Background Idiopathic pulmonary fibrosis (IPF) is a devastating form of chronic lung injury of unknown aetiology characterised by progressive lung scarring. A diagnosis of definite IPF requires High Resolution Computed Tomography (HRCT) appearances indicative of usual interstitial pneumonia (UIP), or in patients with 'possible UIP' CT appearances, histological confirmation of UIP. However the proportion of such patients that undergo SLB varies, perhaps due to a perception of risk of biopsy and additive diagnostic value of biopsy in individual patients. We hypothesised that an underlying UIP pathological pattern may result in increased risk of death and aimed to explore this by comparing the risk of SLB in suspected idiopathic interstitial pneumonia, stratified according to HRCT appearance. Additionally we sought to determine the positive-predictive value of biopsy to diagnose IPF in patients with 'possible UIP HRCT' in our population. In patients with possible UIP who are not biopsied, the clinical value of bronchoalveolar lavage (BAL) is uncertain. We aimed to prospectively study the diagnostic and prognostic value of BAL differential cell count (DCC) in suspected IPF and determine the feasibility of repeat BAL and the relationship between DCC and disease progression in two successive BALs. We hypothesised that BAL DCC between definite and possible IPF was different and that baseline DCC and change in BAL DCC predicted disease progression. Alveolar macrophages (AMs) are an integral part of the lung's reparative mechanism following injury, however in IPF they contribute to pathogenesis by releasing pro-fibrotic mediators promoting fibroblast proliferation and collagen deposition. Expansion of novel subpopulations of pulmonary monocyte-like cells (PMLCs) has been reported in inflammatory lung disease. We hypothesised that a distinct AM polarisation phenotype would be associated with disease progression. We aimed to perform detailed phenotyping of AM and PMLCs in BAL in IPF patients. Several prognostic scoring systems and biomarkers have been described to predict disease progression in IPF but most were derived from clinical trial patients or tertiary referral centres and none have been validated in separate cohorts. We aimed to identify a predictive tool for disease progression utilising physiological, HRCT and serum biomarkers in a unique population of incident treatment naïve IPF patients. Methods Between 01/01/07 and 31/12/13, 611 consecutive incident patients with suspected idiopathic interstitial pneumonia (IIP) presented to the Edinburgh lung fibrosis clinic. Of these patients 222 underwent video-assisted thoracoscopic lung biopsy and histological pattern was determined according to ATS/ERS criteria. Post-operative mortality and complication rates were examined. Fewer than 2% received IPF-directed therapy and less than 1% of the cohort were lost to follow-up. Disease progression was defined as death or ≥10% decline in VC within 12 months of BAL. Cells were obtained by BAL and a panel of monoclonal antibodies; CD14, CD16, CD206, CD71, CD163, CD3, CD4, CD8 and HLA-DR were used to quantify and selectively characterise AMs, resident PMLCs, inducible PMLCs, neutrophils and CD4+/CD8+ T-cells using flow cytometry. Classical, intermediate and non-classical monocyte subsets were also quantified in peripheral blood. Potential biomarkers (n=16) were pre-selected from either previously published studies of IPF biomarkers or our hypothesis-driven profiling. Linear logistic regression was used on each predictor separately to assess its importance in terms of p-value of the associated weight, and the top two variables were used to learn a decision tree. Results Based on the 2011 ATS/ERS criteria, 87 patients were categorised as 'definite UIP', of whom 3 underwent SLB for clinical indications. IPF was confirmed in all 3 patients based on 2013 ATS/ERS/JRS/ALAT diagnostic criteria. 222 patients were diagnosed with 'possible UIP'; 55 underwent SLB, IPF was subsequently diagnosed in 37 patients, 4 were diagnosed with 'probable IPF' and 14 were considered 'not IPF'. In this group, 30 patients were aged 65 years or over and 25/30 (83%) had UIP on biopsy. 306 patients had HRCTs deemed 'inconsistent with UIP', SLB was performed in 168 patients. Post6 operative 30-day mortality was 2.2% overall, and 7.3% in the 'possible UIP' HRCT group. Patients with 'definite IPF' based on HRCT and SLB appearances had significantly better outcomes than patients with 'definite UIP' on HRCT alone (P=0.008, HR 0.44 (95% CI 0.240 to 0.812)). BAL DCC was not different between definite and possible UIP groups, but there were significant differences with the inconsistent with UIP group. In the 12 months following BAL, 33.3% (n=7/21) of patients in the definite UIP group and 29.5% (n=18/61) in the possible UIP group had progressed. There were no significant differences in BAL DCC between progressor and non-progressor groups. Mortality in patients with suspected IPF and a BAL DCC consistent with IPF was no different to those with a DCC inconsistent with IPF (P=0.425, HR 1.590 (95% CI 0.502 to 4.967)). There was no difference in disease progression in either group (P=0.885, HR 1.081 (95% CI 0.376 to 3.106)). There was no statistically significant difference in BAL DCC at 0 and 12 months in either group. There was no significant change in DCC between 0 and 12 month BALs between progressors and non-progressors. Repeat BAL was well tolerated in almost all patients. There was 1 death within 1 month of a first BAL and 1 death within 1 month of a second BAL; both were considered 'probably procedure-related'. AM CD163 and CD71 (transferrin receptor) expression were significantly different between groups (P < 0.0001), with significant increases in the IPF group vs non fibrotic ILD (P < 0.0001) and controls (P < 0.0001 and P < 0.001 respectively). CD71 expression was also significantly increased in the IPF progressor vs non-progressor group (P < 0.0001) and patients with high CD71 expression had significantly poorer survival than the CD71low group (P=0.040, median survival 40.5 and 75.6 months respectively). CD206 (mannose receptor) expression was also significantly higher in the IPF progressor vs non-progressor group (P=0.034). There were no differences in baseline BAL neutrophil, eosinophil or lymphocyte percentages between IPF progressor or non-progressor groups. The percentage of rPMLCs was significantly increased in BAL fluid cells of IPF patients compared to those with non-fibrotic ILD (P < 0.0001) and healthy controls (P < 0.05). Baseline rPMLC percentage was significantly higher in IPF progressors vs IPF non-progressors (P=0.011). Baseline BAL iPMLC:rPMLC ratio was also significantly different between IPF progressor and non-progressor groups (P=0.011). Disease progression was confidently predicted by a combination of clinical and serological variables. In our cohort we identified a predictive tool based on two key parameters, one a measure of lung function and one a single serum biomarker. Both parameters were entered into a decision tree, and when applied to our cohort yielded a sensitivity of 86.4%, specificity of 92.3%, positive predictive value of 90.5% and negative predictive value of 88.9%. We also applied previously reported predictive tools such as the GAP Index, du Bois score and CPI Index to the Edinburgh IPF cohort. Conclusions SLB can be of value in the diagnosis of ILD, however perhaps due to the perceived risks associated with the procedure, only a small percentage of patients undergo SLB despite recommendations that patients have histological confirmation of the diagnosis. Advanced age is a strong predictor for IPF, and in our cohort 83% of patients aged over 65 years with 'possible UIP' HRCT appearances, had UIP on biopsy. BAL and repeat BAL in IPF is feasible and safe (< 1.5% mortality). Of those that underwent repeat BAL, disease progression was not associated with a change in DCC. However, 22% of lavaged patients died or were deemed too frail to undergo a second procedure at 12 months. These data emphasise the importance of BAL in identifying a novel human AM polarisation phenotype in IPF. Our data suggests there is a distinct relationship between AM subtypes, cell-surface expression markers, PMLC subpopulations and disease progression in IPF. This may be utilised to investigate new targets for future therapeutic strategies. / Disease progression in IPF can be predicted by a combination of clinical variables and serum biomarker profiling. We have identified a unique prediction model, when applied to our locally referred, incident, treatment naïve cohort can confidently predict disease progression in IPF. IPF is a heterogeneous disease and there is a definite clinical need to identify 'personalised' prognostic biomarkers which may in turn lead to novel targets and the advent of personalised medicines.

<p>Det här examensarbetet presenterar en evaluering av en <em>Klockkorrigerare av klockpulsbredd</em>. Den består främst av en korrigerare av klockpulsbredd (<em>Duty Cycle Corrector DCC</em>) och även en fördröjningslåst loop (<em>Delayed Locked Loop </em><em>DLL</em>). Det finns många olika korrigerare av klockpulsbredden designade förut, de två populäraste arkitekturerna då har varit enkel eller dubbel återkopplings loop. Den huvudsakliga skillnaden mellan dem är att enkel återkopplings loop använder sig av en öppen loop medan den dubbla varianten istället har en stängd loop. I det här projektet kommer en ny arkitektur att presenteras. Konceptet i den nya designen är att dela upp korrigeraren av klockpulsbredden i två delar, en korrigerare och en detektor. Detektorn får utsignalen från den fördröjningslåsta loopen som insignal och talar om för korrigeraren via två utsignaler ifall signalen behöver justeras. Detektorn är uppdelad i två likadana fördröjningselement, som båda är klockade av utsignalen och dess invers från den fördröjningslåsande loopen, fast i omvänd ordning. Det här gör det möjligt att avgöra om klockpulsbredden av signalen är över eller under 50 %. Om så är fallet kommer den att justeras av korrigeraren för att sedan skickas som insignal till den fördröjningslåsande loopen.</p><p>Abstraktionsnivån för det här projektet har varit systemnivå, detta för att kunna vara riktigt säker på att arkitekturen verkligen fungerar innan ett riktigt chip tillverkas. Tips på framtida projekt är att gå vidare till schemanivå för att slutligen göra en implementering och mätningar på ett riktigt chip av den här <em>Klockkorrigeraren av klockpulsbredd </em>när det är känt att idén fungerar.</p><p> </p>

Neuronal networks are the central functional units of the nervous system. Knowledge about the identity of participating neurons and the assembly of these during development is crucial for the understanding of CNS function. A promising system to dissect the development and functionalities of a neuronal network is the central pattern generator (CPG) for locomotion. We used screening approaches to identify spinal neuronal subpopulations by their specific gene expression, potentially involved in CPG function. Amongst others we found paired-like homeodomain transcription factor 2 (Pitx2) as a cholinergic interneuron marker for partition cells, with a possible role in the spinal network for locomotion. In addition, we present two genes, Chondrolectin (Chodl) and Estrogen-related receptor beta (ERRβ) as novel markers for fast and slow motor neurons, respectively. The neuronal components of the CPG integrate three key functions; rhythm generation, ipsilateral flexors/extensors coordination and bilateral coordination over the midline. Commissural interneurons (CINs) are considered to participate in the latter. During development axons are guided to their targets by the help of axon guidance molecules. Netrin-1 and its receptor DCC (Deleted in Colorectal Cancer) have been shown to play an important role for spinal cord neurons in axon-pathfinding and migration towards the midline. We show that loss of netrin-1 functionally results in a switch from alternating to synchronous left-right locomotor activity and deletion of DCC surprisingly leads to a different phenotype, best described as uncoordination. Thus, during development, netrin-1 and DCC play a critical role for the establishment of a functional balanced CPG. Further we show a selective loss of CINs, predominantly from dorsally originating subtypes, not affecting the ventral-most V3 subtype in netrin-1 mutant mice, but a loss of CINs from all progenitor domains in Dcc mutant mice. Together, our data suggest a netrin-1-independent mechanism for DCC in axon guidance and a role of the most ventral originating CINs as part of the neuronal network controlling synchronous activities over the midline. Another pair of axon guidance molecules, EphA4 and ephrinB3, has been shown to cooperate in preventing ipsilateral interneurons from crossing the spinal midline and if either molecule is deleted in mice, this will result in a defect in left-right coordination of locomotion. We provide in vivo and in vitro evidence that the GTPase-activating protein α2-chimerin, as a downstream molecule of EphA4 signaling, is essential in axon guidance decisions involved in the correct formation of the spinal circuitry for locomotion.

Det här examensarbetet presenterar en evaluering av en Klockkorrigerare av klockpulsbredd. Den består främst av en korrigerare av klockpulsbredd (Duty Cycle Corrector DCC) och även en fördröjningslåst loop (Delayed Locked Loop DLL). Det finns många olika korrigerare av klockpulsbredden designade förut, de två populäraste arkitekturerna då har varit enkel eller dubbel återkopplings loop. Den huvudsakliga skillnaden mellan dem är att enkel återkopplings loop använder sig av en öppen loop medan den dubbla varianten istället har en stängd loop. I det här projektet kommer en ny arkitektur att presenteras. Konceptet i den nya designen är att dela upp korrigeraren av klockpulsbredden i två delar, en korrigerare och en detektor. Detektorn får utsignalen från den fördröjningslåsta loopen som insignal och talar om för korrigeraren via två utsignaler ifall signalen behöver justeras. Detektorn är uppdelad i två likadana fördröjningselement, som båda är klockade av utsignalen och dess invers från den fördröjningslåsande loopen, fast i omvänd ordning. Det här gör det möjligt att avgöra om klockpulsbredden av signalen är över eller under 50 %. Om så är fallet kommer den att justeras av korrigeraren för att sedan skickas som insignal till den fördröjningslåsande loopen. Abstraktionsnivån för det här projektet har varit systemnivå, detta för att kunna vara riktigt säker på att arkitekturen verkligen fungerar innan ett riktigt chip tillverkas. Tips på framtida projekt är att gå vidare till schemanivå för att slutligen göra en implementering och mätningar på ett riktigt chip av den här Klockkorrigeraren av klockpulsbredd när det är känt att idén fungerar.

Les nétrines sont une petite famille de protéines de guidage axonal qui peuvent attirer des axones ou en repousser d’autres lors du développement neuronal. Lors du développement de la rétine, les axones des cellules ganglionnaires de la rétine (CGR) sont attirés vers une source de nétrines au niveau du disque optique leur permettant de quitter la rétine et de former le nerf optique. Afin de pouvoir caractériser le rôle des nétrines dans le système visuel adulte, nous avons investigué l’expression des nétrines et leurs récepteurs dans la rétine de souris adulte. Alors qu’aucune expression de la nétrine-1 n’a été détectée dans la rétine adulte, l’expression de la nétrine-3 a été abondamment détectée au niveau des CGR et des cellules amacrines. Nous démontrons aussi que les récepteurs des nétrines sont exprimés dans la rétine adulte. Alors que DCC semble être confiné au niveau des axones des CGR, néogénine est retrouvé dans les dendrites des CGR et des cellules horizontales. Quant aux protéines de la famille des récepteurs homologues à UNC-5, UNC5B a été détecté dans les somas des CGR et UNC5C dans les cellules de Müller. La découverte que nétrine-3 et ses récepteurs sont abondamment exprimés dans plusieurs types cellulaires de la rétine adulte leur suggère un rôle dans le fonctionnement du système visuel mature. / The netrins are a small family of axonal guidance proteins that can attract or repulse growing axons during neural development. During development of the retina, retinal ganglion cells (RGCs) axons are attracted by a netrin source at the optic disc that permits them to exit the retina and form the optic nerve. To characterise the role of netrins in the adult visual system, we investigated the expression of netrins and their receptors in the adult mouse retina. While expression of netrin-1 has not been detected in the adult retina, netrin- 3 has been abundantly found in RGCs amacrine cells. We also demonstrate that netrin receptors are expressed in the adult retina. DCC was found to be restricted in RGCs axons and neogenin in dendrites of RGCs and horizontal cells. UNC5B proteins were detected at RGC soma and UNC5C proteins in the Müller cells. The finding that netrin-3 and its receptors are abundantly expressed in many cell types of the adult retina suggests a funtional role for them in the mature visual system.

本研究選取台灣加權股價指數、日經225股價指數、南韓綜合股價指數、新加坡海峽指數以及香港恆生指數，從1990年1月5日至2004年12月31日之指數收盤週資料，利用動態條件相關係數（DCC）模型來探討台灣、日本、南韓、新加坡以及香港股票市場間相關係數的動態過程。經由實證本研究歸納結論如下三點： 一、台灣、日本、南韓、新加坡以及香港五個國家股價指數兩兩間的相關係數是會波動的，如同指數在不同時點因事件發生的條件不同而波動一樣，相關係數亦會隨時間點事件發生的條件而改變，不若常數條件相關係數只為固定正值，且受選取時間區間的影響。 二、五個國家由於政經發展相似，且地理與文化背景亦相近，相關係數除台灣－日本、台灣－新加坡以及日本－香港在某些時點為負值外，其餘任何時點皆為正數，與直覺相符。此外，由圖形直觀之，我們發現新加坡－香港的連動程度最高，且除台灣－日本的走勢波動較大而不明顯外，其餘動態相關係數的走勢和緩，在某些時段下還有明顯的趨勢，因此若機構投資人在投資此一區域時，能考量此一趨勢的存在，將能更有效率的運用投資基金；而發行標的為此五個國家股價指數的衍生性金融商品時，發行機構將能更有效的規避風險。 三、現代投資學倡導投資組合管理，其中心理念是藉由資產間的負相關，使得投資報酬不會因非系統風險而降低，對個股而言，指數投資即為分散非系統風險的方法之一；然對區域而言，分散投資個別國家才能達到投資組合最佳化。我們以1997、1998年亞洲金融風暴一例觀察，雖然亞洲金融風暴對亞洲國家而言是全面的，為不可分散的系統風險之一，但由於亞洲各國發生金融危機的時間點不同，因此由圖形中我們可以看出，在亞洲金融風暴時，五個國家股價指數的動態相關係數反而迅速降低，因此投資此五個國家符合資產配置最佳。

La netrine-1 joue un rôle important en tant qu’un élément de guidance pour la croissance axonale au début du développement du système nerveux central. Des études récentes ont démontré une expression de la netrin-1 dans le cerveau antérieur adulte, où elle régule la fonction synaptique et la plasticité dans les neurones corticaux. Cependant, la contribution de la netrine-1 dans la rétine adulte reste encore inconnue. Le but de cette étude est donc de caractériser l'expression de la netrine-1 dans la rétine des souris adultes sauvages (rétine intacte) et malades (rétine blessée). L'expression rétinéene de la netrine-1 et de son récepteur, supprimée dans le cancer colorectal (DCC), a été déterminée, à partir des immunobuvardages, chez des souris post-natales de jour 0 (P0), P14 et adultes. Le recours au double marquage de la netrine-1 avec un anticorps spécifique contre RBPMS, un marqueur sélectif pour les cellules ganglionnaires de la rétine (RGC), a permis l’identification de sa localisation sur les sections transversales de rétine. De plus, les niveaux de netrin-1 ont également été quantifiés à trois et sept jours après l'axotomie du nerf optique. Nous avons démontré que la netrine-1 et DCC sont fortement exprimés dans la rétine à P0, toutefois l’expression de netrin-1 est relativement stable pendant le développent alors que l’expression de DCC est remarquablement réduite à l'âge adulte. De plus, ces expériences ont conclu une expression robuste de la netrin-1 dans le soma RGC adulte et, une expression des récepteurs DCC autour du corps cellulaire. Fait important, nous avons aussi pu démontrer que les niveaux d’expressions de la netrine-1 et DCC sont réduits à trois et sept jours suivant l'axotomie du nerf optique. Cependant, la surexpression de la protéine netrin-1 n'a pas eu un effet significatif sur la survie du RGC par rapport aux témoins injectés par un véhicule. Les résultats obtenus suggèrent que : (i) la netrine-1 est abondamment exprimée dans la rétine néonatale et subit une diminution importante à l'âge adulte, (ii) la netrine-1 et son récepteur DCC sont présents dans les RGC et, (iii) l'expression de la netrine-1 diminue considérablement suite à une lésion axonale. Ensemble, ces résultats suggèrent un rôle pour la netrin-1 dans le système visuel chez les adultes. / Netrin-1 plays a highly-conserved role as a guidance cue directing axonal growth during the early stages of central nervous system development. Recent data has shown that netrin-1 is continued to be expressed in the adult forebrain where it regulates synaptic function and plasticity in cortical neurons. However, the contribution of netrin-1 in the adult retina remains unknown. The purpose of this study was to characterize the expression of netrin-1 in the intact and injured adult mouse retina. The retinal expression of netrin-1 and its receptor, deleted in colorectal cancer (DCC), was examined at postnatal day 0 (P0), P14, and adult mice using western blots. Double labeling of netrin-1 with an antibody against RBPMS, a selective marker for retinal ganglion cells (RGCs), was used to determine its location on retinal cross-sections. Netrin-1 levels were also quantified at 3 and 7 days after optic nerve axotomy. We demonstrate that netrin-1 and DCC are abundantly and widely expressed in the retina at P0, but although the expression level of netrin-1 remains relatively stable during development, the expression level of DCC is markedly downregulated in adulthood. Adult RGC soma were shown to be endowed with robust netrin-1 expression. DCC receptors were also found to be expressed around the cell body. Importantly, we show that netrin-1 and DCC levels are further downregulated at 3 and 7 days after optic nerve axotomy. However, the over-expression of netrin-1 protein failed to exert any significant effect on RGC survival in comparison to vehicle-injected controls. Our data support that: 1) netrin-1 is abundantly expressed in the neonatal retina and undergoes marked downregulation in adulthood, 2) netrin-1 and DCC are present in RGCs, 3) netrin-1 expression decreases rapidly after axonal injury. Together, these results suggest a role for netrin-1 in the mature visual system.

This master thesis deals with extension of the univariate GARCH model to multivari- ate models. We present individual models and deal with methods of their estimation. Then we describe some statistical tests for diagnosting the models. We have programmed in the statistical software R one of them - the Ling-Li test. Afterwards we apply selected models to real data of stock market index S&P 500, stock market index Russell 2000 and stocks of crude oil. For the GO-GARCH model, we compare all available estimation methods and show their differences. Then we compare the results of all models with each other and also with univariate models in terms of estimates of conditional variances, estimates of conditional correlations and also in terms of computational complexity. 1

Axon guidance receptors such as deleted in colorectal cancer (DCC) contribute to the normal formation of neural circuits, and their mutations can be associated with neural defects. In humans, heterozygous mutations in have been linked to congenital mirror movements, which are involuntary movements on one side of the body that mirror voluntary movements of the opposite side. In mice, obvious hopping phenotypes have been reported for bi-allelic mutations, while heterozygous mutants have not been closely examined. We hypothesized that a detailed characterization of heterozygous mice may reveal impaired corticospinal and spinal functions. Anterograde tracing of the motor cortex revealed a normally projecting corticospinal tract, intracortical microstimulation (ICMS) evoked normal contralateral motor responses, and behavioral tests showed normal skilled forelimb coordination. Gait analyses also showed a normal locomotor pattern and rhythm in adult mice during treadmill locomotion, except for a decreased occurrence of out-of-phase walk and an increased duty cycle of the stance phase at slow walking speed. Neonatal isolated spinal cords had normal left-right and flexor-extensor coupling, along with normal locomotor pattern and rhythm, except for an increase in the flexor-related motoneuronal output. Although mice do not exhibit any obvious bilateral impairments like those in humans, they exhibit subtle motor deficits during neonatal and adult locomotion.

Background: With the tremendous growth of the Green Bond (GB) market, understanding the relationship of the GB market with other financial markets gains importance. The Covid19 pandemic causing a recession in most major economies creates an opportunity to see the co-movements of the GB market with other financial markets under a period of economic crisis. Purpose: This study aims to use the economic contraction catalyzed by the 2020’s Covid-19 pandemic as a means to investigate the co-movements between the GB and the treasury bond, corporate bond, stock, and carbon markets during an economic recession. Through this, we intend to find if co-movements of the GB market have changed, and if so, how. Method: As the collected data is time-series data, Augmented Dickey-Fuller and Ljung-Box tests are utilized for preliminary testing. Thereafter, a univariate-GARCH model is used for volatility modeling. Moreover, the DCC-GARCH model has been conducted to determine the co-movements between the markets. Conclusion: The results of the study show that in the case of GB, treasury, and corporate bond markets, no considerable changes were observed in the co-movement among the two different sample periods. Moving to the stock and GB markets, it was found that the co-movement increased at the beginning of the crisis. However, for the whole crisis period, no substantial changes can be seen in comparison to the pre-crisis period. Furthermore, the co-movement between the two markets was found to be weak in general. Moving on to the results obtained for GB and carbon markets, at the start of the crisis, a sharp fall can be observed. When compared to the pre-crisis period, the co-movement showed a slight increase, yet very weak. Furthermore, it was observed that the co-movement between the two markets has been weak during the whole sample period.