An Integrative Investigation of Sources, Fate, and Transport of Bacteria in Milwaukee Coastal Beaches

Beach water quality criteria are determined by the Environmental Protection Agency (EPA) and water quality advisories or closings are issued based on fecal indicator bacteria (FIB) at the beaches. Understanding of sources, fate and transport of FIB at a beach environment is of economic and social interest for public users, beach managers, policy makers and scientists. This is a complex problem and it is a multidisciplinary issue by nature. Scientists have generally taken a reductionist approach to tackle complex environmental issues. However, as alluded by Gallagher and Appenzeller (1999) and adopted by Boehm (2000), many complex systems are best interpreted using an integrative agenda . Sources and transport of bacteria at a beach environment has been studied by Boehm (2012) in this context. Results from such study indicate that large scale feature is best interpreted with information about small-scale interactions. In this dissertation, I examined the sources of fecal indicator bacteria (FIB) in ten Lake Michigan beaches. In depth studies were performed at one study site (Bradford Beach) to investigate possible sources of FIB, including groundwater-lake water interactions and runoff infiltrating through the sand. The impact of hydrological and geophysical factors that are associated with formation of standing water were also investigated, including the potential of FIB reservoirs in the sand matrix to serve as a sink and source of bacteria at the beach environment. In order to better understand bacterial association with particles at a large scale, I examined the small scale interactions between bacteria and particles by developing a new non-invasive optical technique and applying the technique to assess attachment of bacteria to sand particles in a sheared fluid simulating condition found in the surf zone. Finally, I used knowledge obtained from the understanding of small scale interactions to interpret results acquired from a statistical model and time series applied to large scale features at Bradford Beach and Atwater Beach. This work is relevant to the study of sources and transport of bacteria not only in large lakes, but in rivers and oceans. The results also extend to the investigation of other microbial pollutants and their association with particles in a water body and the potential to track the transport of these pollutants in sediments, air and water. References: Boehm, A. (2000). An integrative investigation of particle distributions in natural waters. Department of Chemical and Biochemical Engineering and Materials Science. Irvine, University of California, Irvine: 194. Gallagher, R and T. Appenzeller (1999). Beyond reductionism. Science 284:79. Russell, T. L., K. M. Yamahara and A. B. Boehm (2012). Mobilization and transport of naturally occurring enterococci in beach sands subject to transient infiltration of seawater. Environmental Science and Technology 46:5988-5996

Sequential anomaly detection in the presence of noise and limited feedback

This paper describes a methodology for detecting anomalies from sequentially observed and potentially noisy data. The proposed approach consists of two main elements: (1) {\em filtering}, or assigning a belief or likelihood to each successive measurement based upon our ability to predict it from previous noisy observations, and (2) {\em hedging}, or flagging potential anomalies by comparing the current belief against a time-varying and data-adaptive threshold. The threshold is adjusted based on the available feedback from an end user. Our algorithms, which combine universal prediction with recent work on online convex programming, do not require computing posterior distributions given all current observations and involve simple primal-dual parameter updates. At the heart of the proposed approach lie exponential-family models which can be used in a wide variety of contexts and applications, and which yield methods that achieve sublinear per-round regret against both static and slowly varying product distributions with marginals drawn from the same exponential family. Moreover, the regret against static distributions coincides with the minimax value of the corresponding online strongly convex game. We also prove bounds on the number of mistakes made during the hedging step relative to the best offline choice of the threshold with access to all estimated beliefs and feedback signals. We validate the theory on synthetic data drawn from a time-varying distribution over binary vectors of high dimensionality, as well as on the Enron email dataset.Comment: 19 pages, 12 pdf figures; final version to be published in IEEE Transactions on Information Theor

Ionizing Radiation Detectors

Ionizing radiation has always been present in the natural environment. However, this radiation is not easily detected and since it also possesses high ionizing power and penetration strength, it constitutes a risk to human health when it is found outside of its acceptable limits. The adverse effects of ionizing radiation on human health need to be systematically monitored in order to prevent damage, overexposure, or even death. The detection of the radiation depends on its particular interaction with a sensitive material, and different types of detectors, in different physical states (solid, liquid or gas), are used to measure selective types of ionizing radiation. New materials such as organic semiconductors, for instance, are being targeted for research and as potential candidates for new perspectives on ionizing radiation sensing

Perfil clínico e microbiológico da infecção no pé diabético por bactérias carbapenêmico-resistentes em um hospital do sul do Brasil

Carbapenem-resistant bacteria are a major cause of diabetic foot (DF) infection. They are resistant to almost all available antimicrobial agents and lead to increased hospital costs. The clinical and microbiological characteristics of DF infection due to these microorganisms and the association of DF with outcomes such as mortality and amputation are not yet well established. This was a retrospective cohort study involving 60 vascular surgery patients who were admitted to Nossa Senhora da Conceição Hospital due to DF infection caused by carbapenem-resistant bacteria and who underwent debridement or amputation, and a control group with 60 randomly selected patients. The analyzed parameters were mortality and amputation rates and patients’ epidemiological and microbiological profiles. A significant association was observed between bacterial resistance and previous amputation, previous hospitalizations, and DF ulcer classification into ischemic and neuroischemic; however, there were no differences in mortality and amputation rates between the groups, even after using the Charlson comorbidity index. Although DF infections by carbapenem-resistant bacteria were not statistically associated with worse outcomes, their study is important given that there are few therapeutic options for treating these specific infections.As bactérias carbapenêmico-resistentes são uma causa importante de infecção no pé diabético (PD). Elas são resistentes à maioria dos agentes antimicrobianos disponíveis e estão associadas com aumento dos custos hospitalares. O perfil clínico e microbiológico da infecção no PD por esses microorganismos e a associação do PD com desfechos como mortalidade e amputação não são bem estabelecidos. Foi realizado um estudo de coorte retrospectiva envolvendo 60 pacientes internados na cirugia vascular do Hospital Nossa Senhora da Conceição devido a infecção do PD por bactérias carbapenêmico-resistentes e que foram submetidos a amputação ou desbridamento e um grupo controle de 60 pacientes randomicamente selecionados. Foram analisados o perfil epidemiológico e microbiológico desses pacientes bem como as taxas de mortalidade e amputação. Observou-se uma associação significante entre resistência bacteriana e amputação prévia, hospitalização prévia e classificação do PD em isquêmico e neuro-isquêmico. No entanto, não houve diferença nas taxas de mortalidade e de amputação entre os grupos, mesmo com o uso do escore de comorbidades de Charlson. Apesar das infecções no PD por bactérias carbapenêmico-resistentes não serem associadas estatisticamente com piores desfechos, seu estudo é importante em função das poucas opções terapêuticas disponíveis para tratar essas infecções

Forage mass, nutritive value and persistence of alfalfa and alfalfa mixtures as influenced by forage management

The utilization of alfalfa (Medicago sativa) alone or in mixtures with tall fescue (Lolium arundinaceum (Schreb.) Darbyish) or bermudagrass (Cynodon dactylon (L.) Pers) in the Southeast U.S. must be assessed so better management recommendations can be given. The objective of this first study was to determine the cumulative capacity of alfalfa in monoculture (A) and mixtures with tall fescue (ATF) and bermudagrass (AB), and its indirect improvements on the nutritive (NV). Three species combinations were utilized (A, ATF and AB) and subjected to four harvest frequencies (21, 28, 35 and 42 days) throughout the 2016 and 2017 growing seasons at The University of Tennessee Plateau Research and Education Center (PREC) in Crossville, TN. Samples were collected for analysis of NV and forage mass (FM). Results indicated that on spring of 2016 and 2017, A and ATF showed highest FM values (P \u3c 0.0001). In summer 2016, A and AB had higher FM than ATF (P \u3c 0.0001), however, in summer of 2017 no differences were observed. The NV increased once alfalfa was incorporated into the mixtures, with higher crude protein (CP) and lower neutral detergent fiber (NDF). In conclusion, harvest frequencies above 28 days are recommended for optimum FM accumulation. Yet, harvest frequencies of 42 days tend to have increased lignification thus decreased NV. The second experiment asses the persistence of the same experiment on the third year. Based on FM, results showed that persistence of A (P = 0.0042), AB (P = 0.0002), and ATF (P = 0.0007) decreased at the third year of growth, and different harvest schedules should be followed for each species combination for increased persistence in the field. For A and AB, harvest frequencies should be 35 days and for ATF, 42 days

Structural and functional insights into the role of Carbohydrate Esterases and Carbohydrate-Binding Modules in plant cell wall hydrolysis

Tese de Doutoramento em Ciência e Tecnologia AnimalPlant cell wall polysaccharides offer an extraordinary source of carbon and energy that can be used by various microorganisms, thus constituting a central component of the carbon cycle. The anaerobic thermophilic bacterium Clostridium thermocellum is one of the most prolific degraders of plant cell wall polysaccharides. It produces a multi-enzyme extra-cellular complex of cellulases and hemicellulases, the cellulosome, and these enzymes were shown to have a remarkable biotechnological potential. Based on the recently determined genome sequence of Clostridium thermocellum, we aimed to address several unresolved questions concerning the mechanism of plant cell wall hydrolysis by microbial multi-enzyme complexes.The crystal structure and biochemical properties of the N-terminal carbohydrate esterase domain of Clostridium thermocellum CtCes3-1 were determined (chapter 2). The enzyme is a thermostable acetyl-specific esterase that exhibits a strong preference for acetylated xylan. In adition, we report, in Chapter 3, the characterization of four carbohydrate-binding modules (CBMs) of family 35 that display specificity for Δ4,5-anhydrogalacturonic acid (Δ4,5-GalA), although two of the proteins also interact with glucuronic acid (GlcA). X-ray crystallographic data revealed that the ligand binding site is highly conserved in the four CBM35s. In chapter 4, biochemical properties of a CBM6 (CBM6-1) from Cellvibrio mixtus CmCel5A are presented. The data revealed that CBM6-1 recognizes specifically β1,3-glucans through a previous unknown ligand binding plataform. These studies reveal the different mechanisms by which a highly conserved protein platform (CBM6) can recognise a common ligand. Finally, we identified a novel CBM within the large C. thermocellum cellulosomal protein Cthe_2193 (CtCBM55), which is the founder member of a new CBM family. CtCBM55, in contrast to the previously characterized cellulosomal CBMs, binds to D-galactose and L-arabinose in either anomeric configuration in complex polysaccharides. Ligand specificity is conferred through numerous interactions with the axial O4 of the target sugars, a feature that distinguishes galactose and arabinose from the other major sugars located into plant cell walls.RESUMO - Perspectivas Estruturais e funcionais do papel das carbohidrato esterases e dos modulos de ligação a hidratos de carbono na hidrólise da parede cellular vegetal. - Os polissacáridos da parede celular vegetal constituem uma fonte de carbono e energia que pode ser utilizada por diversos microorganismos desempenhando assim um papel de relevo no ciclo do carbono. A bactéria termofílica anaeróbia Clostridium thermocellum é muito eficaz na degradação dos polissacáridos da parede celular das plantas. Esta produz um complexo multi-enzimático extra-celular de celulases e hemicelulases, denominado celulossoma, demonstrando estas enzimas um extraordinário potencial biotecnológico. Neste trabalho foram determinadas as propriedades bioquímicas e a estrutura cristalográfica do domínio catalítico N-terminal da enzima CtCes3 (CtCes3-1) do Clostridium thermocellum (Capítulo 2). Esta enzima é uma esterase termostável específica para grupos acetilo e que demonstra uma forte preferência por xilano acetilado. É também feita, no Capitulo 3, a caracterização de quatro módulos de ligação a hidratos de carbono (CBMs) da familia 35 que demonstram afinidade para o ácido Δ4,5-anidrogalacturónico (Δ4,5-GalA), apesar de duas das proteínas também interagirem com o acido glucurónico (GlcA). Os dados cristalográficos demonstram que o local de ligação é altamente conservado nos quatro CBM35s. No Capítulo 4, são reveladas as propriedades bioquímicas de um CBM6 da enzima CmCel5A (CBM6-1) do Cellvibrio mixtus. Os dados revelaram que o CBM6-1 reconhece especificamente β1,3-glucanos através de uma plataforma de ligação previamente desconhecida. Estes estudos demonstram os diferentes mecanismos pelos quais uma plataforma proteíca altamente conservada (CBM6) pode reconhecer o mesmo ligando. Finalmente, identificámos um novo CBM da enzima Cthe_2193 (CtCBM55), pertencente ao celulossoma do C. thermocellum, estabelecendo-se assim uma nova família de CBMs. O CtCBM55, ao contrário de outros CBMs do celulossoma, liga-se à D-galactose e à L-arabinose em qualquer configuração anomérica em polissacáridos complexos. A sua especificidade é conferida por varias interacções com o O4 axial dos açucares alvo, uma característica que distingue a galactose e a arabinose dos outros hidratos de carbono que compoêm a parede celular vegetal.This work was funded by Fundação para a Ciência e Tecnologia through individual fellowship SFRH/BD/23784/2005. Co-funded by POCTI/CVT/2004/61162, POCTI/BIA-PRO/2004/59118 and FSE from Ministério da Ciência, Tecnologia e Ensino Superior

Simulation: A Training Resource for Quality Care and Improving Patient Safety

Patient safety is an ever-present topic in the discussion of educators. It has been 20 years since the publication of To Err Is Human, and there are lessons learned, although there is still much to be done. Healthcare systems are becoming increasingly complex, putting the safety of patients at risk. In this context, there is a greater exposure of healthcare professionals to medical-legal liability issues and to becoming victims of situations that are often preventable. Nurses and medical doctors are especially exposed to these situations, since they are visible during procedures, or do so during the points of greater risk during the patient care process. This chapter will review the contribution provided by the curricular integration of simulation-based education as a tool to train technical and nontechnical issues and how this work can be done for the safety of patients through a standardized training plan, under controlled and evaluated processes. We will discuss how resources and elements allow to perform healthcare interventions in a more safely manner. Finally, we will review the existing literature, some experiences, and the available evidence on this topic