC or CaT with measured CaF: 1) the correlation coefficient, 2) the average absolute deviation from measured CaF of the values of CaF predicted by the linear regression of CaF on each CaC, and 3) the number of samples in which CaC or CaT gave a different impression of normality than measured CaF. Application of the 13 published algorithms produced varied results, but none produced substantially better agreement between CaC and CaF than was found between CaT and CaF. The application of additional algorithms derived by multiple linear regression using our data base gave slightly better results than any of the published algorithms, but many values of CaC remained which were disparate from the measured value of CaF. Correction of measured total calcium by using other concurrently obtained chemistry values does not seem to adequately predict calcium status as measured by free calcium.

Autoanalysis

Automated scene analysis of CT scans.

Since the advent of computed tomography, there has been an increasing realization that CT scans contain quantitative as well as qualitative information useful in the diagnostic process. Often however, the use of this information is impeded by the tedious manual outlining of the areas of interest in the scan. To alleviate this problem, we have developed a scene segmentation algorithm which will automatically delineate areas of interest in a CT scan. This procedure uses known information about the expected objects in the scan in conjuction with an algorithm to label those objects. The resultant scene segmentation divides the scan into four anatomical areas: skull, normal brain, high density lesions and CSF. After an area of interest is interactively selected by the clinician, volume, density or other quantitative measures may be computed. Limitations of the algorithm and its clinical applications are discussed.

Absorptiometry, Photon