An intuitive approach for spike removal in Raman spectra based on peaks' prominence and width

BACKGROUND

Raman spectroscopists are familiar with the challenge of dealing with spikes caused by cosmic rays. These artifacts may lead to errors in subsequent data processing steps, such as for example calibration, normalization or spectral search. Spike removal is therefore a fundamental step in Raman spectral data pre-treatment, but access to publicly accessible code for spike removal tools is limited, and their performance for spectra correction often unknown. Therefore, there is a need for development and testing open-source and easy-to-implement algorithms that improve the Raman data processing workflow.

RESULTS

In this work, we present and validate two approaches for spike detection and correction in Raman spectral data from graphene: i) An algorithm based on the peaks' widths and prominences and ii) an algorithm based on the ratio of these two peak features. The first algorithm provides an efficient and reliable approach for spike detection in real and synthetic Raman spectra by imposing thresholds on the peaks' width and prominence. The second approach leverages the prominence/width ratio for outlier detection. It relies on the calculation of a limit of detection based on either one or several spectra, enabling the automatic identification of cosmic ray and low-intensity noise-originated spikes alike. Both algorithms detect low-intensity spikes down to at least ≈10% of the highest Raman peak of spectra with different noise levels. To address their limitations and prove their versatility, the algorithms were further tested in Raman spectra from calcite and polystyrene.

SIGNIFICANCE

Our intuitive, open-source algorithms have been validated and allow automatic correction for a given set of samples. They do not require any pre-processing steps such as calibration or baseline subtraction, and their implementation with Python libraries is computationally efficient, allowing for immediate utilization within existing open-source packages for Raman spectra processing.

The Effect of Hemodialysis on Spectral and Temporal Processing Abilities and Speech Perception in Noise among Individuals with Chronic Kidney Disease

INTRODUCTION

The effect of chronic kidney disease (CKD) on hearing is well documented in the literature. Several studies have investigated the effect of hemodialysis on the peripheral auditory system among individuals with CKD. However, studies investigating the effect of hemodialysis on speech perception and auditory processing abilities are limited. The present study investigated the effect of hemodialysis on few auditory processing abilities and speech perception in noise among adults with CKD.

METHODS

A total of 25 adults with CKD undergoing hemodialysis regularly participated in the study. Spectral ripple discrimination threshold (SRDT), gap detection threshold (GDT), amplitude-modulation detection threshold (AMDT), and speech recognition threshold in noise (SRTn) were measured before and after hemodialysis. Paired samples "t" test was carried out to investigate the effect of hemodialysis on thresholds.

RESULTS

Results showed a significant improvement for SRDT, GDT, AMDT, and SRTn after hemodialysis among individuals with CKD.

DISCUSSION

Hemodialysis showed a positive effect on speech perception in noise and auditory processing abilities among individuals with CKD.

Female preferences for the spectral content of advertisement calls in Cope's gray treefrog (Hyla chrysoscelis)

Amphibians have inner ears with two sensory papillae tuned to different frequency ranges of airborne sounds. In frogs, male advertisement calls possess distinct spectral components that match the tuning of one or both sensory papillae. Female preferences for the spectral content of advertisement calls can depend on signal amplitude and can vary among closely related lineages. In this study of Cope's gray tree frog (Hyla chrysoscelis), we investigated the amplitude dependence of female preferences for the spectral content of male advertisement calls, which have a "bimodal" spectrum with separate low-frequency (1.25 kHz) and high-frequency (2.5 kHz) components. In two-alternative choice tests, females generally preferred synthetic calls with bimodal spectra over "unimodal" calls having only one of the two spectral components. They also preferred unimodal calls with a high-frequency component over one with the low-frequency component. With few exceptions, preferences were largely independent of amplitude across both a 30 dB range of overall signal amplitude and an 11 dB range in the relative amplitudes of the two spectral components. We discuss these results in the context of evolutionary lability in female preferences for the spectral content of advertisement calls in North American tree frogs in the genus Hyla.

Bilateral age-related atrophy in the planum temporale is associated with vowel discrimination difficulty in healthy older adults

In this study we investigated the association between age-related brain atrophy and behavioural as well as electrophysiological markers of vowel perception in a sample of healthy younger and older adults with normal pure-tone hearing. Twenty-three older adults and 27 younger controls discriminated a set of vowels with altered second formants embedded in consonant-vowel syllables. Additionally, mismatch negativity (MMN) responses were recorded in a separate oddball paradigm with the same set of stimuli. A structural magnet resonance scan was obtained for each participant to determine cortical architecture of the left and right planum temporale (PT). The PT was chosen for its function as a major processor of auditory cues and speech. Results suggested that older adults performed worse in vowel discrimination despite normal-for-age pure-tone hearing. In the older group, we found evidence that those with greater age-related cortical atrophy (i.e., lower cortical surface area and cortical volume) in the left and right PT also showed weaker vowel discrimination. In comparison, we found a lateralized correlation in the younger group suggesting that those with greater cortical thickness in only the left PT performed weaker in the vowel discrimination task. We did not find any associations between macroanatomical traits of the PT and MMN responses. We conclude that deficient vowel processing is not only caused by pure-tone hearing loss but is also influenced by atrophy-related changes in the ageing auditory-related cortices. Furthermore, our results suggest that auditory processing might become more bilateral across the lifespan.

rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization

Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove signals from the matrix, according to the matrix chemical composition and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classify m/z signals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows.

Color vision in insects: insights from Drosophila

Color vision is an important sensory capability that enhances the detection of contrast in retinal images. Monochromatic animals exclusively detect temporal and spatial changes in luminance, whereas two or more types of photoreceptors and neuronal circuitries for the comparison of their responses enable animals to differentiate spectral information independent of intensity. Much of what we know about the cellular and physiological mechanisms underlying color vision comes from research on vertebrates including primates. In insects, many important discoveries have been made, but direct insights into the physiology and circuit implementation of color vision are still limited. Recent advances in Drosophila systems neuroscience suggest that a complete insect color vision circuitry, from photoreceptors to behavior, including all elements and computations, can be revealed in future. Here, we review fundamental concepts in color vision alongside our current understanding of the neuronal basis of color vision in Drosophila, including side views to selected other insects.

Speech Recognition in Noise by Children with and without Dyslexia: How is it Related to Reading?

PURPOSE

Developmental dyslexia is commonly viewed as a phonological deficit that makes it difficult to decode written language. But children with dyslexia typically exhibit other problems, as well, including poor speech recognition in noise. The purpose of this study was to examine whether the speech-in-noise problems of children with dyslexia are related to their reading problems, and if so, if a common underlying factor might explain both. The specific hypothesis examined was that a spectral processing disorder results in these children receiving smeared signals, which could explain both the diminished sensitivity to phonological structure - leading to reading problems - and the speech recognition in noise difficulties. The alternative hypothesis tested in this study was that children with dyslexia simply have broadly based language deficits.

PARTICIPANTS

Ninety-seven children between the ages of 7 years; 10 months and 12 years; 9 months participated: 46 with dyslexia and 51 without dyslexia.

METHODS

Children were tested on two dependent measures: word reading and recognition in noise with two types of sentence materials: as unprocessed (UP) signals, and as spectrally smeared (SM) signals. Data were collected for four predictor variables: phonological awareness, vocabulary, grammatical knowledge, and digit span.

RESULTS

Children with dyslexia showed deficits on both dependent and all predictor variables. Their scores for speech recognition in noise were poorer than those of children without dyslexia for both the UP and SM signals, but by equivalent amounts across signal conditions indicating that they were not disproportionately hindered by spectral distortion. Correlation analyses on scores from children with dyslexia showed that reading ability and speech-in-noise recognition were only mildly correlated, and each skill was related to different underlying abilities.

CONCLUSIONS

No substantial evidence was found to support the suggestion that the reading and speech recognition in noise problems of children with dyslexia arise from a single factor that could be defined as a spectral processing disorder. The reading and speech recognition in noise deficits of these children appeared to be largely independent.

Rapid and robust analytical protocol for E. coli STEC bacteria subspecies differentiation using whole cell MALDI mass spectrometry

Whole cell MALDI is regularly used for the identification of bacteria to species level in clinical Microbiology laboratories. However, there remains a need to rapidly characterize and differentiate isolates below the species level to support outbreak management. We describe the implementation of a modified preparative approach for MALDI-MS combined with a custom analytical computational pipeline as a rapid procedure for subtyping Shigatoxigenic E. coli (STEC) and accurately identifying strain-specifying biomarkers. The technique was able to differentiate E. coli O157:H7 from other STEC. Within O157 serotype O157:H7 isolates were readily distinguishable from Sorbitol Fermenting O157 isolates. Overall, nine homogeneous groups of isolates were distinguished, each exhibiting distinct profiles of defining mass spectra features. This offers a robust analytical tool useable in reference/diagnostic public health scenarios.

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine

1H NMR spectra from urine can yield information-rich data sets that offer important insights into many biological and biochemical phenomena. However, the quality and utility of these insights can be profoundly affected by how the NMR spectra are processed and interpreted. For instance, if the NMR spectra are incorrectly referenced or inconsistently aligned, the identification of many compounds will be incorrect. If the NMR spectra are mis-phased or if the baseline correction is flawed, the estimated concentrations of many compounds will be systematically biased. Furthermore, because NMR permits the measurement of concentrations spanning up to five orders of magnitude, several problems can arise with data analysis. For instance, signals originating from the most abundant metabolites may prove to be the least biologically relevant while signals arising from the least abundant metabolites may prove to be the most important but hardest to accurately and precisely measure. As a result, a number of data processing techniques such as scaling, transformation and normalization are often required to address these issues. Therefore, proper processing of NMR data is a critical step to correctly extract useful information in any NMR-based metabolomic study. In this review we highlight the significance, advantages and disadvantages of different NMR spectral processing steps that are common to most NMR-based metabolomic studies of urine. These include: chemical shift referencing, phase and baseline correction, spectral alignment, spectral binning, scaling and normalization. We also provide a set of recommendations for best practices regarding spectral and data processing for NMR-based metabolomic studies of biofluids, with a particular focus on urine.

Advantages of cooled fiber for monitoring laser tissue ablation through temporal and spectral analysis of RF ultrasound signal: A case study

The promising minimally invasive laser thermal therapy technique may be improved if thermal lesions induced into the tissue can be carefully monitored in extension and morphology during the treatment. According to results obtained in several recent experimentations, solutions that avoid tissue carbonization during the treatment have been proposed, in order to allow deeper and longer lasting light penetration in treated tissue and to reduce failures of the applicator tip and fiber optic, dangerous for patients. In the work the advantages in using a cooled fiber are shown, in order not only to induce efficient lesions but also in performing an accurate monitoring by ultrasound. Indeed, one important limit of the ultrasound control is caused by the gas bubbles generation, which represent an acoustic barrier that invalidate the ultrasonic image representation of the treated tissue. Ultrasonic radiofrequency signals were acquired from the same bovine liver ex vivo sample by using both bare and cooled fiber and processed to produce B-mode and spectral parametric images by implementing TUV (Thermotherapy Ultrasonic View) algorithm. Radiofrequency signals, B-mode and TUV images were analysed and compared in order to evaluate the different tissue heating processes during ablation and the different lesion extensions induced into the tissue after the treatment. Cooled fiber avoided carbonization and strongly reduced gas bubbles generation inducing a larger lesion and allowing a more effective ultrasound monitoring. Moreover by correlating optical images of the lesions and the corresponding Integral TUV images, by using Dice and Jaccard coefficients, it was proven that TUV algorithm is able to characterize the tissue portions differently modified by ablation exhibiting better performances in the case of cooled fiber and revealing to be a potential tool capable to improve the laser delivery settings control.

Representation of spectro-temporal features of spoken words within the P1-N1-P2 and T-complex of the auditory evoked potentials (AEP)

The purpose of the study was to determine whether P1-N1-P2 and T-complex morphology reflect spectro-temporal features within spoken words that approximate the natural variation of a speaker and whether waveform morphology is reliable at group and individual levels, necessary for probing auditory deficits. The P1-N1-P2 and T-complex to the syllables /pət/ and /sət/ within 70 natural word productions each were examined. EEG was recorded while participants heard nonsense word pairs and performed a syllable identification task to the second word in the pairs. Single trial auditory evoked potentials (AEP) to the first words were analyzed. Results found P1-N1-P2 and T-complex to reflect spectral and temporal feature processing. Also, results identified preliminary benchmarks for single trial response variability for individual subjects for sensory processing between 50 and 600ms. P1-N1-P2 and T-complex, at least at group level, may serve as phenotypic signatures to identify deficits in spectro-temporal feature recognition and to determine area of deficit, the superior temporal plane or lateral superior temporal gyrus.

Phonological, temporal and spectral processing in vowel length discrimination is impaired in German primary school children with developmental dyslexia

It is still unclear whether phonological processing deficits are the underlying cause of developmental dyslexia, or rather a consequence of basic auditory processing impairments. To avoid methodological confounds, in the current study the same task and stimuli of comparable complexity were used to investigate both phonological and basic auditory (temporal and spectral) processing in dyslexia. German dyslexic children (Grades 3 and 4) were compared to age- and grade-matched controls in a vowel length discrimination task with three experimental conditions: In a phonological condition, natural vowels were used, differing both with respect to temporal and spectral information (in German, vowel length is phonemic, and vowel length differences are characterized by both temporal and spectral information). In a temporal condition, spectral information differentiating between the two vowels of a pair was eliminated, whereas in a spectral condition, temporal differences were removed. As performance measure, the sensitivity index d' was computed. At the group level, dyslexic children's performance was inferior to that of controls for phonological as well as temporal and spectral vowel length discrimination. At an individual level, nearly half of the dyslexic sample was characterized by deficits in all three conditions, but there were also some children showing no deficits at all. These results reveal on the one hand that phonological processing deficits in dyslexia may stem from impairments in processing temporal and spectral information in the speech signal. On the other hand they indicate, however, that not all dyslexic children might be characterized by phonological or auditory processing deficits.