Dataset Information

Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification.

ABSTRACT: Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting.

SUBMITTER: Lu S

PROVIDER: S-EPMC5338801 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification.

Lu Sha S Mirchevska Gordana G Phatak Sayali S SS Li Dongmei D Luka Janos J Calderone Richard A RA Fonzi William A WA

PloS one 20170306 3

Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HR ...[more]

PMID: 28264030

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Project description:Post-stroke complications are the second most frequent cause of death and the third leading cause of disability worldwide. The motor function of post-stroke patients is often assessed by measuring the postural sway in the patients during quiet standing, based on sway measures, such as sway area and velocity, which are obtained from temporal variations of the center of pressure. However, such approaches to establish a relationship between the sway measures and patients' demographic factors have hardly been successful (e.g., days after onset). This study instead evaluates the postural sway features of post-stroke patients using the clustering method of machine learning. First, we collected the stroke patients' multi-variable motion-capture standing-posture data and processed them into t s long data slots. Then, we clustered the t-s data slots into K cluster groups using the dynamic-time-warping partition-around-medoid (DTW-PAM) method. The DTW measures the similarity between two temporal sequences that may vary in speed, whereas PAM identifies the centroids for the DTW clustering method. Finally, we used a post-hoc test and found that the sway amplitudes of markers in the shoulder, hip, knee, and center-of-mass are more important than their sway frequencies. We separately plotted the marker amplitudes and frequencies in the medial-lateral direction during a 5-s data slot and found that the post-stroke patients' postural sway frequency lay within the bandwidth of 0.5-1.5 Hz. Additionally, with an increase in the onset days, the cluster index of cerebral hemorrhage patients gradually transits in a four-cluster solution. However, the cerebral infarction patients did not exhibit such pronounced transitions over time. Moreover, we found that the postural-sway amplitude increased in clusters 1, 3, and 4. However, the amplitude of cluster 2 did not follow this pattern, owing to age effects related to the postural sway changes with age. A rehabilitation doctor can utilize these findings as guidelines to direct the post-stroke patient training.

Dataset Information

Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification.

Publications

Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification.

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