Image segmentation and pigment mapping of cultural heritage based on spectral imaging

The goal of the work reported in this dissertation is to develop methods for image segmentation and pigment mapping of paintings based on spectral imaging. To reach this goal it is necessary to achieve sufficient spectral and colorimetric accuracies of both the spectral imaging system and pigment mapping. The output is a series of spatial distributions of pigments (or pigment maps) composing a painting. With these pigment maps, the change of the color appearance of the painting can be simulated when the optical properties of one or more pigments are altered. These pigment maps will also be beneficial for enriching the historical knowledge of the painting and aiding conservators in determining the best course for retouching damaged areas of the painting when metamerism is a factor. First, a new spectral reconstruction algorithm was developed based on Wyszecki’s hypothesis and the matrix R theory developed by Cohen and Kappauf. The method achieved both high spectral and colorimetric accuracies for a certain combination of illuminant and observer. The method was successfully tested with a practical spectral imaging system that included a traditional color-filter-array camera coupled with two optimized filters, developed in the Munsell Color Science Laboratory. The spectral imaging system was used to image test paintings, and the method was used to retrieve spectral reflectance factors for these paintings. Next, pigment mapping methods were brought forth, and these methods were based on Kubelka-Munk (K-M) turbid media theory that can predict spectral reflectance factor for a specimen from the optical properties of the specimen’s constituent pigments. The K-M theory has achieved practical success for opaque materials by reduction in mathematical complexity and elimination of controlling thickness. The use of the general K-M theory for the translucent samples was extensively studied, including determination of optical properties of pigments as functions of film thickness, and prediction of spectral reflectance factor of a specimen by selecting the right pigment combination. After that, an investigation was carried out to evaluate the impact of opacity and layer configuration of a specimen on pigment mapping. The conclusions were drawn from the comparisons of prediction accuracies of pigment mapping between opaque and translucent assumption, and between single and bi-layer assumptions. Finally, spectral imaging and pigment mapping were applied to three paintings. Large images were first partitioned into several small images, and each small image was segmented into different clusters based on either an unsupervised or supervised classification method. For each cluster, pigment mapping was done pixel-wise with a limited number of pigments, or with a limited number of pixels and then extended to other pixels based on a similarity calculation. For the masterpiece The Starry Night, these pigment maps can provide historical knowledge about the painting, aid conservators for inpainting damaged areas, and digitally rejuvenate the original color appearance of the painting (e.g. when the lead white was not noticeably darkened)

HSP90 inhibitors stimulate DNAJB4 protein expression through a mechanism involving N6-methyladenosine.

Small-molecule inhibitors for the 90-kDa heat shock protein (HSP90) have been extensively exploited in preclinical studies for the therapeutic interventions of human diseases accompanied with proteotoxic stress. By using an unbiased quantitative proteomic method, we uncover that treatment with three HSP90 inhibitors results in elevated expression of a large number of heat shock proteins. We also demonstrate that the HSP90 inhibitor-mediated increase in expression of DNAJB4 protein occurs partly through an epitranscriptomic mechanism, and is substantially modulated by the writer, eraser, and reader proteins of N6-methyladenosine (m6A). Furthermore, exposure to ganetespib leads to elevated modification levels at m6A motif sites in the 5'-UTR of DNAJB4 mRNA, and the methylation at adenosine 114 site in the 5'-UTR promotes the translation of the reporter gene mRNA. This m6A-mediated mechanism is also at play upon heat shock treatment. Cumulatively, we unveil that HSP90 inhibitors stimulate the translation of DNAJB4 through an epitranscriptomic mechanism

Methods of spectral reflectance reconstruction for a sinarback 54 digital camera

There is an urgent need to build digital image databases with adequate colorimetric accuracy for museums, achieves and libraries. Traditional colorimetric imaging suffers from the possibilities of metameric problem, while spectral imaging can facilitate accurate tristimulus estimation and possibilities for spectral reconstruction of each pixel. Spectral image archives can be used to render accurate images both spectrally and colorimetrically to the original target for any illuminant and observer. The most convenient and practical capture system for spectral imaging combines a commercial trichromatic camera with two absorption filters to define image spectrally. Two images were taken for each target; so six-channel multichannel images were obtained. Three methods of spectral color reproduction were evaluated: pseudoinverse method, canonical correlation regression (CCR), and Matrix R method. The CCR method can obtain the highest spectral accuracy among these methods, just because it incorporates fifteen cross product terms in the simulation. The Matrix R method can reach the same spectral accuracy as the pseudoinverse method, and the spectral accuracy of both methods could be improved if they also use the same cross product terms. On the other hand, the Matrix R can achieve the best colorimetric accuracy for a certain combination of illuminant and observer. Thus, the Matrix R is a very promising method for achieving artwork images with sufficient spectral and colorimetric accuracy

Using the Matrix R method for spectral image archives

Conventional color digital cameras can only produce three-channel images so they are limited when high-quality color reproduction is required. Alternatively, spectral imaging increases the number of channels and can retrieve spectral reflectance for each scene pixel. The major goal of spectral imaging is high spectral accuracy, while it may also be beneficial to achieve high colorimetric accuracy for a specific viewing condition. A new spectral reconstruction method, called the matrix R method, was developed to achieve both goals simultaneously. An experiment was performed to test this method. The experimental results have been very promising; average color difference for all targets evaluated was about 1.3 CIEDE2000 and 2.0% RMS. These results suggest that this new method is a promising method for building digital image databases for museums, archives and libraries

Intragenic homogenization and multiple copies of prey-wrapping silk genes in Argiope garden spiders.

BackgroundSpider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk proteins encoded by members of the spidroin gene family. Spidroins are dominated by tandem repeats flanked by short, non-repetitive N- and C-terminal coding regions. The remarkable mechanical properties of spider silks have been largely attributed to the repeat sequences. However, the molecular evolutionary processes acting on spidroin terminal and repetitive regions remain unclear due to a paucity of complete gene sequences and sampling of genetic variation among individuals. To better understand spider silk evolution, we characterize a complete aciniform spidroin gene from an Argiope orb-weaving spider and survey aciniform gene fragments from congeneric individuals.ResultsWe present the complete aciniform spidroin (AcSp1) gene from the silver garden spider Argiope argentata (Aar_AcSp1), and document multiple AcSp1 loci in individual genomes of A. argentata and the congeneric A. trifasciata and A. aurantia. We find that Aar_AcSp1 repeats have >98% pairwise nucleotide identity. By comparing AcSp1 repeat amino acid sequences between Argiope species and with other genera, we identify regions of conservation over vast amounts of evolutionary time. Through a PCR survey of individual A. argentata, A. trifasciata, and A. aurantia genomes, we ascertain that AcSp1 repeats show limited variation between species whereas terminal regions are more divergent. We also find that average dN/dS across codons in the N-terminal, repetitive, and C-terminal encoding regions indicate purifying selection that is strongest in the N-terminal region.ConclusionsUsing the complete A. argentata AcSp1 gene and spidroin genetic variation between individuals, this study clarifies some of the molecular evolutionary processes underlying the spectacular mechanical attributes of aciniform silk. It is likely that intragenic concerted evolution and functional constraints on A. argentata AcSp1 repeats result in extreme repeat homogeneity. The maintenance of multiple AcSp1 encoding loci in Argiope genomes supports the hypothesis that Argiope spiders require rapid and efficient protein production to support their prolific use of aciniform silk for prey-wrapping and web-decorating. In addition, multiple gene copies may represent the early stages of spidroin diversification

Identification and characterization of bovine regulator of telomere length elongation helicase gene (RTEL): molecular cloning, expression distribution, splice variants and DNA methylation profile

BACKGROUND: The genetic basis of telomere length heterogeneity among mammalian species is still not well understood. Recently, a gene named regulator of telomere length elongation helicase (RTEL) was identified and predicted to be an essential participant in species-specific telomere length regulation in two murine species. To obtain broader insights into its structure and biological functions and to ascertain whether RTEL is also a candidate gene in the regulation of telomere length diversity in other mammalian species, data from other mammals may be helpful. RESULTS: Here we report the cDNA cloning, genomic structure, chromosomal location, alternative splicing pattern, expression distribution and DNA methylation profile of the bovine homolog of RTEL. The longest transcript of bovine RTEL is 4440 nt, encompassing 24.8 kb of genomic sequence that was mapped to chromosome 13q2.2. It encodes a conserved helicase-like protein containing seven characterized helicase motifs in the first 750 aa and a PIP box in the C-terminus. Four splice variants were identified within the transcripts in both the coding and 5'-untranslated regions; Western blot revealed that the most abundant splice variant SV-1 was translated to a truncated isoform of RTEL. The different 5'UTRs imply alternative transcription start sites in the promoter; Bovine RTEL was transcribed at the blastocyst stage, and expression levels were highest in adult testis, liver and ovary. DNA methylation analysis of tissues that differed significantly in expression level indicated that relatively low DNA methylation is associated with higher expression. CONCLUSION: In this study, we have identified and characterized a bovine RTEL homolog and obtained basic information about it, including gene structure, expression distribution, splice variants and profile of DNA methylation around two putative transcription start sites. These data may be helpful for further comparative and functional analysis of RTEL in mammals

Conifers in Mountains of China

China has the largest area of mountains of all countries, with about 70% of land territory covered with mountains and plateaus. Thanks to vastness, mountainousness, highly heterogeneous habitats and long history of biological evolution, China boasts of extremely high biodiversity (more than 30,000 species of seed plants). The objectives of this chapter are to investigate conifer species and to analyze their multi-dimensional distribution in China. Our conclusions include: (1) China has 244 species of conifers belonging to 32 genera in 4 families (Pinaceae, Cupressaceae, Podocarpaceae and Taxaceae), accounting for 38.37, 49.29 and 66.67% of the global totals, respectively; (2) there are totally 115 conifer species endemic to China, falling in 23 genera of 4 families; (3) conifers and coniferous forests are widely distributed in China, from north to south and from east to west, more prominently in its numerous and high mountains and plateaus; (4) some conifer species appear even at very high elevations, e.g., Juniperus tibetica forests at 4800–4900 m above sea level in the southeastern Tibetan Plateau; and (5) China has established a large number of nature reserves and promulgated and implemented a series of laws and regulations to protect its rare and precious conifer resources