Using node ordering to improve Structure MCMC for Bayesian Model Averaging

In this thesis, I address an important problem of estimating the structure of Bayesian network models using Bayesian model averaging approach. Bayesian networks are probabilistic graphical models which are widely used for probabilistic inference and causal modeling. Learning the structure of Bayesian networks can reveal insights into the causal structure of the underlying domain. Owing to the super exponential structure space, it is a challenging task to find the most suitable network model that explains the data. The problem is worsened when the amount of available data is modest, as there might be numerous models with non negligible posterior. Therefore, we are interested in the calculation of posterior of a feature like presence of an edge from one particular node to another or a particular set being a parent of a specific node. The contribution of this thesis includes a Markov Chain Monte Carlo simulation approach to sample network structures from a posterior and then using Bayesian model averaging approach to estimate the posterior of various features

Determine the functional and radiological outcome of T3 proximal femur nail in the treatment of intertrochanteric fracture of femur

Background: T3 is the new generation nail used for fixation of intertrochanteric fractures. The lag screw is designed to transfer the load of the femoral head into the nail shaft by bridging the fracture line to allow fast and secure fracture healing. The load carrying thread design of the T3 lag screw provides large surface contact to the cancellous bone, this provides high resistance against cut out.Methods: 30 subjects attending the study were operated with T3 proximal femur nail in the treatment of intertrochanteric fracture of femur. Prospective, randomised case-controlled study done over period of 1 year.Results: Significant results were obtained while comparing the mean RUSH score and mean Harris hip score at different postoperative follow-up time intervals with good to excellent outcome and less operative time and low complications rate.Conclusions: T3 is the new generation nail used for fixation of intertrochanteric fractures and is a dependable implant for the fixation. It has good to excellent outcomes and takes less operative time with low complication rates. The anatomical shape of the nail is universal for all indications involving the treatment of intertrochanteric fractures. The load carrying thread design of the T3 lag screw provides large surface contact to the cancellous bone, thus providing high resistance against cut out. The set screw prevents rotation of the lag screw. The T3 has a single screw passing into the neck of the femur and its Set Screw that is passed into the proximal part of the femoral nail sits into the groove of the Lag screw, thus providing rotational stability

Occurrence of Grapevine Leafroll-Associated Virus Complex in Napa Valley

Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n = 36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n = 134) were GLRaV positive. Of the positives, 81% (n = 109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n = 5), while the remaining samples (15%, n = 20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n = 306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n = 31) were positive for GLRaVs and 90% of positive blocks (n = 28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events

Using node ordering to improve Structure MCMC for Bayesian Model Averaging

In this thesis, I address an important problem of estimating the structure of Bayesian network models using Bayesian model averaging approach. Bayesian networks are probabilistic graphical models which are widely used for probabilistic inference and causal modeling. Learning the structure of Bayesian networks can reveal insights into the causal structure of the underlying domain. Owing to the super exponential structure space, it is a challenging task to find the most suitable network model that explains the data. The problem is worsened when the amount of available data is modest, as there might be numerous models with non negligible posterior. Therefore, we are interested in the calculation of posterior of a feature like presence of an edge from one particular node to another or a particular set being a parent of a specific node. The contribution of this thesis includes a Markov Chain Monte Carlo simulation approach to sample network structures from a posterior and then using Bayesian model averaging approach to estimate the posterior of various features.</p

Exergy analysis of a heating ventilation and air conditioning (HVAC) system

According to the first law of thermodynamics, energy can neither be created nor destroyed; except that energy can be changed from one form to the other. Exergy refers to the maximum useful work that can be obtained from a system at a given state in a given environment. This implies that the conservation law applies to energy but it is subjected to exergy. Thus, using exergy analysis, a system can be optimized by analyzing the weakness of the exergy where the useful work obtained is not maximum or efficient. In this paper, the principle of exergy will be analyzed considering the Heating, Ventilation, and Air Conditioning (HVAC) systems, taking into account possible solutions of system designs. Analytical reviews and results will be used to determine the most efficient system by reducing the amount of exergy being used and thus reducing the amount of energy that is being consumed

A divergent variant of <it>Grapevine leafroll-associated virus 3</it> is present in California

<p>Abstract</p> <p>Background</p> <p>Grapevine leafroll-associated viruses are a problem for grape production globally. Symptoms are caused by a number of distinct viral species. During a survey of Napa Valley vineyards (California, USA), we found evidence of a new variant of <it>Grapevine leafroll-associated virus 3</it> (GLRaV-3). We isolated its genome from a symptomatic greenhouse-raised plant and fully sequenced it.</p> <p>Findings</p> <p>In a maximum likelihood analysis of representative GLRaV-3 gene sequences, the isolate grouped most closely with a recently sequenced variant from South Africa and a partial sequence from New Zealand. These highly divergent GLRaV-3 variants have predicted proteins that are more than 10% divergent from other GLRaV-3 variants, and appear to be missing an open reading frame for the p6 protein.</p> <p>Conclusions</p> <p>This divergent GLRaV-3 phylogroup is already present in grape-growing regions worldwide and is capable of causing symptoms of leafroll disease without the p6 protein.</p

Cord Blood Adductomics Reveals Oxidative Stress Exposure Pathways of Bronchopulmonary Dysplasia

Fetal and neonatal exposures to perinatal oxidative stress (OS) are key mediators of bronchopulmonary dysplasia (BPD). To characterize these exposures, adductomics is an exposure science approach that captures electrophilic addition products (adducts) in blood protein. Adducts are bound to the nucleophilic cysteine loci of human serum albumin (HSA), which has a prolonged half-life. We conducted targeted and untargeted adductomics to test the hypothesis that adducts of OS vary with BPD. We studied 205 preterm infants (≤28 weeks) and 51 full-term infants from an ongoing birth cohort. Infant plasma was collected at birth (cord blood), 1-week, 1-month, and 36-weeks postmenstrual age. HSA was isolated from plasma, trypsin digested, and analyzed using high-performance liquid chromatography-mass spectrometry to quantify previously annotated (known) and unknown adducts. We identified 105 adducts in cord and postnatal blood. A total of 51 known adducts (small thiols, direct oxidation products, and reactive aldehydes) were increased with BPD. Postnatally, serial concentrations of several known OS adducts correlated directly with supplemental oxygen exposure. The application of large-scale adductomics elucidated OS-mediated pathways of BPD. This is the first study to investigate the "neonatal-perinatal exposome" and to identify oxidative stress-related exposure biomarkers that may inform antioxidant strategies to protect the health of future generations of infants