Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data.

Measuring persistence in inflation: evidence for Angola

The purpose of this paper is to examine the degree of persistence in five inflation indicators for Angola, and to identify the implications for decision making. Our results suggest that when structural breaks are accounted for, all five inflation indicators are stationary. Second, our findings suggest that persistence is not too high. Moreover, the degree of persistence is similar among the five inflation indicators and throughout the sample period. Finally, our results also show that extracting the most volatile components of the headline inflation indicator does not generate a new inflation indicator that is less volatile and more persistent than the original. These results have important policy implications as the National Bank of Angola is preparing to change its monetary policy focus to a more inflation-targeting regime

A Retrospective Claims Analysis of Medication Adherence and Persistence Among Patients Taking Antidepressants for the Treatment of Major Depressive Disorder (MDD)

Thesis (Master's)--University of Washington, 2015

Home bias persistence in foreign direct investments

The purpose of this paper is to analyse the issues related to home bias and foreign direct investments (FDIs). We study the role of physical, cultural, and institutional distances from home on FDI decisions taken by corporations to assess whether the globalization of the past two decades has reduced their influence. Using the ‘home bias’ framework from the finance literature and the gravity model from the economics literature, we utilize a large sample of both developed and emerging markets, using FDI flows of 6263 unique bilateral country pairs over a 30-year period. We find strong empirical evidence of persistent home bias in FDI outflows, and we show that not only physical distance but also cultural and institutional similarities between host and source countries remain a decisive factor in foreign corporate investment decisions. We also show that such home bias is persistent over time and is observed around the world.

The Persistence of Memory

This paper analyzes several natural and man-made complex phenomena in the perspective of dynamical systems. Such phenomena are often characterized by the absence of a characteristic length-scale, long range correlations and persistent memory, which are features also associated to fractional order systems. For each system, the output, interpreted as a manifestation of the system dynamics, is analyzed by means of the Fourier transform. The amplitude spectrum is approximated by a power law function and the parameters are interpreted as an underlying signature of the system dynamics. The complex systems under analysis are then compared in a global perspective in order to unveil and visualize hidden relationships among them.

Testing for volatility persistence change: The effect of the credit crisis on the Portuguese banks

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

Leverage instability and persistence: Evidence from the United States and Europe

We find that leverage behavior both in level and time-series variation is very similar between the United States and Europe throughout the 1990-2013 period. Leverage regimes are simultaneously unstable and persistent for both regions. We define instability as the extent to which firms largely deviate from their long-term leverage mean, while persistence as the extent to which today’s leverage influences its future levels. We then show that this simultaneous evidence imply a mean-reversion behavior of leverage and discuss some of its implications for future research on this field.

Phenotypic heterogeneity of antigen-specific CD4 cells under different conditions of antigen persistence and antigen load

RESUME Nous n'avons pas de connaissance précise des facteurs à l'origine de l'hétérogénéité phénotypique des cellules T CD4 mémoires. Une troisième population phénotypique des cellules T CD4 mémoires, caractérisée par les marqueurs CD45RA+CCR7- a été identifiée dans cette étude. Cette population présente un état de différentiation avancée, comme en témoigne son histoire de réplication, ainsi que sa capacité de prolifération homéostatique. Les réponses des cellules T CD4 mémoires à différentes conditions de persistance et charge antigénique ont trois patterns phénotypiques différents, caractérisés par les marqueurs CD45RA et CCR7. La réponse CD4 mono -phénotypique CD45RA-CCR7+ ou CD45RA- CCR7- est associée à des conditions d'élimination de l'antigène (telle la réponse CD4 tétanos spécifique) ou à des conditions de persistance antigénique et de virémie élevée (telle la réponse HIV chronique ou la primo-infection CMV) respectivement. D'autre part, les réponses T CD4 multi -phénotypiques CD45RA-CCR7+ sont associées à des conditions d'exposition antigénique prolongée et de faible virémie (telles les infections CMV, EBV et HSV ou les infections HIV chez les long term non progressons). La réponse mono -phénotypique CD45RA- CCR7+ est propre aux cellules T CD4 secrétant de IL2, définies également comme centrales mémoires, la réponse CD45RA- CCR7- aux cellules T CD4 secrétant de l'IFNγ et finalement la réponse mufti-phénotypique aux cellules T CD4 secrétant à la fois de l'IL2 et de l' IFNγ. En conclusion, ces résultats témoignent d'une régulation de l'hétérogénéité phénotypique par l'exposition et la charge antigénique. ABSTRACT The factors responsible for the phenotypic heterogeneity of memory CD4 T cells are unclear. In the present study, we have identified a third population of memory CD4 T cells characterized as CD45RA+CCRT that, based on its replication history and the homeostatic proliferative capacity, was at an advanced stage of differentiation. Three different phenotypic patterns of memory CD4 T cell responses were delineated under different conditions of antigen (Ag) persistence and load using CD45RA and CCR7 as markers of memory T cells. Mono-phenotypic CD45RA'CCR7+ or CD45RA'CCR7' CD4 T cell responses were associated with conditions of Ag clearance (tetanus toxoid-specific CD4 T cell response) or Ag persistence and high load (chronic HIV-1 and primary CMV infections), respectively. Multi-phenotypic CD45RA CCR7+, CD45RA'CCRT and CD45RA+CCRT CD4 T cell responses were associated with protracted Ag exposure and low load (chronic CMV, EBV and HSV infections and HIV-1 infection in long-term nonprogressors). The mono-phenotypic CD45RA'CCR7+ response was typical of central memory (TCM) IL-2-secreting CD4 T cells, the mono-phenotypic CD45RA CCRT response of effector memory (TEM) IFN-γ -secreting CD4 T cells and the multi-phenotypic response of both IL-2- and IFN-γ -secreting cells. The present results indicate that the heterogeneity of different Ag-specific CD4 T cell responses is regulated by Ag exposure and Ag load.

Analyses, persistence an degradation of the synthetic pyrethroid insecticides permethrin and fenvalerate

Studies on persistence and degradation of the synthetic pyrethroid insecticides, permethrin and fenvalerate, were carried out under natural environmental conditions of the Niagara Peninsula. Permethrin and fenvalerate were treated on apple foliage atrat~s of 0.21 kg(AI)!ha and 0.14 kg(AI)/ha, respectively. The initial cis- and trans-permethrin spray deposits were found to be 13.5 ppm and 19.2 ppm, respectively and 38.0 ppm was observed for the fenvalerate treated sample. Twenty-three days and 84 days after spray application, permethrin residues were 4.0 ppm and 2.7 ppm for the cis-isomer, whereas they were 7.9 ppm and 4.7 ppm for the trans-isomer, respectively. Residues of fenvalerate 23 days and 84 days after spray application were 13.4 ppm and 8.0 ppm, respectively. The values of observed half-life of cis-permethrin, trans-permethrin and fenvalerate were found to be 42 days, 46 days and 51 days, respectively. Studies were extended to quantitatively determine some of the major degradation compounds of permethrin and fenvalerate, which were expected to be produced as results of ester cleavage of the parent compounds. A permethrin treated sample, 84 days after initial spray application, showed 0.25 and 0.8 ppm of cis- and trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylic acid (C12CA (18), respectively. These two acids were not found as free acids, but found as conjugated compounds. The other expected degradation compounds, 3-phenoxybenzyl alcohol (PBalc (~)),3-phenoxybenz.aldehyde (PBald (38)) and 2- (4-chlorophenyl) isovaleric acid (CPIA (31)) were not detected by the methods employed in this study. The results indicate that these degradation compounds were not present, or, if they were present, their concentrations were too low to detect by the methods used.

The identification, distribution and persistence of oxamyl and its degradation products in planted corn seed, seedling root and soil from oxamyl-treated corn seeds

A simple method was developed for treating corn seeds with oxamyl. It involved soaking the seeds to ensure oxamyl uptake, centrifugation to draw off excess solution, and drying under a stream of air to prevent the formation of fungus. The seeds were found to have an even distribution of oxamyl. Seeds remained fungus-free even 12 months after treatment. The highest nonphytotoxic treatment level was obtained by using a 4.00 mg/mL oxamyl solution. Extraction methods for the determination of oxamyl (methyl-N'N'-dimethyl-N-[(methylcarbamoyl)oxy]-l-thiooxamimidate), its oxime (methyl-N',N'-dimethyl-N-hydroxy-1-thiooxamimidate), and DMCF (N,N-dimethyl-1-cyanoformanade) in seed" root, and soil were developed. Seeds were processed by homogenizing, then shaking in methanol. Significantly more oxamyl was extracted from hydrated seeds as opposed to dry seeds. Soils were extracted by tumbling in methanol; recoveries range~ from 86 - 87% for oxamyl. Root was extracted to 93% efficiency for oxamyl by homogenizing the tissue in methanol. NucharAttaclay column cleanup afforded suitable extracts for analysis by RP-HPLC on a C18 column and UV detection at 254 nm. In the degradation study, oxamyl was found to dissipate from the seed down into the soil. It was also detected in the root. Oxime was detected in both the seed and soil, but not in the root. DMCF was detected in small amounts only in the seed.

Habit Formation and the Persistence of Monetary Shocks

This paper studies the persistent effects of monetary shocks on output. Previous empirical literature documents this persistence, but standard general equilibrium models with sticky prices fail to generate output responses beyond the duration of nominal contracts. This paper constructs and estimates a general equilibrium model with price rigidities, habit formation, and costly capital adjustment. The model is estimated via Maximum Likelihood using US data on output, the real money stock, and the nominal interest rate. Econometric results suggest that habit formation and adjustment costs to capital play an important role in explaining the output effects of monetary policy. In particular, impulse response analysis indicates that the model generates persistent, hump-shaped output responses to monetary shocks.

Explaining the Persistence of Commodity Prices

This paper extends the Competitive Storage Model by incorporating prominent features of the production process and financial markets. A major limitation of this basic model is that it cannot successfully explain the degree of serial correlation observed in actual data. The proposed extensions build on the observation that in order to generate a high degree of price persistence, a model must incorporate features such that agents are willing to hold stocks more often than predicted by the basic model. We therefore allow unique characteristics of the production and trading mechanisms to provide the required incentives. Specifically, the proposed models introduce (i) gestation lags in production with heteroskedastic supply shocks, (ii) multiperiod forward contracts, and (iii) a convenience return to inventory holding. The rational expectations solutions for twelve commodities are numerically solved. Simulations are then employed to assess the effects of the above extensions on the time series properties of commodity prices. Results indicate that each of the features above partially account for the persistence and occasional spikes observed in actual data. Evidence is presented that the precautionary demand for stocks might play a substantial role in the dynamics of commodity prices.

Tests GMM pour caractériser le biais de simultanéité de la persistence de volatilité.

Rapport de stage (maîtrise en finance mathématique et computationnelle)

Impact of type of drug insurance on adherence, persistence and costs of antidepressant drugs : a Quebec population-based study

Contexte: À date, il existe peu de données sur l’adhésion, la persistance et les coûts associés aux antidépresseurs selon le type d’assurance médicament (privé ou public). Objectif: Comparer selon le régime d’assurance médicament (privé ou public), l'adhésion, la persistance et les coûts des antidépresseurs. Méthodes de recherche: Une étude de cohorte appariée a été réalisée en utilisant des bases de données du Québec. Sujets: Nous avons sélectionné 194 patients assurés par un régime privé et 1923 patients assurés par le régime public de la Régie de l’assurance maladie du Québec (RAMQ) (18-64 ans) qui ont rempli au moins une ordonnance pour un antidépresseur entre décembre 2007 et septembre 2009. Mesures: L’adhésion, mesurée sur une période d’un an, a été estimée en utilisant le proportion of prescribed days covered (PPDC). Un modèle de régression linéaire a été utilisé afin d’estimer la différence moyenne en PPDC entre les patients assurés par un régime privé et ceux assurés par le régime public de la RAMQ. La persistance a été comparé entre ces deux groupes avec un modèle de régression de survie Cox, et le coût mensuel d'antidépresseurs ($ CAN) a été comparé entre ces deux groupes en utilisant un modèle de régression linéaire. Résultats: Le PPDC parmi les patients assurés par un régime privé était de 86,4% (intervalle de confiance (IC) 95%: 83,3%-89,5%) versus 81,3% (IC 95%: 80,1%-82,5%) pour les patients assurés par le régime public de la RAMQ, pour une différence moyenne ajustée de 6,7% (IC 95%: 3,0%-10,4%). La persistance après un an parmi les patients assurés par un régime privé était de 49,5% versus 18,9% pour les patients assurés par le régime public de la RAMQ (p <0,001), et le rapport de risque ajusté était de 0,48 (IC 95%: 0,30-0,76). Comparativement aux patients assurés par le régime public de la RAMQ, les patients ayant une assurance privée ont payé 14,94 $ CAD (95% CI: $12,30-$17,58) de plus par mois en moyenne pour leurs antidépresseurs. Conclusion: Les patients assurés par un régime privé avaient une meilleure adhésion, persistance, mais avaient aussi un plus haut coût pour leurs antidépresseurs que ceux assurés par le régime public de la RAMQ. Cette différence de coûts peut être due aux différentes exigences de paiement en pharmacie entre les deux régimes ainsi qu’aux limites des honoraires des pharmaciens imposés par le régime public.

Impact of pesticides on indicator and pathogenic microorganism persistence under laboratory and field conditions

On s’intéresse aux impacts des pesticides sur la microflore des plantes surtout dans le contexte des légumes contaminés par des agents pathogènes. Le but de cette étude est d'évaluer l'impact de certains pesticides sur la persistance de micro-organismes indicateurs et pathogènes. En laboratoire, la persistance d’E. coli et de Salmonella en présence de quatre pesticides (Ripcord 400EC, Copper 53W, Bioprotec CAF, Serenade MAX) a été étudiée. Les plaques de Pétrifilm et le milieu sélectif XLD sont utilisés pour énumérer les populations d’E. coli et de Salmonella. Il a été démontré que le Serenade MAX favorisait la croissance microbienne, le Bioprotec CAF et le Ripcord 400EC soutenaient la survie microbienne et le Copper 53W inhibait la croissance, à la fois d’E. coli et de Salmonella. En conditions terrain, Ripcord 400EC, Copper 53W, Bioprotec CAF ont été étudiés sur une culture de brocoli irriguée avec de l'eau expérimentalement contaminée par E. coli. Dans tous les traitements, un impact de l’irrigation a été observé sur les populations de levures et de moisissures (diminution) et les bactéries aérobies totales (augmentation). Une prévalence supérieure d’E. coli a été observée dans les parcelles traitées avec le Bioprotec CAF comparativement aux traitements au Copper 53W, ce qui est en accord avec les résultats observés lors de l'essai en laboratoire. Cependant, l'analyse statistique n'a montré aucune différence significative entre les traitements appliqués. Les effets directs des pesticides sur les micro-organismes sont confirmés dans des conditions de laboratoire mais demeurent méconnus dans les conditions expérimentales au champ.