Knowledge-Guided Bayesian Support Vector Machine Methods For High-Dimensional Data

Support vector machines (SVM) is a popular classification method for analysis of high dimensional data such as genomics data. Recently, new SVM methods have been developed to achieve variable selection through either frequentist regularization or Bayesian shrinkage. The Bayesian framework provides a probabilistic interpretation for SVM and allows direct uncertainty quantification. In this dissertation, we develop four knowledge-guided SVM methods for the analysis of high dimensional data. In Chapter 1, I first review the theory of SVM and existing methods for incorporating the prior knowledge, represented bby graphs into SVM. Second, I review the terminology on variable selection and limitations of the existing methods for SVM variable selection. Last, I introduce some Bayesian variable selection techniques as well as Markov chain Monte Carlo (MCMC) algorithms . In Chapter 2, we develop a new Bayesian SVM method that enables variable selection guided by structural information among predictors, e.g, biological pathways among genes. This method uses a spike and slab prior for feature selection combined with an Ising prior for incorporating structural information. The performance of the proposed method is evaluated in comparison with existing SVM methods in terms of prediction and feature selection in extensive simulations. Furthermore, the proposed method is illustrated in analysis of genomic data from a cancer study, demonstrating its advantage in generating biologically meaningful results and identifying potentially important features. The model developed in Chapter 2 might suffer from the issue of phase transition \citep{li2010bayesian} when the number of variables becomes extremely large. In Chapter 3, we propose another Bayesian SVM method that assigns an adaptive structured shrinkage prior to the coefficients and the graph information is incorporated via the hyper-priors imposed on the precision matrix of the log-transformed shrinkage parameters. This method is shown to outperform the method in Chapter 2 in both simulations and real data analysis.. In Chapter 4, to relax the linearity assumption in chapter 2 and 3, we develop a novel knowledge-guided Bayesian non-linear SVM. The proposed method uses a diagonal matrix with ones representing feature selected and zeros representing feature unselected, and combines with the Ising prior to perform feature selection. The performance of our method is evaluated and compared with several penalized linear SVM and the standard kernel SVM method in terms of prediction and feature selection in extensive simulation settings. Also, analyses of genomic data from a cancer study show that our method yields a more accurate prediction model for patient survival and reveals biologically more meaningful results than the existing methods. In Chapter 5, we extend the work of Chapter 4 and use a joint model to identify the relevant features and learn the structural information among them simultaneously. This model does not require that the structural information among the predictors is known, which is more powerful when the prior knowledge about pathways is limited or inaccurate. We demonstrate that our method outperforms the method developed in Chapter 4 when the prior knowledge is partially true or inaccurate in simulations and illustrate our proposed model with an application to a gliobastoma data set. In Chapter 6, we propose some future works including extending our methods to more general types of outcomes such as categorical or continuous variables

The roles of a light-dependent protochlorophyllide oxidoreductase (LPOR), and ATP-dependent dark operative protochlorophyllide oxidoreductase (DPOR) in chlorophyll biosynthesis

Chlorophyll is a green photosynthetic pigment, and photosynthesis drives the global carbon cycle. The reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate stage of biosynthesis of chlorophyll (Chl) is catalyzed by light-independent protochlorophyllide reducatse (DPOR), and the light-dependent protochlorophyllide oxidoreductase (LPOR). The search was done to all manuscript sections according to terms chlorophyll, a light-dependent protochlorophyllide oxidoreductase, ATP-dependent dark operative protochlorophyllide oxidoreductase, chlorophyll, photosynthesis and chlorophyllide. Within the framework of photosynthesis and chlorophyll, this review article was aimed to provide an overview of the functional studies in chlorophyll biosynthesis, protein crystal structure, disclosure of action mechanisms, and possible future available direction of LPOR and DPOR in the biosynthesis of chlorophyll

Prevalence of human herpesvirus 8 infection in systemic lupus erythematosus

<p>Abstract</p> <p>Background</p> <p>For decades, scientists have tried to understand the environmental factors involved in the development of systemic lupus erythematosus (SLE), in which viral infections was included. Previous studies have identified Epstein-Barr virus (EBV) to incite SLE. Human herpesvirus 8 (HHV-8), another member of the gammaherpesvirus family, shares a lot in common with EBV. The characteristics of HHV-8 make it a well-suited candidate to trigger SLE.</p> <p>Results</p> <p>In the present study, serum samples from patients (n = 108) with diagnosed SLE and matched controls (n = 122) were collected, and the prevalence of HHV-8 was compared by a virus-specific nested PCR and a whole virus enzyme-linked immunoassay (EIA). There was significant difference in the prevalence of HHV-8 DNA between SLE patients and healthy controls (11 of 107 vs 1 of 122, <it>p </it>= 0.001); significant difference was also found in the detection of HHV-8 antibodies (19 of 107 vs 2 of 122, <it>p </it>< 0.001).</p> <p>We also detected the antibodies to Epstein-Barr virus viral capsid antigen (EBV-VCA) and Epstein-Barr nuclear antigen-1 (EBNA-1). Both patients and controls showed high seroprevalence with no significant difference (106 of 107 vs 119 of 122, <it>p </it>= 0.625).</p> <p>Conclusion</p> <p>Our finding indicated that there might be an association between HHV-8 and the development of SLE.</p

Health-related quality of life after mandibular resection for oral cancer: reconstruction with free fibula flap

Objectives: Mandibular resection for oral cancer is often necessary to achieve an adequate margin of tumor clear - ance. Mandibular resection has been associated with a poor health-related quality of life (HRQOL), particularly before free fibula flap to reconstruct the defect. The aim of this study was to evaluate health-related quality of life in patients who have had mandibular resections of oral cancer and reconstruction with free fibula flap. Study D esigns: There were 115 consecutive patients between 2008 and 2011 who were treated by primary surgery for oral squamous cell carcinoma, 34 patients had a mandibular resection. HRQOL was assessed by means of the 14-item Oral Health Impact Profile (OHIP-14) and University of Washington Quality of Life (UW-QOL) question - naires after 12 months postoperatively. Results: In the UW-QOL the best-scoring domain was mood, whereas the lowest scores were for chewing and saliva. In the OHIP-14 the lowest-scoring domain was social disability, followed by handicap, and psychological disability. Conclusions: Mandible reconstruction with free fibula flap would have significantly influenced on patients' quality of life and oral functions. The socio-cultural data show a fairly low level of education for the majority of patients

Identifying crystal accumulation in granitoids through amphibole composition and in situ zircon O isotopes in North Qilian Orogen

Granitoids are the main constituents of the continental crust, and an understanding of their petrogenesis is key to the origin and evolution of continents. Whether crystal fractionation is the dominant way to generate evolved magmas has long been debated, mostly because such processes would produce large volumes of complementary cumulates, which remains elusive. Mafic magmatic enclaves (MMEs) are ubiquitous in granitoids and their presence was initially recognized as cumulates. However, because many MMEs lack obvious evidence of accumulation, such as the classic cumulate textures and modal layering, the cumulate origin of MMEs has been abandoned and the model of magma mixing between mafic and felsic magmas has become popular. In this study, we conduct a combined study of amphibole composition and in situ O isotopes in zircons on three suites of orogenic granitoids with MMEs from the North Qilian Orogenic Belt (NQOB). We find that the MMEs and their host granodiorites show overlapping zircon δ18O values, affirming that they share the same parental magmas. The amphibole compositions indicate that amphiboles from the MMEs are not in equilibrium with a melt whose composition was that of the bulk-rock. These new data, together with the published bulk-rock data, suggest that the MMEs in our study have clear cumulate signatures and are thus of cumulate origin. Our study provides evidence for crystal accumulation in granitoids in the NQOB. This new understanding calls for re-examination on the petrogenesis of some intermediate magmatic rocks (granitoid/andesite) in discussing models of continental crustal growth

Survey on nitrogenase evolution by considering the importance of nitrogenase, its structure, and mechanism of nitrogenase

Nitrogenase is a complicated enzyme that actives the ATP-dependent reduction of dinitrogen (N2) to ammonia (NH3). The aim of this manuscript is to review the nitrogenase evolution with considering nitrogenase, structure of nitrogenase, action mechanism of nitrogenase and oxygen sensitive mechanism of nitrogenase. The searches focused on publications from 1980 to February 2023, using PubMed, Google Scholar, Science Direct, and Scopus databases. In the term of evolution, the nitrogen cycle has experienced highly changes; at the beginning of life and suggested the exact anoxic scenario, the comparatively sufficient ammonium was possibly used in an assimilation/mineralization cycle by protocellular organisms. The main nif gene products which are active in nitrogen fixation are nifH, nifD, nifK, nifT, nifY/nafY, nifE, nifN, nifX, nifU, nifS, nifV, nifW, nifZ, nifM, nifF, nifL, nifA, nifB, fdxN, nifQ, and nifJ. The main vnf gene products which are active in nitrogen fixation are vnfA, vnfE, vnfN, vnfX, vnfH, vnfFd, vnfD, vnfG, vnfK, and vnfY. Oxygen can be either detrimental or beneficial for diazotrophs in organisms suitable for an aerobic catabolism, and it supports the production of a substrate for nitrogenase (ATP), but it can also impede the activity and suppress the synthesis of this enzyme.

Five Plants Used in the Traditional Asian Medicine, Their Functional Phytochemicals and Medicinal Properties

The interest toward natural components in treatment and prevention of several diseases such as diabetes, cancer, coronary disease, arthritis, etc. have been increased in recent years. Common thistle is an annual/biennial broad-leaf weed which is rich in insulin, a starch which passes directly through the digestive system. Its root in diuretic, tonic, antiphlogistic, astringent and hepatic in traditional medicine as well as an important remedy for toothache. Ramsons is an erect perennial native to Eurasia and the most notable pharmacological benefits of ramsons are antibacterial activity, treats stomach problems, useful for chronic disease, many benefits for blood pressure and high cholesterol, appropriate for skin, suitable for inflammations and infections, aids in detoxification, ameliorate aggravations and allergies. The outstanding pharmacological benefits of lychee is helping to remove blemishes and reduce sunburns, to prevent signs of aging, promoting hair growth and providing a distinct shine, prevention of cataracts, anticancer effects, improve digestion, promoting cardiovascular health, regulating blood circulation, anti-influenza activity, anti-inflammatory activity, preventing blood vessel rupture, strengthening bones, increasing the libido and preventing anemia. The most notable health benefits of five flavor berries are increasing energy, anti-inflammatory activity, improving muscular activity, improving vision, increasing cellular health, and preventing liver disease, premature aging and protection against diabetes, radiation, and regulation of blood glucose levels, improve mental health, modulating blood pressure, improving digestion and preventing infection. Ajwain oil has a wide range of pharmaceutical applications such as antifungal, antibacterial, antioxidant, anti-inflammatory, antibacterial, nematicidal, stomachic, carminative, antiseptic, aromatic, digestive, antiseptic, and emmenagogue activities. The present review aims to present some of the most important pharmacological and health benefits five important medicinal plants in traditional Asian medicine which can be studied more due to their valuable chemical components to prevent and treatment of diseases

A Review of Lysimeter Studies and Experiments by Considering Agricultural Production

Lysimeters have been used to obtain accurate information for developing calibrating, and validating crop evapotranspiration and crop coefficients for many plants and crops. Lysimeters are also an unique equipment for studying the transport of solutes when saline waters are used, and therefore, for assessing alkalization and salinization hazards. Three main types of lysimeters are used: constatnt water-table lysimeters, drainage lysimeters, and weighing lysimeters. The weighing lysimeters provide scientist the basic information for research related to the evapotranspiration, and they are commonly divided into two types, continuous weighing and intermittent weighing. Lysimeters are foremost devices, typically tanks or containers, that define a specific boundary to contain soil water and permit measurement of either the soil-water balance or the volume of water percolating vertically and its quality. The limitations are expense which depends on design, variable experimental conditions such as climatic/environmental factors which are usually not controlled, the spatial variability is normally less, they are not appropriate for every plant species and even every soil type. The main goal of lysimeter is defining the crop coefficient (Kc) which used to convert Etr to equivalent crop ET (Etc) values, and determining agronomical parameters of crops which are planted on the field of lysimeter. All weather data like air temperature, humidity, solar radiation, and potential evaporation should be obtained onsite, and the frequency and time of measurements should be at least daily. For crop products, the management such as fertilization, sowing tillage, seed bed preparation, and harvest of the lysimeter including its surrounding area is carried out on the basis of good agricultural practice. it may be required to complement natural precipitation by irrigation. The main purpose of this literature review is to give a brief summary about lysimeters, and survey the impacts of lysimeter studies and crops production. The information provides is obtained from randomized control experiments, review articles, and analytical studies and observations which were gathered from numerous literature sources such as Scopus, PubMed, Google Scholar,and Science Direct

PARP1: Liaison of Chromatin Remodeling and Transcription

Simple Summary: Poly(ADP-ribose) polymerase 1 (PARP1) is perhaps the most studied member of the PARP superfamily and participates in numerous cellular processes. PARP1 inhibitors have been approved as drugs to treat various cancers in clinics, based on its role in DNA repair. Yet, there is a growing body of evidence showing multitasking function of PARP1 in regulation of gene expression. In this review article, we discuss the current knowledge of PARP1 and its conducted enzymatic process, i.e., PARylation, with an emphasis on gene expression by the interaction with transcription factors and regulation of chromatin conformation, dependent or independent of DNA damage. The molecular action mode of PARP1 in gene transcription may present as a potential target for therapeutic intervention of inflammation-related diseases and also for cancer therapy. Abstract Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation

COVID-19 and bilingual children’s home language environment: Digital media, socioeconomic status, and language status

Input is considered crucial in bilingual children’s language development. This is especially true for bilingual children’s mother tongue language learning given its common reduction in input opportunities due to the dominance of one language within society, as seen in countries and regions from Wales to Singapore. Previous studies tend to focus on the quantity and quality of conventional active communication and resources (e.g., speaking and reading with parents) on bilingual children’s language development, and substantially, fewer studies have explored this topic from the perspective of digital media. However, the COVID-19 pandemic has accentuated the critical role of digital media in various aspects of life, including bilingual children’s home language environment. Thus, to holistically understand bilingual children’s daily language input patterns, it is imperative to explore both their conventional and digital media input resources. The current study focuses on English-Mandarin bilingual children in Singapore and would like to explore (1) whether their conventional and digital media language environments have been affected by the COVID-19 pandemic and (2) whether the societal status of a language and familial socioeconomic status (SES) would affect bilingual children’s conventional and digital media input. Survey data from 162 parents of English-Mandarin bilingual preschoolers (3 to 6 years old) were used to explore the two research questions. Two online parental questionnaires were employed for data collection. One-way repeated-measures MANOVA and path models were used to address the questions. The results indicated that input patterns from nuclear family members had not been affected by COVID-19; however, the amount and frequency of conventional and digital media materials and activities increased significantly since COVID-19. Higher-SES families possessed more conventional materials and conducted conventional activities more often, while lower-SES families possessed more digital media materials. Both conventional and digital media materials and activities were richer in English than in Mandarin. Higher-SES families perceived digital media usage for learning to be of less importance than lower-SES families. The implications for early bilingual learning following COVID-19 are discussed