BIFNOM: Binary-Coded Features on Normal Maps.
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ABSTRACT:
SUBMITTER: Miyashita L
PROVIDER: S-EPMC8156490 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectivesTo assess the feasibility of a CNN-based liver registration algorithm to generate difference maps for visual display of spatiotemporal changes in liver PDFF, without needing manual annotations.MethodsThis retrospective exploratory study included 25 patients with suspected or confirmed NAFLD, who underwent PDFF-MRI at two time points at our institution. PDFF difference maps were generated by applying a CNN-based liver registration algorithm, then subtracting follow-up from baseline PDFF maps. The difference maps were post-processed by smoothing (5 cm2 round kernel) and applying a categorical color scale. Two fellowship-trained abdominal radiologists and one radiology resident independently reviewed difference maps to visually determine segmental PDFF change. Their visual assessment was compared with manual ROI-based measurements of each Couinaud segment and whole liver PDFF using intraclass correlation (ICC) and Bland-Altman analysis. Inter-reader agreement for visual assessment was calculated (ICC).ResultsThe mean patient age was 49 years (12 males). Baseline and follow-up PDFF ranged from 2.0 to 35.3% and 3.5 to 32.0%, respectively. PDFF changes ranged from - 20.4 to 14.1%. ICCs against the manual reference exceeded 0.95 for each reader, except for segment 2 (2 readers ICC = 0.86-0.91) and segment 4a (reader 3 ICC = 0.94). Bland-Altman limits of agreement were within 5% across all three readers. Inter-reader agreement for visually assessed PDFF change (whole liver and segmental) was excellent (ICCs > 0.96), except for segment 2 (ICC = 0.93).ConclusionsVisual assessment of liver segmental PDFF changes using a CNN-generated difference map strongly agreed with manual estimates performed by an expert reader and yielded high inter-reader agreement.Key points• Visual assessment of longitudinal changes in quantitative liver MRI can be performed using a CNN-generated difference map and yields strong agreement with manual estimates performed by expert readers.
| S-EPMC8906007 | biostudies-literature
Project description:For epidemic prevention and control, the identification of SARS-CoV-2 subpopulations sharing similar micro-epidemiological patterns and evolutionary histories is necessary for a more targeted investigation into the links among COVID-19 outbreaks caused by SARS-CoV-2 with similar genetic backgrounds. Genomic sequencing analysis has demonstrated the ability to uncover viral genetic diversity. However, an objective analysis is necessary for the identification of SARS-CoV-2 subpopulations. Herein, we detected all the mutations in 186 682 SARS-CoV-2 isolates. We found that the GC content of the SARS-CoV-2 genome had evolved to be lower, which may be conducive to viral spread, and the frameshift mutation was rare in the global population. Next, we encoded the genomic mutations in binary form and used an unsupervised learning classifier, namely PhenoGraph, to classify this information. Consequently, PhenoGraph successfully identified 303 SARS-CoV-2 subpopulations, and we found that the PhenoGraph classification was consistent with, but more detailed and precise than the known GISAID clades (S, L, V, G, GH, GR, GV and O). By the change trend analysis, we found that the growth rate of SARS-CoV-2 diversity has slowed down significantly. We also analyzed the temporal, spatial and phylogenetic relationships among the subpopulations and revealed the evolutionary trajectory of SARS-CoV-2 to a certain extent. Hence, our results provide a better understanding of the patterns and trends in the genomic evolution and epidemiology of SARS-CoV-2.
| S-EPMC8385964 | biostudies-literature
Project description:Historically there has been a virtual absence of constructive methods to produce broad classes of "certifiably random" infinite sequences, despite considerable interest in this endeavor. Previously, we proved a theorem that yielded explicit algorithms to produce diverse sets of normal numbers, reasonable candidates for random sequences, given their limiting equidistribution of subblocks of all lengths. Herein, we develop this algorithmic approach much further, systematizing the normal number generation process in several ways. We construct delineated, distinct sets of normal numbers (classified by the extent to which initial segments deviate from maximal irregularity), with virtually any allowable specified rate of convergence to 0 of this deviation, encompassing arbitrarily fast and slow rates, and accommodating asymmetric behavior above or below a centered median. As a corollary, we provide an explicit construction of a normal number that satisfies the Law of the Iterated Logarithm. We also produce distinct families of "biased" normal numbers, with virtually any specified rate of convergence of the bias (to 0). This latter theory is in part motivated by the remarkable observation that the binary version of Champernowne's number, which is also normal, is biased-any initial segment has more 1s than 0s. Finally, we construct an interesting normal sequence with arbitrarily fast convergence to equidistribution of singleton blocks, yet arbitrarily slow convergence of pairs, which has profound implications both for probability theory, and for metrics to evaluate the "near-randomness" of sequences.
| S-EPMC3511067 | biostudies-literature
Project description:The data presented here is related to the article titled, "Using handwriting to infer a writer's country of origin for forensic intelligence purposes" (Agius et al., 2017) [1]. This article reports original writer, spatial and construction characteristic data for thirty-seven English Australian writers and thirty-seven Vietnamese writers. All of these characteristics were coded and recorded in Microsoft Excel 2013 (version 15.31). The construction characteristics coded were only extracted from seven characters, which were: 'g', 'h', 'th', 'M', '0', '7' and '9'. The coded format of the writer, spatial and construction characteristics is made available in this Data in Brief in order to allow others to perform statistical analyses and modelling to investigate whether there is a relationship between the handwriting features and the nationality of the writer, and whether the two nationalities can be differentiated. Furthermore, to employ mathematical techniques that are capable of characterising the extracted features from each participant.
| S-EPMC5752089 | biostudies-other
Project description:BackgroundThe steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information.ResultsIn this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed.ConclusionsBy using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at http://pelopas.uop.gr/~egian/VIP/index.html.
| S-EPMC3176264 | biostudies-literature
Project description:ObjectiveTo evaluate the diagnostic accuracy of keratoconus using deep learning of the colour-coded maps measured with the swept-source anterior segment optical coherence tomography (AS-OCT).DesignA diagnostic accuracy study.SettingA single-centre study.ParticipantsA total of 304 keratoconic eyes (grade 1 (108 eyes), 2 (75 eyes), 3 (42 eyes) and 4 (79 eyes)) according to the Amsler-Krumeich classification, and 239 age-matched healthy eyes.Main outcome measuresThe diagnostic accuracy of keratoconus using deep learning of six colour-coded maps (anterior elevation, anterior curvature, posterior elevation, posterior curvature, total refractive power and pachymetry map).ResultsDeep learning of the arithmetical mean output data of these six maps showed an accuracy of 0.991 in discriminating between normal and keratoconic eyes. For single map analysis, posterior elevation map (0.993) showed the highest accuracy, followed by posterior curvature map (0.991), anterior elevation map (0.983), corneal pachymetry map (0.982), total refractive power map (0.978) and anterior curvature map (0.976), in discriminating between normal and keratoconic eyes. This deep learning also showed an accuracy of 0.874 in classifying the stage of the disease. Posterior curvature map (0.869) showed the highest accuracy, followed by corneal pachymetry map (0.845), anterior curvature map (0.836), total refractive power map (0.836), posterior elevation map (0.829) and anterior elevation map (0.820), in classifying the stage.ConclusionsDeep learning using the colour-coded maps obtained by the AS-OCT effectively discriminates keratoconus from normal corneas, and furthermore classifies the grade of the disease. It is suggested that this will become an aid for improving the diagnostic accuracy of keratoconus in daily practice.Clinical trial registration number000034587.
| S-EPMC6773416 | biostudies-literature
Project description:Here, data related to the electrical activity of the human skin are presented in detail. The 3D electrical activity maps in normal and diabetic individuals are shown and described using raw data obtained with Photon-Pixel coupling. Average electrical activity matrices are shown by subject, gender and group. Distributions of the electrical activity data are shown in connection with the ventral and dorsal side of the human torso. For a better understanding of the electrical activity data, critical parameters of the individuals that participated in the study are also presented.
| S-EPMC6216044 | biostudies-literature
Project description:Johnston's organ is the largest mechanosensory organ in Drosophila. It contributes to hearing, touch, vestibular sensing, proprioception, and wind sensing. In this study, we used in vivo 2-photon calcium imaging and unsupervised image segmentation to map the tuning properties of Johnston's organ neurons (JONs) at the site where their axons enter the brain. We then applied the same methodology to study two key brain regions that process signals from JONs: the antennal mechanosensory and motor center (AMMC) and the wedge, which is downstream of the AMMC. First, we identified a diversity of JON response types that tile frequency space and form a rough tonotopic map. Some JON response types are direction selective; others are specialized to encode amplitude modulations over a specific range (dynamic range fractionation). Next, we discovered that both the AMMC and the wedge contain a tonotopic map, with a significant increase in tonotopy-and a narrowing of frequency tuning-at the level of the wedge. Whereas the AMMC tonotopic map is unilateral, the wedge tonotopic map is bilateral. Finally, we identified a subregion of the AMMC/wedge that responds preferentially to the coherent rotation of the two mechanical organs in the same angular direction, indicative of oriented steady air flow (directional wind). Together, these maps reveal the broad organization of the primary and secondary mechanosensory regions of the brain. They provide a framework for future efforts to identify the specific cell types and mechanisms that underlie the hierarchical re-mapping of mechanosensory information in this system.
| S-EPMC5952606 | biostudies-literature
Project description:"Locked-in" patients lose their ability to communicate naturally due to motor system dysfunction. Brain-computer interfacing offers a solution for their inability to communicate by enabling motor-independent communication. Straightforward and convenient in-session communication is essential in clinical environments. The present study introduces a functional near-infrared spectroscopy (fNIRS)-based binary communication paradigm that requires limited preparation time and merely nine optodes. Eighteen healthy participants performed two mental imagery tasks, mental drawing and spatial navigation, to answer yes/no questions during one of two auditorily cued time windows. Each of the six questions was answered five times, resulting in five trials per answer. This communication paradigm thus combines both spatial (two different mental imagery tasks, here mental drawing for "yes" and spatial navigation for "no") and temporal (distinct time windows for encoding a "yes" and "no" answer) fNIRS signal features for information encoding. Participants' answers were decoded in simulated real-time using general linear model analysis. Joint analysis of all five encoding trials resulted in an average accuracy of 66.67 and 58.33% using the oxygenated (HbO) and deoxygenated (HbR) hemoglobin signal respectively. For half of the participants, an accuracy of 83.33% or higher was reached using either the HbO signal or the HbR signal. For four participants, effective communication with 100% accuracy was achieved using either the HbO or HbR signal. An explorative analysis investigated the differentiability of the two mental tasks based solely on spatial fNIRS signal features. Using multivariate pattern analysis (MVPA) group single-trial accuracies of 58.33% (using 20 training trials per task) and 60.56% (using 40 training trials per task) could be obtained. Combining the five trials per run using a majority voting approach heightened these MVPA accuracies to 62.04 and 75%. Additionally, an fNIRS suitability questionnaire capturing participants' physical features was administered to explore its predictive value for evaluating general data quality. Obtained questionnaire scores correlated significantly (r = -0.499) with the signal-to-noise of the raw light intensities. While more work is needed to further increase decoding accuracy, this study shows the potential of answer encoding using spatiotemporal fNIRS signal features or spatial fNIRS signal features only.
| S-EPMC7174771 | biostudies-literature
Project description:We measured human ability to detect texture patterns in a signal detection task. Observers viewed sequences of 20 blue or yellow tokens placed horizontally in a row. They attempted to discriminate sequences generated by a random generator ("a fair coin") from sequences produced by a disrupted Markov sequence (DMS) generator. The DMSs were generated in two stages: first a sequence was generated using a Markov chain with probability, pr = 0.9, that a token would be the same color as the token to its left. The Markov sequence was then disrupted by flipping each token from blue to yellow or vice versa with probability, pd-the probability of disruption. Disruption played the role of noise in signal detection terms. We can frame what observers are asked to do as detecting Markov texture patterns disrupted by noise. The experiment included three conditions differing in pd (0.1, 0.2, 0.3). Ninety-two observers participated, each in only one condition. Overall, human observers' sensitivities to texture patterns (d' values) were markedly less than those of an optimal Bayesian observer. We considered the possibility that observers based their judgments not on the entire texture sequence but on specific features of the sequences such as the length of the longest repeating subsequence. We compared human performance with that of multiple optimal Bayesian classifiers based on such features. We identify the single- and multiple-feature models that best match the performance of observers across conditions and develop a pattern feature pool model for the signal detection task considered.
| S-EPMC10627294 | biostudies-literature