Long-term relationships among pesticide applications, mobility, and soil erosion in a vineyard watershed

Agricultural pesticide use has increased worldwide during the last several decades, but the long-term fate, storage, and transfer dynamics of pesticides in a changing environment are poorly understood. Many pesticides have been progressively banned, but in numerous cases, these molecules are stable and may persist in soils, sediments, and ice. Many studies have addressed the question of their possible remobilization as a result of global change. In this article, we present a retro-observation approach based on lake sediment records to monitor micropollutants and to evaluate the long-term succession and diffuse transfer of herbicides, fungicides, and insecticide treatments in a vineyard catchment in France. The sediment allows for a reliable reconstruction of past pesticide use through time, validated by the historical introduction, use, and banning of these organic and inorganic pesticides in local vineyards. Our results also revealed how changes in these practices affect storage conditions and, consequently, the pesticides’ transfer dynamics. For example, the use of postemergence herbicides (glyphosate), which induce an increase in soil erosion, led to a release of a banned remnant pesticide (dichlorodiphenyltrichloro- ethane, DDT), which had been previously stored in vineyard soil, back into the environment. Management strategies of ecotoxico- logical risk would be well served by recognition of the diversity of compounds stored in various environmental sinks, such as agriculture soil, and their capability to become sources when environmental conditions change.

A thermodynamic model for di-trioctahedral chlorite from experimental and natural data in the system MgO-FeO-Al2O3-SiO2-H2O. Applications to P-T sections and geothermometry

We present a new thermodynamic activity-composition model for di-trioctahedral chlorite in the system FeO–MgO–Al2O3–SiO2–H2O that is based on the Holland–Powell internally consistent thermodynamic data set. The model is formulated in terms of four linearly independent end-members, which are amesite, clinochlore, daphnite and sudoite. These account for the most important crystal-chemical substitutions in chlorite, the Fe–Mg, Tschermak and di-trioctahedral substitution. The ideal part of end-member activities is modeled with a mixing-on-site formalism, and non-ideality is described by a macroscopic symmetric (regular) formalism. The symmetric interaction parameters were calibrated using a set of 271 published chlorite analyses for which robust independent temperature estimates are available. In addition, adjustment of the standard state thermodynamic properties of sudoite was required to accurately reproduce experimental brackets involving sudoite. This new model was tested by calculating representative P–T sections for metasediments at low temperatures (<400 °C), in particular sudoite and chlorite bearing metapelites from Crete. Comparison between the calculated mineral assemblages and field data shows that the new model is able to predict the coexistence of chlorite and sudoite at low metamorphic temperatures. The predicted lower limit of the chloritoid stability field is also in better agreement with petrological observations. For practical applications to metamorphic and hydrothermal environments, two new semi-empirical chlorite geothermometers named Chl(1) and Chl(2) were calibrated based on the chlorite + quartz + water equilibrium (2 clinochlore + 3 sudoite = 4 amesite + 4 H2O + 7 quartz). The Chl(1) thermometer requires knowledge of the (Fe3+/ΣFe) ratio in chlorite and predicts correct temperatures for a range of redox conditions. The Chl(2) geothermometer which assumes that all iron in chlorite is ferrous has been applied to partially recrystallized detrital chlorite from the Zone houillère in the French Western Alps.

Metabolomics in plant-herbivore interactions: challenges and applications

Metabolomics as the study of the entire set of metabolites of a given organism is an important frontier in life sciences. As a tool that captures the ‘front end’ of cellular machineries, metabolomics is particularly suited to investigate biotic interactions, including for instance the interplay between plants and insects. In this review, we discuss the opportunities and challenges of metabolomics to study plant–herbivore interactions. We first present a brief overview of the typical analytical workflows used in metabolomics and their associated issues, in particular those related to metabolome coverage and compound identification. Second, recent advances in the field of plant–herbivore relationships that are promoted by non-targeted approaches are reviewed, with examples ranging from classical herbivore resistance patterns to plant-mediated interactions across different spatial scales and volatile-mediated tritrophic interactions. Through general considerations and the discussion of a few selected case studies, our review highlights the potential and challenges of metabolomics as a research approach to understand biological interfaces.

Layer-by-layer grown scalable redox-active ruthenium-based molecular multilayer thin films for electrochemical applications and beyond

Here we report the first study on the electrochemical energy storage application of a surface-immobilized ruthenium complex multilayer thin film with anion storage capability. We employed a novel dinuclear ruthenium complex with tetrapodal anchoring groups to build well-ordered redox-active multilayer coatings on an indium tin oxide (ITO) surface using a layer-by-layer self-assembly process. Cyclic voltammetry (CV), UV-Visible (UV-Vis) and Raman spectroscopy showed a linear increase of peak current, absorbance and Raman intensities, respectively with the number of layers. These results indicate the formation of well-ordered multilayers of the ruthenium complex on ITO, which is further supported by the X-ray photoelectron spectroscopy analysis. The thickness of the layers can be controlled with nanometer precision. In particular, the thickest layer studied (65 molecular layers and approx. 120 nm thick) demonstrated fast electrochemical oxidation/reduction, indicating a very low attenuation of the charge transfer within the multilayer. In situ-UV-Vis and resonance Raman spectroscopy results demonstrated the reversible electrochromic/redox behavior of the ruthenium complex multilayered films on ITO with respect to the electrode potential, which is an ideal prerequisite for e.g. smart electrochemical energy storage applications. Galvanostatic charge–discharge experiments demonstrated a pseudocapacitor behavior of the multilayer film with a good specific capacitance of 92.2 F g−1 at a current density of 10 μA cm−2 and an excellent cycling stability. As demonstrated in our prototypical experiments, the fine control of physicochemical properties at nanometer scale, relatively good stability of layers under ambient conditions makes the multilayer coatings of this type an excellent material for e.g. electrochemical energy storage, as interlayers in inverted bulk heterojunction solar cell applications and as functional components in molecular electronics applications.

Analysis of iodine-129 in environmental materials: Quality assurance and applications

The long-lived radionuclide 129I (T 1/2 = 15.7 My) occurs in the nature in very low concentrations. Since the middle of our century the environmental levels of 129I have been dramatically changed as a consequence of civil and military use of nuclear fission. Its investigation in environmental materials is of interest for environmental surveillance, retrospective dosimetry and for the use as a natural and man-made fracers of environmental processes. We are comparing two analytical methods which presently are capable of determining 129I in environmental materials, namely radiochemical neutron activation analysis (RNAA) and accelerator mass spectrometry (AMS). Emphasis is laid upon the quality control and detection capabilities for the analysis of 129I in environmental materials. Some applications are discussed.

Electrochemical CO2 Reduction - A Critical View on Fundamentals, Materials and Applications

The electrochemical reduction of CO2 has been extensively studied over the past decades. Nevertheless, this topic has been tackled so far only by using a very fundamental approach and mostly by trying to improve kinetics and selectivities toward specific products in half-cell configurations and liquid-based electrolytes. The main drawback of this approach is that, due to the low solubility of CO2 in water, the maximum CO2 reduction current which could be drawn falls in the range of 0.01–0.02 A cm–2. This is at least an order of magnitude lower current density than the requirement to make CO2-electrolysis a technically and economically feasible option for transformation of CO2 into chemical feedstock or fuel thereby closing the CO2 cycle. This work attempts to give a short overview on the status of electrochemical CO2 reduction with respect to challenges at the electrolysis cell as well as at the catalyst level. We will critically discuss possible pathways to increase both operating current density and conversion efficiency in order to close the gap with established energy conversion technologies.

Study of Basic Wood Decay Mechanisms and Their Biotechnological Applications

The overall objective of this thesis was to gain further understanding of the non-enzymatic mechanisms involved in brown-rot wood decay, especially the role of pH, oxalic acid, and low molecular catecholate compounds on the dissolution and reduction of iron, and the formation of reactive oxygen species. Another focus of this study will be the potential application of a biomimetic free radical generating system inspired from fungi wood decay process, especially the non-enzymatic mechanism. The possible pathways of iron uptake and iron redox cycling in non-enzymatic brown-rot decay were investigated in this study. UV-Vis spectroscopy and HPLC were employed to study the kinetics and pathways of the interaction between iron and model catecholate compounds under different pH and chelator/iron molar ratio conditions. Iron chelation and reduction during early non-enzymatic wood decay processes have been studied in this thesis. The results indicate that the effects of the chelator/iron ratio, the pH, and other reaction parameters on the hydroxyl radical generation in a Fenton type system can be determined using ESR spin-trapping techniques. Data also support the hypothesis that superoxide radicals are involved in chelator-mediated Fenton processes. The mechanisms involved in free radical activation of Thermal Mechanical Pulp fibers were investigated. The activation of TMP fibers was evaluated by ESR measurement of free phenoxy radical generation on solid fibers. The results indicate that low molecular weight chelators can improve Fenton reactions, thus in turn stimulating the free radical activation of TMP fibers. A mediated Fenton system was evaluated for decolorization of several types of dyes. The result shows that the Fenton system mediated by a catecholate-type chelator effectively reduced the color of a diluted solution of synthetic dyes after 90 minutes of treatment at room temperature. The results show that compared to a neat Fenton process, the mediated Fenton decolorization process increased the production, and therefore the effective longevity, of hydroxyl radical species to increase the decolorization efficiency.

The public health applications of law enforcement medical direction: A practical experience with the Dallas Police Department

In 2008, 132 law enforcement officers were killed in the line of duty in The United States. Additionally, some have explored both the public health implications of interactions with law enforcement as well as the potential benefits of the use of law enforcement officers as public health and emergency healthcare providers. By virtue of these novel analyses and techniques, professional medical direction of the emerging specialty of law enforcement medicine is needed. This paper, an analysis of law enforcement medical direction through a look at the Dallas Police Medical Direction Program, seeks to examine origins of law enforcement medicine through a comprehensive literature review, as well as begin to define to core competencies of law enforcement medical direction. ^ The unique intersection of public health, medicine and law enforcement, and the subsequent specialty that is developing to manage this interface, is in its relative infancy. An analysis of this nature is in order to begin to lay down the foundations necessary for future study and improvements in the field. ^

Bayesian and survival model for tumor relapse status and disease-specific survival, with applications to breast cancer

Breast cancer is the most common non-skin cancer and the second leading cause of cancer-related death in women in the United States. Studies on ipsilateral breast tumor relapse (IBTR) status and disease-specific survival will help guide clinic treatment and predict patient prognosis.^ After breast conservation therapy, patients with breast cancer may experience breast tumor relapse. This relapse is classified into two distinct types: true local recurrence (TR) and new ipsilateral primary tumor (NP). However, the methods used to classify the relapse types are imperfect and are prone to misclassification. In addition, some observed survival data (e.g., time to relapse and time from relapse to death)are strongly correlated with relapse types. The first part of this dissertation presents a Bayesian approach to (1) modeling the potentially misclassified relapse status and the correlated survival information, (2) estimating the sensitivity and specificity of the diagnostic methods, and (3) quantify the covariate effects on event probabilities. A shared frailty was used to account for the within-subject correlation between survival times. The inference was conducted using a Bayesian framework via Markov Chain Monte Carlo simulation implemented in softwareWinBUGS. Simulation was used to validate the Bayesian method and assess its frequentist properties. The new model has two important innovations: (1) it utilizes the additional survival times correlated with the relapse status to improve the parameter estimation, and (2) it provides tools to address the correlation between the two diagnostic methods conditional to the true relapse types.^ Prediction of patients at highest risk for IBTR after local excision of ductal carcinoma in situ (DCIS) remains a clinical concern. The goals of the second part of this dissertation were to evaluate a published nomogram from Memorial Sloan-Kettering Cancer Center, to determine the risk of IBTR in patients with DCIS treated with local excision, and to determine whether there is a subset of patients at low risk of IBTR. Patients who had undergone local excision from 1990 through 2007 at MD Anderson Cancer Center with a final diagnosis of DCIS (n=794) were included in this part. Clinicopathologic factors and the performance of the Memorial Sloan-Kettering Cancer Center nomogram for prediction of IBTR were assessed for 734 patients with complete data. Nomogram for prediction of 5- and 10-year IBTR probabilities were found to demonstrate imperfect calibration and discrimination, with an area under the receiver operating characteristic curve of .63 and a concordance index of .63. In conclusion, predictive models for IBTR in DCIS patients treated with local excision are imperfect. Our current ability to accurately predict recurrence based on clinical parameters is limited.^ The American Joint Committee on Cancer (AJCC) staging of breast cancer is widely used to determine prognosis, yet survival within each AJCC stage shows wide variation and remains unpredictable. For the third part of this dissertation, biologic markers were hypothesized to be responsible for some of this variation, and the addition of biologic markers to current AJCC staging were examined for possibly provide improved prognostication. The initial cohort included patients treated with surgery as first intervention at MDACC from 1997 to 2006. Cox proportional hazards models were used to create prognostic scoring systems. AJCC pathologic staging parameters and biologic tumor markers were investigated to devise the scoring systems. Surveillance Epidemiology and End Results (SEER) data was used as the external cohort to validate the scoring systems. Binary indicators for pathologic stage (PS), estrogen receptor status (E), and tumor grade (G) were summed to create PS+EG scoring systems devised to predict 5-year patient outcomes. These scoring systems facilitated separation of the study population into more refined subgroups than the current AJCC staging system. The ability of the PS+EG score to stratify outcomes was confirmed in both internal and external validation cohorts. The current study proposes and validates a new staging system by incorporating tumor grade and ER status into current AJCC staging. We recommend that biologic markers be incorporating into revised versions of the AJCC staging system for patients receiving surgery as the first intervention.^ Chapter 1 focuses on developing a Bayesian method to solve misclassified relapse status and application to breast cancer data. Chapter 2 focuses on evaluation of a breast cancer nomogram for predicting risk of IBTR in patients with DCIS after local excision gives the statement of the problem in the clinical research. Chapter 3 focuses on validation of a novel staging system for disease-specific survival in patients with breast cancer treated with surgery as the first intervention. ^

Biomedical informatics applications for epilepsy management: A systematic review

Epilepsy is a very complex disease which can have a variety of etiologies, co-morbidities, and a long list of psychosocial factors4. Clinical management of epilepsy patients typically includes serological tests, EEG's, and imaging studies to determine the single best antiepileptic drug (AED). Self-management is a vital component of achieving optimal health when living with a chronic disease. For patients with epilepsy self-management includes any necessary actions to control seizures and cope with any subsequent effects of the condition9; including aspects of treatment, seizure, and lifestyle. The use of computer-based applications can allow for more effective use of clinic visits and ultimately enhance the patient-provider relationship through focused discussion of determinants affecting self-management. ^ The purpose of this study is to conduct a systematic literature review on informatics application in epilepsy self-management in an effort to describe current evidence for informatics applications and decision support as an adjunct to successful clinical management of epilepsy. Each publication was analyzed for the type of study design utilized. ^ A total of 68 publications were included and categorized by the study design used, development stage, and clinical domain. Descriptive study designs comprised of three-fourths of the publications and indicate an underwhelming use of prospective studies. The vast majority of prospective studies also focused on clinician use to increase knowledge in treating patients with epilepsy. ^ Due to the chronic nature of epilepsy and the difficulty that both clinicians and patients can experience in managing epilepsy, more prospective studies are needed to evaluate applications that can effectively increase management activities. Within the last two decades of epilepsy research, management studies have employed the use of biomedical informatics applications. While the use of computer applications to manage epilepsy has increased, more progress is needed.^

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION

My dissertation focuses on two aspects of RNA sequencing technology. The first is the methodology for modeling the overdispersion inherent in RNA-seq data for differential expression analysis. This aspect is addressed in three sections. The second aspect is the application of RNA-seq data to identify the CpG island methylator phenotype (CIMP) by integrating datasets of mRNA expression level and DNA methylation status. Section 1: The cost of DNA sequencing has reduced dramatically in the past decade. Consequently, genomic research increasingly depends on sequencing technology. However it remains elusive how the sequencing capacity influences the accuracy of mRNA expression measurement. We observe that accuracy improves along with the increasing sequencing depth. To model the overdispersion, we use the beta-binomial distribution with a new parameter indicating the dependency between overdispersion and sequencing depth. Our modified beta-binomial model performs better than the binomial or the pure beta-binomial model with a lower false discovery rate. Section 2: Although a number of methods have been proposed in order to accurately analyze differential RNA expression on the gene level, modeling on the base pair level is required. Here, we find that the overdispersion rate decreases as the sequencing depth increases on the base pair level. Also, we propose four models and compare them with each other. As expected, our beta binomial model with a dynamic overdispersion rate is shown to be superior. Section 3: We investigate biases in RNA-seq by exploring the measurement of the external control, spike-in RNA. This study is based on two datasets with spike-in controls obtained from a recent study. We observe an undiscovered bias in the measurement of the spike-in transcripts that arises from the influence of the sample transcripts in RNA-seq. Also, we find that this influence is related to the local sequence of the random hexamer that is used in priming. We suggest a model of the inequality between samples and to correct this type of bias. Section 4: The expression of a gene can be turned off when its promoter is highly methylated. Several studies have reported that a clear threshold effect exists in gene silencing that is mediated by DNA methylation. It is reasonable to assume the thresholds are specific for each gene. It is also intriguing to investigate genes that are largely controlled by DNA methylation. These genes are called “L-shaped” genes. We develop a method to determine the DNA methylation threshold and identify a new CIMP of BRCA. In conclusion, we provide a detailed understanding of the relationship between the overdispersion rate and sequencing depth. And we reveal a new bias in RNA-seq and provide a detailed understanding of the relationship between this new bias and the local sequence. Also we develop a powerful method to dichotomize methylation status and consequently we identify a new CIMP of breast cancer with a distinct classification of molecular characteristics and clinical features.