Efficient path-based computations on pedigree graphs with compact encodings

A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increasingly important. In large pedigree graphs, path-based methods for efficiently computing genealogical measurements, such as inbreeding and kinship coefficients of individuals, depend on efficient identification and processing of paths. In this paper, we propose a new compact path encoding scheme on large pedigrees, accompanied by an efficient algorithm for identifying paths. We demonstrate the utilization of our proposed method by applying it to the inbreeding coefficient computation. We present time and space complexity analysis, and also manifest the efficiency of our method for evaluating inbreeding coefficients as compared to previous methods by experimental results using pedigree graphs with real and synthetic data. Both theoretical and experimental results demonstrate that our method is more scalable and efficient than previous methods in terms of time and space requirements

Processing of spectral information in the dragonfly lamina

In this thesis, intracellular recordings were made from the photoreceptors and large monopolar cells (LMCs) of the dragonfly, Hemicordulia tau, to study the spectral information processing in the early vision of the insect compound eye. Photoreceptors recorded from the ventral region of the compound eye could be divided into five groups (360 nm, 420 nm, 460 nm, 530 nm and 590 nm) according to their peak spectral sensitivities. Compared to the previous study by S. Laughlin in 1974, where only three spectral classes of photoreceptors were reported, the 420 nm and 600 nm classes of photoreceptors are a new discovery. The spectral sensitivities of five types of LMC (cell type 1-5) were also recorded. Cell type 1 exhibits a broad spectral sensitivity function with maximal sensitivity between 480 nm and 510 nm. The spectral sensitivity of cell type 2 has two peaks, one in the region between 500 nm and 550 nm and another in the UV region. The spectral sensitivities of cell types 3 and 4 are similar to the 420 nm and 530 nm photoreceptors, respectively. The main sensitivity peak of cell type 4 is in the 500-550 nm region. The spectral sensitivity of cell type 5 is also similar to 530 nm photoreceptor, but the main sensitivity peak is at 500 nm. When dark-adapted, the monopolar cells had peak spectral sensitivities that were similar to single photoreceptors, or appeared to pool the outputs of receptors with different spectral sensitivities. In some cases, spectral sensitivity changed markedly upon light adaptation. For example, when cell type 2 was light-adapted by 550 nm, its sensitivity to UV light was suppressed. On the other hand, when cell type 5 was light-adapted by 550 nm, the absolute sensitivity to 520 nm was increased, though the spectral sensitivity remained the same as in the dark-adapted state. These effects cannot be explained by selective spectral adaptation. Rather, they suggest that this cell type receives synaptic input from more than one spectral class of photoreceptor, and that adaptation alters the computation of this input in unexpected ways. A control experiment on fly LMCs, which are known to receive input from a single spectral class of photoreceptors, showed no spectral sensitivity change in the light­ adapted state, as expected. These results suggest that the changes of spectral sensitivity in the light-adapted lamina monopolar cells of the dragonfly are mediated by the interaction of different spectral types of photoreceptors. Previous studies in fly lamina (Laughlin, 1974b; Srinivasan et al., 1982; Laughlin and Osorio, 1989) indicated that lateral inhibition affects the spatial and temporal properties of lamina cells. Because the lateral inhibition of the LMC could be mediated by extracellular photocurrents or particular synaptic inputs (Laughlin, 1974a,b; Shaw,1975), I attempted to identify the origin of the lateral inputs by measuring their spectral sensitivities as well as looking at their spatio-temporal properties with white-noise stimulation. The spectral sensitivities of the inhibitory inputs recorded from two types of UV-sensitive LMCs (cell types 2 and 4) in the dark-adapted state were different from their spectral sensitivities measured from the hyperpolarizing centre in the dark­ adapted state, but similar to those on 550 nm light adaptation. That is, the surround spectral sensitivity of cell type 2 has a single peak in 500-520 nm region, while cell type 4 has its sensitivity peak at 340-360 nm. These results suggest that a synaptic lateral inhibitory input to the hyperpolarizing centre of the LMC receptive field is provided from neighbouring lamina cartridges. Experiments with white-noise stimulation were carried out to determine the characteristics of the inhibition and the shape of its receptive field. Two spatial configurations Were used for the white-noise experiments: one having the spatial form of a checkerboard and the other a spot with a surrounding annuals. Analysis of the kernels obtained from checkboard white-noise experiments reveals that the inhibitory signal has a longer latency than that from the excitatory centre. The spatio-temporal receptive fields of the dragonfly LMCs show that the shapes of the inhibitory fields are diverse, but most of them are hi-lobed. None of the dragonfly LMCs has a receptive field with concentric centre-surround configuration. The nonlinear properties of the LMCs were examined using spot-annulus white-noise stimulus. The reversed polarity found between the second-order kernels of the hyperpolarizing centre and depolarising surround indicate an inverted, nonlinear signal contributed by the surrounding cartridges. These observations are consistent with the presence of synaptic lateral inhibition, in addition to the electrical field inhibition that has been postulated as the primary mechanism for generating the inhibitory fields of lamina neurons in the insect eye (Laughlin, 1974b; Shaw, 1975). Since the lateral inhibition provides both spatial and spectral antagonism to the LMCs, it is evident that colour opponency plays an important role in the processing of spectral information in the dragonfly lamina

Analysis on tailed distributed arithmetic codes for uniform binary sources

Distributed Arithmetic Coding (DAC) is a variant of Arithmetic Coding (AC) that can realise Slepian-Wolf Coding (SWC) in a nonlinear way. In the previous work, we defined Codebook Cardinality Spectrum (CCS) and Hamming Distance Spectrum (HDS) for DAC. In this paper, we make use of CCS and HDS to analyze tailed DAC, a form of DAC mapping the last few symbols of each source block onto non-overlapped intervals as traditional AC. We first derive the exact HDS formula for tailless DAC, a form of DAC mapping all symbols of each source block onto overlapped intervals, and show that the HDS formula previously given is actually an approximate version. Then the HDS formula is extended to tailed DAC. We also deduce the average codebook cardinality, which is closely related to decoding complexity, and rate loss of tailed DAC with the help of CCS. The effects of tail length are extensively analyzed. It is revealed that by increasing tail length to a value not close to the bitstream length, closely-spaced codewords within the same codebook can be removed at the cost of a higher decoding complexity and a larger rate loss. Finally, theoretical analyses are verified by experiments

Hamming distance spectrum of DAC codes for equiprobable binary sources

Distributed Arithmetic Coding (DAC) is an effective technique for implementing Slepian-Wolf coding (SWC). It has been shown that a DAC code partitions source space into unequal-size codebooks, so that the overall performance of DAC codes depends on the cardinality and structure of these codebooks. The problem of DAC codebook cardinality has been solved by the so-called Codebook Cardinality Spectrum (CCS). This paper extends the previous work on CCS by studying the problem of DAC codebook structure.We define Hamming Distance Spectrum (HDS) to describe DAC codebook structure and propose a mathematical method to calculate the HDS of DAC codes. The theoretical analyses are verified by experimental results

3-D neurohistology of transparent tongue in health and injury with optical clearing

Tongue receives extensive innervation to perform taste, sensory, and motor functions. Details of the tongue neuroanatomy and its plasticity in response to injury offer insights to investigate tongue neurophysiology and pathophysiology. However, due to the dispersed nature of the neural network, standard histology cannot provide a global view of the innervation. We prepared transparent mouse tongue by optical clearing to reveal the spatial features of the tongue innervation and its remodeling in injury. Immunostaining of neuronal markers, including PGP9.5 (pan-neuronal marker), calcitonin gene-related peptide (sensory nerves), tyrosine hydroxylase (sympathetic nerves), and vesicular acetylcholine transporter (cholinergic parasympathetic nerves and neuromuscular junctions), was combined with vessel painting and nuclear staining to label the tissue network and architecture. The tongue specimens were immersed in the optical-clearing solution to facilitate photon penetration for 3-dimensiontal (3-D) confocal microscopy. Taking advantage of the transparent tissue, we simultaneously revealed the tongue microstructure and innervation with subcellular-level resolution. 3-D projection of the papillary neurovascular complex and taste bud innervation was used to demonstrate the spatial features of tongue mucosa and the panoramic imaging approach. In the tongue injury induced by 4-nitroquinoline 1-oxide administration in the drinking water, we observed neural tissue remodeling in response to the changes of mucosal and muscular structures. Neural networks and the neuromuscular junctions were both found rearranged at the peri-lesional region, suggesting the nerve-lesion interactions in response to injury. Overall, this new tongue histological approach provides a useful tool for 3-D imaging of neural tissues to better characterize their roles with the mucosal and muscular components in health and disease

Diversity of the Photoreceptors and Spectral Opponency in the Compound Eye of the Golden Birdwing, Troides aeacus formosanus

The compound eye of the Golden Birdwing, Troides aeacus formosanus (Papilionidae, Lepidoptera), is furnished with three types of ommatidia, which are clearly different in pigmentation around the rhabdom. Each ommatidium contains nine photoreceptors, whose spectral sensitivities were analyzed electrophysiologically. We identified nine spectral types of photoreceptor with sensitivities peaking at 360 nm (UV), 390 nm (V), 440 nm (B), 510 nm (BG), 540 nm (sG), 550 nm (dG), 580 nm (O), 610 nm (R), and 630 nm (dR) respectively. The spectral sensitivities of the V, O, R and dR receptors did not match the predicted spectra of any visual pigments, but with the filtering effects of the pigments around the rhabdom, they can be reasonably explained. In some of the receptors, negative-going responses were observed when they were stimulated at certain wavelengths, indicating antagonistic interactions between photoreceptors