Physico-geochemical and mineral composition of neem tree soils and relation to organic properties

The Neem tree, the oil of which has a long history of pesticide, fertilizer and medicinal use in India, has been studied extensively for its organic compounds. Here we present a physical, mineralogical and geochemical database resulting from the analyses of two Neem soil profiles (epipedons) in India. Neem tree derivatives are used in the manufacture of a variety of products, from anti-bacterial drugs and insecticides to fertilizers and animal feeds. A preliminary geochemical and mineralogical analysis of Neem soils is made to explore the potential for chemical links between Neem tree derivatives and soils. Physical soil characteristics, including colour, texture and clay mineralogy, suggest the two pedons formed under different hydrological regimes, and hence, are products of different leaching environments, one well-drained site, the other poorly drained. Geochemically, the two Neem soils exhibit similarities, with elevated concentrations of Th and rare earth elements. These elements are of interest because of their association with phosphates, especially monazite and apatite, and the potential link to fertilizer derivatives. Higher concentrations of trace elements in the soils may be linked to nutritional derivatives and to cell growth in the Neem tree.

The ins of the striatum: Utilizing chemogenetics to define the contribution of cortical and thalamic afferents during addiction behaviors

Thesis (Ph.D.)--University of Washington, 2016-08

Salicaceae Endophytes: Growth Promotion Potential in Rice (Oryza sativa L.) and Maize (Zea mays L.) and Bio-Control of Plant Pathogen

Thesis (Ph.D.)--University of Washington, 2016-08

Pathologies of Patriarchy: Death, Suffering, Care and Coping in the Gendered Gaps of HIV/AIDS Interventions in Nigeria

Thesis (Ph.D.)--University of Washington, 2016-08

Renal Drug Transporters – Clinical Significance and Role in Drug-Drug Interactions

Thesis (Ph.D.)--University of Washington, 2016-07

Disappeared Persons and Homicide in El Salvador

During 2012-2013, the homicide rate in El Salvador came down from 69.9 to 42.2 per 100,000 population following a truce between the leaders of the two major gangs, “Mara Salvatrucha” and “Barrio 18”, and government. But despite the apparent successes of the truce, it was speculated that the drop in murders could have been due to the killers simply hid the bodies of their victims. This paper aims at determining whether gangs effectively disappeared their victims to cut down the official counts of murders, or they committed these crimes for other reasons. The results from this study suggest that Salvadoran gangs had been using disappearance as a resource to gain sustained social control among residents of already gang-dominated areas, that together with homicide, disappearance is part of a process of territorial spread and strategic strengthening by which these groups are enhancing their capabilities to interfere in the alliances of Mexican drug trafficking organizations with Central American criminal organizations specializing in the transshipment of drugs and in providing access to local markets to distribute and sell drugs. Our findings show that the risk for disappearance has been large even before the truce was in place and that actually, it continues as such and going through a process of geographic expansion.

Off-label prescription of drugs at hospital

Objectives: To develop a procedure for management of off-label medications, and to analyze the treatments, indications, and hospital units which will request them more frequently, as well as which variables will have an impact on the authorization decision, and its economic impact. Methods: A procedure was designed where clinicians would complete request forms and the Hospital Unit would prepare reports assessing their efficacy, safety, convenience, and cost. The request forms for the past five years were analyzed. Results: A total of 834 applications were received, and 88.1% of these were accepted. The authorization rates were higher for Paediatric Units (95.7% vs. 86.6%; p<0.05). The reasons for considering prescriptions as off-label were: different indication (73.2%), different combination (10.2%), different line of treatment (8.6%) and different age (8%). A 73.4% of requests were for antineoplastic drugs, and the most frequently prescribed were rituximab (120) and bevacizumab (103). The quality of evidence supporting the prescriptions was moderate-low, though no direct relationship with the likelihood of approval was demonstrated (p = 0.413). The cost of the approved medications was 8,567,537 €, and the theoretical savings for those drugs rejected was of 2,268,642 €. There was a statistically significant decrease in the authorization rate (p < 0.05, Student's t test) when spending increased. Conclusions: The responsibility for assessing off-label prescriptions has fallen on the Pharmacy Unit. It has not been demonstrated that the quality of evidence represents a decisive variable for approval of treatment; on the other hand, age and cost have demonstrated a significant impact.

Hazardous drugs: new challenges, new opportunities

Occupational exposure to hazardous drugs can cause harmful effects on health professionals and several protective measures must be taken. Nevertheless, classification of hazardous drugs is not the same in all the published repertoires and the terminology is still confusing: hazardous drugs, biohazardous drugs or risky drugs are terms improperly described and can define very different drugs with a very different hazard profiles. In Spain, there is not an updated official list of hazardous drugs, and healthcare professionals must consider and follow other published lists. In our opinion, it is mandatory to do a consensus among these professionals, administration and labor union organizations in order to clarify some conflictive questions not only in healthcare settings but in investigational and academic scenarios too. These multidisciplinary groups should be involved also in teaching new and non-experienced personnel and in the knowledge reinforcement for the experienced ones.

Women’s involvement in clinical trials: historical perspective and future implications

The importance of considering the differences between the male and female sex in clinical decision-making is crucial. However, it has been acknowledged in recent decades that clinical trials have not always adequately enrolled women or analyzed sex-specific differences in the data. As these deficiencies have hindered the progress of understanding women’s response to medications, agencies in the United States have worked towards the inclusion of women in clinical trials and appropriate analysis of sex-specific data from clinical trials. This review outlines the history and progress of women’s inclusion in clinical trials for prescription drugs and presents considerations for researchers, clinicians, and academicians on this issue.

DATA DRIVEN APPROACHES TO IDENTIFY DETERMINANTS OF HEART DISEASES AND CANCER RESISTANCE

Cancer and cardio-vascular diseases are the leading causes of death world-wide. Caused by systemic genetic and molecular disruptions in cells, these disorders are the manifestation of profound disturbance of normal cellular homeostasis. People suffering or at high risk for these disorders need early diagnosis and personalized therapeutic intervention. Successful implementation of such clinical measures can significantly improve global health. However, development of effective therapies is hindered by the challenges in identifying genetic and molecular determinants of the onset of diseases; and in cases where therapies already exist, the main challenge is to identify molecular determinants that drive resistance to the therapies. Due to the progress in sequencing technologies, the access to a large genome-wide biological data is now extended far beyond few experimental labs to the global research community. The unprecedented availability of the data has revolutionized the capabilities of computational researchers, enabling them to collaboratively address the long standing problems from many different perspectives. Likewise, this thesis tackles the two main public health related challenges using data driven approaches. Numerous association studies have been proposed to identify genomic variants that determine disease. However, their clinical utility remains limited due to their inability to distinguish causal variants from associated variants. In the presented thesis, we first propose a simple scheme that improves association studies in supervised fashion and has shown its applicability in identifying genomic regulatory variants associated with hypertension. Next, we propose a coupled Bayesian regression approach -- eQTeL, which leverages epigenetic data to estimate regulatory and gene interaction potential, and identifies combinations of regulatory genomic variants that explain the gene expression variance. On human heart data, eQTeL not only explains a significantly greater proportion of expression variance in samples, but also predicts gene expression more accurately than other methods. We demonstrate that eQTeL accurately detects causal regulatory SNPs by simulation, particularly those with small effect sizes. Using various functional data, we show that SNPs detected by eQTeL are enriched for allele-specific protein binding and histone modifications, which potentially disrupt binding of core cardiac transcription factors and are spatially proximal to their target. eQTeL SNPs capture a substantial proportion of genetic determinants of expression variance and we estimate that 58% of these SNPs are putatively causal. The challenge of identifying molecular determinants of cancer resistance so far could only be dealt with labor intensive and costly experimental studies, and in case of experimental drugs such studies are infeasible. Here we take a fundamentally different data driven approach to understand the evolving landscape of emerging resistance. We introduce a novel class of genetic interactions termed synthetic rescues (SR) in cancer, which denotes a functional interaction between two genes where a change in the activity of one vulnerable gene (which may be a target of a cancer drug) is lethal, but subsequently altered activity of its partner rescuer gene restores cell viability. Next we describe a comprehensive computational framework --termed INCISOR-- for identifying SR underlying cancer resistance. Applying INCISOR to mine The Cancer Genome Atlas (TCGA), a large collection of cancer patient data, we identified the first pan-cancer SR networks, composed of interactions common to many cancer types. We experimentally test and validate a subset of these interactions involving the master regulator gene mTOR. We find that rescuer genes become increasingly activated as breast cancer progresses, testifying to pervasive ongoing rescue processes. We show that SRs can be utilized to successfully predict patients' survival and response to the majority of current cancer drugs, and importantly, for predicting the emergence of drug resistance from the initial tumor biopsy. Our analysis suggests a potential new strategy for enhancing the effectiveness of existing cancer therapies by targeting their rescuer genes to counteract resistance. The thesis provides statistical frameworks that can harness ever increasing high throughput genomic data to address challenges in determining the molecular underpinnings of hypertension, cardiovascular disease and cancer resistance. We discover novel molecular mechanistic insights that will advance the progress in early disease prevention and personalized therapeutics. Our analyses sheds light on the fundamental biological understanding of gene regulation and interaction, and opens up exciting avenues of translational applications in risk prediction and therapeutics.

Growth and development of three key summer grasses in Australian cotton systems

Awnless barnyard grass, feathertop Rhodes grass, and windmill grass are important weeds in Australian cotton systems. In October 2014, an experiment was established to investigate the phenological plasticity of these species. Seed of these species were planted in a glasshouse every four weeks and each cohort grown for 6 months. A developmental response to day length was observed in barnyard grass but not in the other species. Days to maturity increased with each planting for feathertop Rhodes and windmill grass for the first six cohorts. Barnyard grass showed a similar pattern in growth for seeds planted from October to December with an increase in the onset of maturity from 51 to 58 days. However, the onset of maturity for cohorts planted between January and March decreased to between 50 and 52 days. All species had a decrease in the total number of panicles produced from the first four plantings. Feathertop Rhodes grass planted in October produced 41 panicles compared to those planted at the end of December producing 30 panicles, barnyard grass had a decrease from 99 to 47 panicles and windmill grass 37 to 15 panicles on average. By comparing the development of these key weed species over 12 months, detailed information on the phenological plasticity of these species will be obtained. This information will contribute to more informed management decisions by improving our understanding of appropriate weed control timings or herbicide rates depending on weed emergence and development.

New developments in UAV remote sensing for pest management and the implications for cotton

Efficient crop monitoring and pest damage assessments are key to protecting the Australian agricultural industry and ensuring its leading position internationally. An important element in pest detection is gathering reliable crop data frequently and integrating analysis tools for decision making. Unmanned aerial systems are emerging as a cost-effective solution to a number of precision agriculture challenges. An important advantage of this technology is it provides a non-invasive aerial sensor platform to accurately monitor broad acre crops. In this presentation, we will give an overview on how unmanned aerial systems and machine learning can be combined to address crop protection challenges. A recent 2015 study on insect damage in sorghum will illustrate the effectiveness of this methodology. A UAV platform equipped with a high-resolution camera was deployed to autonomously perform a flight pattern over the target area. We describe the image processing pipeline implemented to create a georeferenced orthoimage and visualize the spatial distribution of the damage. An image analysis tool has been developed to minimize human input requirements. The computer program is based on a machine learning algorithm that automatically creates a meaningful partition of the image into clusters. Results show the algorithm delivers decision boundaries that accurately classify the field into crop health levels. The methodology presented in this paper represents a venue for further research towards automated crop protection assessments in the cotton industry, with applications in detecting, quantifying and monitoring the presence of mealybugs, mites and aphid pests.

The importance of cotton disease surveys in Queensland for monitoring endemic diseases and detecting new pathogens and pests

The cotton industry in Australia funds biannual disease surveys conducted by plant pathologists. The objective of these surveys is to monitor the distribution and importance of key endemic pests and record the presence or absence of new or exotic diseases. Surveys have been conducted in Queensland since 2002/03, with surveillance undertaken by experienced plant pathologists. Monitoring of endemic diseases indicates the impact of farming practices on disease incidence and severity. The information collected gives direction to cotton disease research. Routine diagnostics has provided early detection of new disease problems which include 1) the identification of Nematospora coryli, a pathogenic yeast associated with seed and internal boll rot; and 2) Rotylenchulus reniformis, a plant-parasitic nematode. This finding established the need for an intensive survey of the Theodore district revealing that reniform was prevalent across the district at populations causing up to 30% yield loss. Surveys have identified an exotic defoliating strain (VCG 1A) and non-defoliating strains of Verticillium dahliae, which cause Verticillium wilt. An intensive study of the diversity of V. dahliae and the impact these strains have on cotton are underway. Results demonstrate the necessity of general multi-pest surveillance systems in broad acre agriculture in providing (1) an ongoing evaluation of current integrated disease management practices and (2) early detection for a suite of exotic pests and previously unknown pests.

Is there a relation between environmental exposure to teratogenic substances during pregnancy and congenital anomalies in the newborn? A pilot study in Portugal

Background: Maternal occupation as a proxy of environmental exposure has been consistently associated with specific congenital anomalies (CA) in the foetus and newborn. On the other hand, geographical location of the mother such as place of residence and place of work have not been used as proxy for environmental exposures during pregnancy. We designed a pilot study aiming to investigate the association between maternal place of residence and workplace during pregnancy and CA in Portugal. Methods: Cases and controls are identified in the maternity unit. Cases are all live births with at least one CA delivered in the Barreiro hospital located in a heavy industrial area near Lisboa. Controls are the two normal births following each case. Residents outside the study area, stillbirths and women who decline to participate or are incapable of giving consent are excluded. A health professional interviews the mothers using a questionnaire adapted from the registry form of the Portuguese national registry of CA and includes information on places during pregnancy (residence, workplace, leisure), and demographic characterization as place of birth, infant sex, weight, description of CA, age of mother, ethnicity, maternal birth place. Maternal health and obstetric history, education, smoking, alcohol, drugs and medication use is also collected as potential confounders. Results: The pilot study started in January 2016 and at the moment two cases and four controls have been recruited without refusals. The study will continue to be implemented and it is proposed to start in other hospital units during 2016.