Idiopathic pulmonary fibrosis (IPF) is a disease of unknown pathogenesis characterized by scarring of the lung and declining respiratory function. Originating from bone marrow, circulating monocytes can be recruited into the lung tissue and polarized toward the alternatively activated (M2) profibrotic macrophage phenotype. Recent literature has shown that cluster of differentiation 14 positive (CD14+) monocytes are more abundant in IPF patient blood and are associated with disease outcome and acute exacerbation. Additionally, a 52-gene risk profile from peripheral blood mononuclear cells for outcome prediction in IPF was recently published. Here, we began by characterizing macrophages in human IPF lung tissue. We then assembled a biobank and examined transcriptomic characteristics of blood-derived circulating monocytes from IPF patients. Various histological assessments were completed on a tissue microarray including lung biopsies from 24 IPF patients and 17 controls, to characterize M2 macrophage expression in human tissue. Whole blood samples were collected from 50 IPF patients and 12 control subjects. CD14+ monocytes were isolated and mRNA was extracted for bulk RNA sequencing. Data were analyzed for differential expression (DE), and Gene Set Enrichment Analysis (GSEA) was performed to examine enrichment of the previously published 52-gene risk profile in our dataset. We found that M2 macrophage expression was increased in IPF lung tissue compared to controls. CD14+ monocyte levels were significantly elevated in IPF patients in our cohort compared to control participants, and was negatively correlated with forced vital capacity (FVC). DE analysis comparing IPF and control monocytes yielded a 35-gene signature, with 16 up-regulated genes and 19 down-regulated genes. When comparing the signature related to long transplant-free survival from the published dataset to our data, GSEA demonstrated that this signature is enriched in donors from our dataset, supporting concurrence between the meanings of the two datasets. Overall, these results provide insight to identify targets to modulate monocyte/macrophage function in IPF and potentially affect progressive disease. / Thesis / Master of Science (MSc) / Idiopathic pulmonary fibrosis (IPF) is a disease of unknown cause that results in excessive scarring of the lungs and progressive impairment in lung function. We believe that white blood cells called monocytes and macrophages play a key role in the development and progression of this disease. Overall, it is thought that monocytes, which circulate in the blood, enter the lung tissue and become macrophages. These macrophages then lead to the formation of scar tissue, which is characteristic to IPF. In order to better understand how these cells contribute to IPF, we studied their properties in blood and lung biopsies from IPF patients. We found significant differences between monocytes/macrophages in IPF than those in healthy controls, that may help explain disease progression. We hope that these findings will provide insight into causes of the IPF, and potential avenues for therapeutic intervention.

The purpose of this thesis is to examine the potential of a novel method for analysis and characterization of coal mine dust. Respirable dust has long been an industry concern due to the association of overexposure leading to the development occupational lung disease. Recent trends of increased incidence of occupational lung disease in miners, such as silicosis and Coal Workers Pneumoconiosis, has shown there is a need for a greater understanding of the respirable fraction of dust in underground coal mines. This study will examine the development of a comprehensive standard methodology for characterization of respirable dust via thermogravimetric analysis (TGA). This method was verified with laboratory-generated respirable dust samples analogous to those commonly observed in underground coal mines. Results of this study demonstrate the ability of the novel TGA method to characterize dust efficiently and effectively. Analysis of the dust includes the determination of mass fractions of coal and non-coal, as well as mass fractions of coal, carbonate, and non-carbonate minerals for larger respirable dust samples. Characterization occurs through the removal of dust particulates from the filter and analysis with TGA, which continuously measures change in mass with specific temperature regions associated with chemical changes for specific types of dust particulates. Results obtained from the verification samples reveal that this method can provide powerful information that may help to increase the current understanding of the health risks linked with exposure to certain types of dust, specifically those found in underground coal mines. / Master of Science

Inhalation of respirable dust in coal mines is a serious occupational health hazard which can lead to the development of chronic and irreversible lung diseases, such as Coal Worker's Pneumoconiosis (CWP) and Progressive Massive fibrosis (PMF). After the passage of the Federal Coal Mine Health and Safety Act (CMHSA) in the late 1960's the prevalence of CWP among US coal miners decreased. However, since the late 1990's a resurgence of lung diseases has been reported, particularly in central Appalachia. On the other hand, dust monitoring data suggest that concentrations of respirable coal mine dust (RCMD) and crystalline silica have been on a downward trend. This contradiction has prompted keen interest in detailed characterization of RCMD to shed light on dust constituents-and their sources. Such information might help miners understand where and under what conditions specific sources contribute to RCMD, and how dust controls and monitoring could be enhanced to mitigate the exposure to respirable hazards. Respirable dust particles generated in coal mines are generally associated with three primary sources: the coal strata that is mined and generates mostly coal particles that could contribute for lung diseases, the rock strata that is cut along with the coal and generates most of the respirable silica and silicates, and the rock dust products that are the main source of carbonates which could produce respiratory irritations. Thermogravimetric Analysis (TGA) is one of many analytical tools that might be used for dust characterization. Its primary benefit is that it can be used to apportion the total sample mass into three mass fractions (i.e., coal, carbonates, non-carbonates) which should be roughly associated with the primary dust sources (i.e., coal strata, rock dust products, rock strata) in many coal mines. This thesis consists of two main chapters: Chapter 1, outlines the research motivation, recaps the efforts to establish a standard TGA method for RCMD, and shows results of the validation experiments that were performed in the current work to enable application of the TGA method to a large set of RCMD and laboratory-generated dust samples. In Chapter 2, 46 lab-generated samples from primary dust source materials collected in 15 coal mines, and 129 respirable dust samples from 23 US coal mines are analyzed using the TGA method validated in Chapter 1. Results for both sets of samples are presented and the mine samples are interpreted based on sampling location, mining method and region. Additionally, Chapter 3 summarizes recommendations for future work. / Master of Science / The chronic exposure to dust generated in underground coal operations represents a serious health concern among coal miners that can lead to the development of lung diseases such as Coal Workers Pneumoconiosis (CWP or "black lung). Despite of dust compliance monitoring data that have shown that the concentrations of dust have been declining, since the late 1990's the number of US coal miners diagnosed with lung diseases has been increasing, especially in central Appalachia. This contradiction has prompted keen interest in detailed characterization of respirable coal mine dust (RCMD) to shed light on dust constituents-and their sources. Such information might help miners understand where and under what conditions specific sources contribute to RCMD, and how dust controls and monitoring could be enhanced to mitigate the exposure to respirable hazards. Thermogravimetric Analysis (TGA) has been proposed as an alternative approach for dust characterization. Its primary benefit is that it can be used to apportion the total sample mass into three mass fractions (i.e., coal, carbonates, non-carbonates) which should be roughly associated with the primary dust sources (i.e., coal strata, rock dust products, rock strata) in many coal mines. This thesis consists of two main chapters: Chapter 1, outlines the research motivation, recaps the efforts to establish a standard TGA method for RCMD, and shows results of the validation experiments that were performed in the current work to enable application of the TGA method to a large set of RCMD and laboratory-generated dust samples. In Chapter 2, 46 lab-generated samples from primary dust source materials collected in 15 coal mines, and 129 respirable dust samples from 23 US coal mines are analyzed using the TGA method validated in Chapter 1. Results for both sets of samples are presented and the mine samples are interpreted based on sampling location, mining method and region. Additionally, Chapter 3 summarizes recommendations for future work.

The purpose of this thesis is to examine applications of thermal and laser-based methods to monitor airborne particulates in underground coal mines. Specifically, coal and mixed mineral mine dust, as well as, diesel particulate matter (DPM). These particulates have historically, and continue to have, significant health impacts on underground miners. Chapters 1 and 2 of this thesis concentrate on using a novel method of thermogravimetric analysis (TGA) to characterize respirable coal and mixed mineral mine dust and presents the results of this method being applied to samples collected in Appalachia coal mines. Appalachia has been a geographic "hotspot" for the rise in occupational lung disease amongst underground coal miners, which began in 1990's after decades of steady decline. This has led researchers to propose there could be something unique about the respirable dust composition in Appalachia coal mines, which resulted in the surge of lung disease cases; however, the knowledge base regarding the actual composition of respirable coal mine dust is limited. The results of this thesis show that most of the mass fraction of respirable Appalachia coal mine dust is not coal, but rather carbonates and non-carbonate minerals (i.e. silica and silicates). These findings are significant as many researchers now suspect silica and silicates to be the true culprit in the occupational lung disease of coal miners. DPM presents an additional occupational health hazard to underground coal miners where diesel equipment is used and is difficult to monitor due to its complex nature. In underground metal/non-metal mines, airborne DPM is regulated and monitored using carbon surrogates. However, due to the potential interference from coal-sourced carbon, DPM in coal mines is monitored only by taking samples at the tailpipe of each piece of equipment. This thesis aims to investigate the potential for a laser-based instrument, the FLIR Airtec, to be used in underground coal mines. In particular, what effect the coal dust will have on the instrument, as it measures DPM by way of elemental carbon (EC). The results of this study show that while the Airtec will not over-estimate coal-sourced EC, there could be some sampling artifacts associated with its operation in coal mines, which may inhibit its effectiveness. / Master of Science / The purpose of this thesis is to examine applications of thermal and laser-based methods to monitor airborne particulates in underground coal mines. Airborne particulates such as, coal dust, silica and other mixed mineral dust, and diesel particulate matter (DPM) have historically, and continue to this day, to have health impacts on underground coal miners. Characterizing and monitoring the composition and concentration of these particulates is crucial from a health and safety engineering approach. Chapters 1 and 2 of this thesis concentrate on using a novel method of thermogravimetric analysis (TGA) to get the mass fraction composition of respirable coal mine dust, while Chapter 3 examines potential interferences with using a DPM monitor in underground coal mines (e.g. it is currently only used in underground metal/non-metal mines). The results of Chapters 1 and 2 indicate that the majority of the mass fraction of respirable coal mine dust is actually not coal, but rather carbonate and non-carbonate minerals (i.e. silica and silicates). This is significant from a health and safety viewpoint as many researchers now suspect silica and silicates may be the true culprits in the occupational lung disease which still plagues underground coal miners to this day. The results of Chapter 3 show that while the DPM monitor in the study could potentially be used to monitor DPM in an underground coal mine, there could be some operational issues presented by airborne coal dust, which would not be present in an underground metal/non-metal mine.

Idiopathic Pulmonary Fibrosis (IPF) is a debilitating respiratory disorder that is characterized by a progressive decline in lung function. Originating through unknown etiology, it is essentially an unchecked wound healing response that causes the build-up of excessive scar tissue in the lung interstitial tissue with a heavy toll on the patient’s respiratory capacity. Pro-fibrotic alternatively activated macrophages (M2) have been linked as an important contributor to the fibrotic remodeling of the lung. Previous Ask research indicates that targeting M2 macrophages is possible through the use of the Dectin-1 receptor, a transmembrane cell surface receptor found in high abundance on M2 macrophages. Activating the Dectin-1 receptor through the use of beta-glucan, a ligand the receptor has a high affinity for, initiates a pro-inflammatory response within the naturally immunosuppressive macrophage and can alter its activity to be less fibrogenic. Our data suggest that M2 polarization of naïve macrophages can be inhibited in vitro by beta-glucan microparticles. Additionally, we have found that polarized M2 macrophages adopt M1-like characteristics when treated with beta-glucan microparticles, in a process that is largely Dectin-1 dependent. M2 cell surface marker CD206, increased levels of which are associated with rapidly progressing IPF, shows significantly decreased frequency of expression in M2 macrophages treated with beta-glucan microparticles. Our assessment for cell-specific uptake of beta-glucan microparticles suggests an important role of the Dectin-1 receptor for significantly increased uptake in murine wild-type M2 macrophages relative to their Dectin-1 knockout counterpart. The use of beta-glucan microparticles as a potential anti-fibrotic therapeutic was assessed in the bleomycin model of fibrotic lung disease. Mice given bleomycin and treated with beta-glucan displayed decreased soluble collagen content and TGFB expression within lung homogenate relative to fibrotic bleomycin control mice. Overall, these results provide insight into the use of beta-glucan as a potential activity modulator of macrophage function in IPF and the possibility of its use as a therapeutic. / Thesis / Master of Science (MSc)

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with worsening respiratory symptoms and physiological impairment. Pulmonary fibrosis is a chronic lung disease characterized by forming scar tissue (fibrosis) in the lungs. Alternatively activated macrophages (M2) known as pro-fibrotic are known to contribute to the fibrotic remodeling of the lung. In addition to the polarization of slices from naïve to pro-fibrotic, the addition of anti-fibrotic therapeutics reprogram slices back to a naïve condition. To polarize the slices, naïve slices are incubated with a previously investigated method in the lab known as the polarization cocktail. The polarization cocktail can be achieved by adding of IL-4, IL-6 and IL-13 to naïve(M0) slices in the Precision Cut lung slice (PCLS) model. For the therapeutic model, slices are incubated with the polarization cocktail and subsequently with the therapeutic. Our results have shown that the precision cut lung slice model can mimic previously investigated in-vivo experiments with the polarization cocktail. Secondly, the addition of therapeutics result in the slices exhibiting lower amounts of M2 markers and arginase activity concluding the model is suitable for the polarization and reprogramming of macrophages. / Thesis / Master of Science in Medical Sciences (MSMS)

Introdução: A doença intersticial pulmonar (DIP) é uma forma de acometimento visceral grave pela esclerose sistêmica (ES), correspondendo na atualidade à principal causa de mortalidade pela doença. Atualmente, a tomografia computadorizada de alta resolução pulmonar (TCAR) é considerada o padrão-ouro no seu diagnóstico. Estudos recentes têm proposto diversos algoritmos clínicos para a predição diagnóstica e prognóstica da DIP-ES, objetivando ampliar sua detecção precoce e auxiliar na determinação de sua evolução e prognóstico. Objetivo: Testar os algoritmos clínicos propostos na literatura na predição diagnóstica e prognóstica na DIP-ES, estimar sua prevalência e avaliar a associação da extensão do acometimento pulmonar na TCAR com mortalidade em uma coorte de pacientes com ES. Métodos: Estudo de coorte prospectivo, incluindo 177 pacientes com ES recrutados no período de abril de 2000 a abril de 2009, avaliados através de entrevista, exame físico, exames laboratoriais, provas de função pulmonar e TCAR. Algoritmos clínicos (A, B e C), combinando dados da ausculta pulmonar, radiografia de tórax e capacidade vital forçada (CVF), foram aplicados para o diagnóstico de diferentes extensões da pneumopatia intersticial na TCAR. Curvas de Kaplan-Meier e Regressão de Cox uni e multivariada foram utilizadas para analisar a associação dos algoritmos e da extensão de DIP na TCAR com a mortalidade. Resultados: A prevalência estimada de DIP na TCAR do baseline foi de 57,1% e 79 pacientes (44,6%) morreram em uma mediana de 11,1 anos de seguimento. Para identificação de DIP com extensão ≥10 e ≥20% na TCAR, todos os algoritmos apresentaram uma alta sensibilidade (>89%) e um likelihoodratio negativo muito baixo (<0,16). Para fins prognósticos, sobrevida foi reduzida para todos os algoritmos, com destaque para o algoritmo C, o qual identifica DIP considerando a presença de crepitantes na ausculta pulmonar, alterações na radiografia de tórax ou CVF <80% (HR 3,47; IC 95% 1,62-7,42). Pacientes com doença extensa como proposto por Goh e Wells (extensão >20% na TCAR ou, em casos indeterminados, CVF <70%) apresentam uma significativa redução na sobrevida (HR 3,42; IC 95% 2,12-5,52). Sobrevida não foi diferente entre pacientes com extensão ≥10 ou ≥20% na TCAR e análise de mortalidade em 10 anos sugere que extensão >10% na TCAR apresenta uma boa capacidade preditiva para mortalidade, embora não haja um ponto de corte claro a partir do qual ocorra um maior incremento na mortalidade. Conclusão: Algoritmos clínicos apresentam uma alta sensibilidade e um likelihood ratio negativo muito baixo para o diagnóstico de extensões de DIP com relevância clínica e prognóstica (≥10 e ≥20%) e foram fortemente associados com mortalidade. Assim sendo, a utilização desses algoritmos pode evitar a necessidade de realização de TCAR em alguns casos. / Introduction: Interstitial lung disease (ILD) is a form of severe visceral involvement by systemic sclerosis (SSc) and currently is the primary cause of death by disease. Thoracic high-resolution computed tomography (HRCT) is considered the gold standard for diagnosis. Recent studies have proposed several clinical algorithms to predict the diagnosis of SSc-ILD, aiming to expand its early detection and estimate prognosis. Objective: To test the clinical algorithms to predict the presence and prognosis of SSc-ILD, to estimate the prevalence of SSc-ILD, and to evaluate the association of extent of ILD with mortality in a cohort of SSc patients. Methods: Prospective cohort study, including 177 SSc patients assessed by clinical evaluation, laboratory tests, pulmonary function tests, and HRCT. Clinical algorithms, combining lung auscultation, chest radiography and % predicted forced vital capacity (FVC), were applied for the diagnosis of different extents of ILD on HRCT. Univariate and multivariate Cox proportional models were used to analyze the association of algorithms and the extent of ILD on HRCT with the risk of death using hazard ratios (HR). Results: The prevalence of ILD was 57.1% on baseline HRCT and 79 patients died (44.6%) in a median follow-up of 11.1 years. For identification of ILD with extent ≥10 and ≥20% on HRCT, all algorithms presented a high sensitivity (>89%) and a very low negative likelihood ratio (<0.16). For prognosis, survival was decreased for all algorithms, especially the algorithm C (HR 3.47, 95% CI 1.62-7.42), which identified the presence of ILD based on crackles on lung auscultation, findings on chest X-ray or FVC <80%. Extensive disease as proposed by Goh and Wells (extent of ILD >20% on HRCT or, in indeterminate cases, FVC <70%) had a significantly higher risk of death (HR 3.42, 95% CI 2.12 to 5.52). Survival was not different between patients with extent of 10 or 20% of ILD on HRCT, and analysis of 10-year mortality suggested that a threshold of 10% may also have a good predictive value for mortality. However, there is no clear cutoff above which mortality is sharply increased. Conclusion: Clinical algorithms had a good diagnostic performance for extent of SSc-ILD on HRCT with clinical and prognostic relevance (≥10 and ≥20%), and were also strongly related to mortality. Therefore, they probably could be used to obviate the requirement of HRCT in some cases.

<p>The progress of chronic disorders such as heart failure and chronic obstructive pulmonary disease affects various aspects of life. They have an deep impact on patients´experience of health and wellbeing and their functional qualities and quality of life. Several studies have in an extensive way described heart failure and chronic obstructive pulmonary disease in its own domain but few qualitative studies consider coexistence of the disorders from a caring science perspective. The aim was to describe the meaning of living with heart failure and chronic obstructive pulmonary disease from a lifeworld perspective. With a phenomenological and reflecting lifeworld approach it´s possible to describe eight patients daily experiences of living with severe and chronic disorders from their own narratives. A general structure describing the phenomenon emerges from the analysis as an acceptance of an unpredictable and changed situation in life. When bodily strengths are balanced and adjusted due to the condition of the disorders harmony will appear in life. The phenomenon´s general structure is illustrated through five constituents; <em>the failing body, make sacrifice, living the life that exist, placing one´s life in the hands of others </em>and <em>to lose one´s identity.</em></p>

The progress of chronic disorders such as heart failure and chronic obstructive pulmonary disease affects various aspects of life. They have an deep impact on patients´experience of health and wellbeing and their functional qualities and quality of life. Several studies have in an extensive way described heart failure and chronic obstructive pulmonary disease in its own domain but few qualitative studies consider coexistence of the disorders from a caring science perspective. The aim was to describe the meaning of living with heart failure and chronic obstructive pulmonary disease from a lifeworld perspective. With a phenomenological and reflecting lifeworld approach it´s possible to describe eight patients daily experiences of living with severe and chronic disorders from their own narratives. A general structure describing the phenomenon emerges from the analysis as an acceptance of an unpredictable and changed situation in life. When bodily strengths are balanced and adjusted due to the condition of the disorders harmony will appear in life. The phenomenon´s general structure is illustrated through five constituents; the failing body, make sacrifice, living the life that exist, placing one´s life in the hands of others and to lose one´s identity.

Occupational exposure to endotoxin-rich swine barn air induces respiratory diseases and loss of lung function. Barn exposure induces recruitment of pulmonary intravascular monocytes/macrophages (PIMMs) and subsequent increased host sensitivity to <i>Escherichia coli</i> LPS challenge. Therefore, to further clarify the biology of PIMMs we examined the role of recruited PIMMs in a rat <i>Escherichia coli</i>-induced lung inflammation model. Following sepsis, lung inflammation was induced with recruitment of PIMMs and subsequently, <i>Escherichia coli</i> LPS challenge exacerbated the lung inflammation with localization of multiple inflammatory cytokines in PIMMs to suggest their possible involvement in modulating lung inflammation in this model.<p> In order to delineate mechanisms of barn air induced lung dysfunction, a rat model of occupational exposure was characterized to show that one and five exposures to the barn environment induced acute lung inflammation and increased airway hyperresponsiveness (AHR). Following 20 exposures, AHR was dampened to indicate adaptive responses. Barn air contains high levels of endotoxin which led us to investigate its role in lung inflammation and AHR. Exposure of mice with either a functional TLR4 (WT) or non-functional TLR4 (mutants) to barn air revealed dependence of lung inflammation but not AHR on a functional TLR4.<p> I investigated whether exposure to barn air alters host responses to a subsequent microbial challenge. Following one day barn exposure and <i>Escherichia coli</i> LPS challenge, lung inflammation was exacerbated with increased granulocytes and IL-1β levels compared to one day barn exposed rats without <i>Escherichia coli</i> LPS challenge. However, increased granulocytes and IL-1β levels in barn exposed and <i>Escherichia coli</i> LPS challenged rats were not different from control rats treated with <i>Escherichia coli</i> LPS indicating a lack of priming effect of barn exposure. However, above results are suggestive of an underlying risk of increased lung inflammation following secondary microbial infection in naïve barn workers.<p> Lastly, I investigated the expression and activity of novel signalling molecules called <i>N</i>-myristoyltransferase and calcineurin in barn air and <i>E. coli</i> LPS induced lung inflammation models. Following one day barn exposure, increased protein expression but not activity of <i>N</i>-myristoyltransferase and calcineurin was shown. However, there is a need to identify the specific role of these two molecules in barn air induced lung inflammation. To conclude, animal models of barn exposure are useful tools to understand mechanisms of lung inflammation and AHR. However, there is still a need to examine endotoxin-independent nature of AHR and roles of other molecules of the innate immune system in regulating barn air induced effects.