On the importance of low-frequency signals in functional and molecular photoacoustic computed tomography

In photoacoustic computed tomography (PACT) with short-pulsed laser excitation, wideband acoustic signals are generated in biological tissues with frequencies related to the effective shapes and sizes of the optically absorbing targets. Low-frequency photoacoustic signal components correspond to slowly varying spatial features and are often omitted during imaging due to the limited detection bandwidth of the ultrasound transducer, or during image reconstruction as undesired background that degrades image contrast. Here we demonstrate that low-frequency photoacoustic signals, in fact, contain functional and molecular information, and can be used to enhance structural visibility, improve quantitative accuracy, and reduce spare-sampling artifacts. We provide an in-depth theoretical analysis of low-frequency signals in PACT, and experimentally evaluate their impact on several representative PACT applications, such as mapping temperature in photothermal treatment, measuring blood oxygenation in a hypoxia challenge, and detecting photoswitchable molecular probes in deep organs. Our results strongly suggest that low-frequency signals are important for functional and molecular PACT

Idealized computational models for auditory receptive fields

This paper presents a theory by which idealized models of auditory receptive fields can be derived in a principled axiomatic manner, from a set of structural properties to enable invariance of receptive field responses under natural sound transformations and ensure internal consistency between spectro-temporal receptive fields at different temporal and spectral scales. For defining a time-frequency transformation of a purely temporal sound signal, it is shown that the framework allows for a new way of deriving the Gabor and Gammatone filters as well as a novel family of generalized Gammatone filters, with additional degrees of freedom to obtain different trade-offs between the spectral selectivity and the temporal delay of time-causal temporal window functions. When applied to the definition of a second-layer of receptive fields from a spectrogram, it is shown that the framework leads to two canonical families of spectro-temporal receptive fields, in terms of spectro-temporal derivatives of either spectro-temporal Gaussian kernels for non-causal time or the combination of a time-causal generalized Gammatone filter over the temporal domain and a Gaussian filter over the logspectral domain. For each filter family, the spectro-temporal receptive fields can be either separable over the time-frequency domain or be adapted to local glissando transformations that represent variations in logarithmic frequencies over time. Within each domain of either non-causal or time-causal time, these receptive field families are derived by uniqueness from the assumptions. It is demonstrated how the presented framework allows for computation of basic auditory features for audio processing and that it leads to predictions about auditory receptive fields with good qualitative similarity to biological receptive fields measured in the inferior colliculus (ICC) and primary auditory cortex (A1) of mammals.Comment: 55 pages, 22 figures, 3 table

Development of method of matched morphological filtering of biomedical signals and images

Formalized approach to the analysis of biomedical signals and images with locally concentrated features is developed on the basis of matched morphological filtering taking into account the useful signal models that allowed generalizing the existing methods of digital processing and analysis of biomedical signals and images with locally concentrated features. The proposed matched morphological filter has been adapted to solve such problems as localization of the searched structural elements on biomedical signals with locally concentrated features, estimation of the irregular background aimed at the visualization quality improving of biological objects on X-ray biomedical images, pathologic structures selection on mammogram. The efficiency of the proposed methods of matched morphological filtration of biomedical signals and images with locally concentrated features is proved by experiments

The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m1A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m1A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored to the simultaneous analysis of RT-arrest and misincorporation patterns. By application to a variety of native and synthetic RNA preparations, we found a characteristic signature of m1A, which, in addition to an arrest rate, features misincorporation as a significant component. Detailed analysis suggests that the signature depends on RNA structure and on the nature of the nucleotide 3’ of m1A in the template RNA, meaning it is sequence dependent. The RT-signature ofm1Awas used for inspection and confirmation of suspected modification sites and resulted in the identification of hitherto unknown m1A residues in trypanosomal tRNA

3D Imaging of Gems and Minerals by Multiphoton Microscopy

Many optical approaches have been used to examine the composition and structure of gemstones, both recently and throughout history. The nonlinear optical behavior of different gemstones has not been investigated, and the higher order terms to the refractive index represent an unused tool for qualifying and examining a stone. We have used a multiphoton microscope to examine the nonlinear optical properties of 36 different gemstones and demonstrate that it is a useful tool for imaging them three-dimensionally up to the millimeter scale below the sample surface. The polarization dependence of second harmonic generation signals was used to examine the crystal orientations inside the minerals.Comment: 9 pages, five figure