System Characterizations and Optimized Reconstruction Methods for Novel X-ray Imaging

In the past decade there have been many new emerging X-ray based imaging technologies developed for different diagnostic purposes or imaging tasks. However, there exist one or more specific problems that prevent them from being effectively or efficiently employed. In this dissertation, four different novel X-ray based imaging technologies are discussed, including propagation-based phase-contrast (PB-XPC) tomosynthesis, differential X-ray phase-contrast tomography (D-XPCT), projection-based dual-energy computed radiography (DECR), and tetrahedron beam computed tomography (TBCT). System characteristics are analyzed or optimized reconstruction methods are proposed for these imaging modalities. In the first part, we investigated the unique properties of propagation-based phase-contrast imaging technique when combined with the X-ray tomosynthesis. Fourier slice theorem implies that the high frequency components collected in the tomosynthesis data can be more reliably reconstructed. It is observed that the fringes or boundary enhancement introduced by the phase-contrast effects can serve as an accurate indicator of the true depth position in the tomosynthesis in-plane image. In the second part, we derived a sub-space framework to reconstruct images from few-view D-XPCT data set. By introducing a proper mask, the high frequency contents of the image can be theoretically preserved in a certain region of interest. A two-step reconstruction strategy is developed to mitigate the risk of subtle structures being oversmoothed when the commonly used total-variation regularization is employed in the conventional iterative framework. In the thirt part, we proposed a practical method to improve the quantitative accuracy of the projection-based dual-energy material decomposition. It is demonstrated that applying a total-projection-length constraint along with the dual-energy measurements can achieve a stabilized numerical solution of the decomposition problem, thus overcoming the disadvantages of the conventional approach that was extremely sensitive to noise corruption. In the final part, we described the modified filtered backprojection and iterative image reconstruction algorithms specifically developed for TBCT. Special parallelization strategies are designed to facilitate the use of GPU computing, showing demonstrated capability of producing high quality reconstructed volumetric images with a super fast computational speed. For all the investigations mentioned above, both simulation and experimental studies have been conducted to demonstrate the feasibility and effectiveness of the proposed methodologies

Tinkering Evolution of Post-Transcriptional RNA Regulons: Puf3p in Fungi as an Example

Genome-wide studies of post-transcriptional mRNA regulation in model organisms indicate a “post-transcriptional RNA regulon” model, in which a set of functionally related genes is regulated by mRNA–binding RNAs or proteins. One well-studied post-transcriptional regulon by Puf3p functions in mitochondrial biogenesis in budding yeast. The evolution of the Puf3p regulon remains unclear because previous studies have shown functional divergence of Puf3p regulon targets among yeast, fruit fly, and humans. By analyzing evolutionary patterns of Puf3p and its targeted genes in forty-two sequenced fungi, we demonstrated that, although the Puf3p regulon is conserved among all of the studied fungi, the dedicated regulation of mitochondrial biogenesis by Puf3p emerged only in the Saccharomycotina clade. Moreover, the evolution of the Puf3p regulon was coupled with evolution of codon usage bias in down-regulating expression of genes that function in mitochondria in yeast species after genome duplication. Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles

Antagonistic Changes in Sensitivity to Antifungal Drugs by Mutations of an Important ABC Transporter Gene in a Fungal Pathogen

Fungal pathogens can be lethal, especially among immunocompromised populations, such as patients with AIDS and recipients of tissue transplantation or chemotherapy. Prolonged usage of antifungal reagents can lead to drug resistance and treatment failure. Understanding mechanisms that underlie drug resistance by pathogenic microorganisms is thus vital for dealing with this emerging issue. In this study, we show that dramatic sequence changes in PDR5, an ABC (ATP-binding cassette) efflux transporter protein gene in an opportunistic fungal pathogen, caused the organism to become hypersensitive to azole, a widely used antifungal drug. Surprisingly, the same mutations conferred growth advantages to the organism on polyenes, which are also commonly used antimycotics. Our results indicate that Pdr5p might be important for ergosterol homeostasis. The observed remarkable sequence divergence in the PDR5 gene in yeast strain YJM789 may represent an interesting case of adaptive loss of gene function with significant clinical implications

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Effects of Salinity and Water Depth on Germination of Phragmites australis in Coastal Wetland of the Yellow River Delta

Phragmites australis, a perennial herb and a widespread species, is widely distributed in coastal wetland in the Yellow River Delta. Laboratory experiments were carried out to assess the effects of water and salinity on seed germination of P. australis and recovery response after seed transferred to distilled water. The germination responses of seeds were determined over a wide range of salinities of 0, 0.5, 1, 2, 2.5, and 3% and water depths of 0, 2, 4, 6, 8, 10, and 15?cm. Final percent germination and germination speed except for at 0.5% salinity treatment were decreased with increasing salinities. Lower salinity (0.5%) could stimulate germination of P. australis, while seed germination was nearly inhibited completely at salinity 3%. P. australis percent germination was decreased with water depth increasing except 2?cm water depth treatment. Percent germination and speed were great and fast at lower water depth. After end of the recovery period, the final percent germination of P. australis after high salinity treatments (2, 2.5, and 3%) was up to 80%, while those after low salinity treatments were lower than 1%, and percent germination after different water depth treatments was zero. The results indicate that it is possible to accelerate the degraded coastal wetland restoration process of P. australis population by sexual ways in the Yellow River Delta.Phragmites australis, a perennial herb and a widespread species, is widely distributed in coastal wetland in the Yellow River Delta. Laboratory experiments were carried out to assess the effects of water and salinity on seed germination of P. australis and recovery response after seed transferred to distilled water. The germination responses of seeds were determined over a wide range of salinities of 0, 0.5, 1, 2, 2.5, and 3% and water depths of 0, 2, 4, 6, 8, 10, and 15?cm. Final percent germination and germination speed except for at 0.5% salinity treatment were decreased with increasing salinities. Lower salinity (0.5%) could stimulate germination of P. australis, while seed germination was nearly inhibited completely at salinity 3%. P. australis percent germination was decreased with water depth increasing except 2?cm water depth treatment. Percent germination and speed were great and fast at lower water depth. After end of the recovery period, the final percent germination of P. australis after high salinity treatments (2, 2.5, and 3%) was up to 80%, while those after low salinity treatments were lower than 1%, and percent germination after different water depth treatments was zero. The results indicate that it is possible to accelerate the degraded coastal wetland restoration process of P. australis population by sexual ways in the Yellow River Delta

Partially reduced graphene oxide and chitosan nanohybrid membranes for selective retention of divalent cations.

A tremendous quantity of brackish water with a high proportion of divalent cations is in great need of water softening. Layer-stacked graphene oxide membranes show potential in membrane processing due to their molecular sieving properties, but show poor selective retention of cations due to unstable interlayer spacing and electrostatic interaction. In this study, a partially reduced graphene oxide (prGO) and chitosan (CS) nanohybrid membrane (prGO-CS) was fabricated to achieve the selective retention of divalent cations by adjusting the configuration and controlling the surface charge. The prGO-CS membrane, which included a CS skin and embedded prGO sheets, showed a performance boost of 98.0% rejection of Mg2+ and 95.5% rejection of Ca2+ when compared with a CS membrane. The membrane showed good water softening performance for brackish water under low operation pressure with a high Na+/Mg2+ selectivity of 33.8. The excellent performance was attributed to the dense structure and positive charge of prGO-CS

A Comparison of the Development of Wetland Restoration Techniques in China and Other Nations

Based on retrieved results of literature and patents related to international wetland ecological restoration, the current status and development of ecological restoration techniques for degraded wetlands in both China and international states were analyzed synthetically. The results showed that the United States was the pioneering country in studies on the wetland ecological restoration, while China began to pay widespread attention from 2000. Compared to the international developed countries, the start time of concern for wetland ecological restoration in China was about 10 years later. The phytoremediation and engineering restoration were the most popular among all the wetland ecological restoration techniques. Besides the United States, the number of publications increased most quickly in China since 2004. The Louisiana State University published most of the researching findings among the international institutions related to wetland ecological restoration. The Chinese Academy of Sciences was the most important institution for wetland restoration study in China. The analysis of the wetland ecological restoration practice in China and international states indicated that the study and application of combined bioremediation techniques would receive more attention for wetland ecological restoration in the future