Adaptive Markov chain Monte Carlo and Bayesian filtering for state space models

This thesis is concerned with the state and parameter estimation in state space models. The estimation of states and parameters is an important task when mathematical modeling is applied to many different application areas such as the global positioning systems, target tracking, navigation, brain imaging, spread of infectious diseases, biological processes, telecommunications, audio signal processing, stochastic optimal control, machine learning, and physical systems. In Bayesian settings, the estimation of states or parameters amounts to computation of the posterior probability density function. Except for a very restricted number of models, it is impossible to compute this density function in a closed form. Hence, we need approximation methods. A state estimation problem involves estimating the states (latent variables) that are not directly observed in the output of the system. In this thesis, we use the Kalman filter, extended Kalman filter, Gauss–Hermite filters, and particle filters to estimate the states based on available measurements. Among these filters, particle filters are numerical methods for approximating the filtering distributions of non-linear non-Gaussian state space models via Monte Carlo. The performance of a particle filter heavily depends on the chosen importance distribution. For instance, inappropriate choice of the importance distribution can lead to the failure of convergence of the particle filter algorithm. In this thesis, we analyze the theoretical Lᵖ particle filter convergence with general importance distributions, where p ≥2 is an integer. A parameter estimation problem is considered with inferring the model parameters from measurements. For high-dimensional complex models, estimation of parameters can be done by Markov chain Monte Carlo (MCMC) methods. In its operation, the MCMC method requires the unnormalized posterior distribution of the parameters and a proposal distribution. In this thesis, we show how the posterior density function of the parameters of a state space model can be computed by filtering based methods, where the states are integrated out. This type of computation is then applied to estimate parameters of stochastic differential equations. Furthermore, we compute the partial derivatives of the log-posterior density function and use the hybrid Monte Carlo and scaled conjugate gradient methods to infer the parameters of stochastic differential equations. The computational efficiency of MCMC methods is highly depend on the chosen proposal distribution. A commonly used proposal distribution is Gaussian. In this kind of proposal, the covariance matrix must be well tuned. To tune it, adaptive MCMC methods can be used. In this thesis, we propose a new way of updating the covariance matrix using the variational Bayesian adaptive Kalman filter algorithm.

Characterization of the phosphorylation of thylakoid membrane proteins from cyanobacterium synechococcus sp. PCC 6301 in light state 1 and light state 2

The distribution of excitation energy between the two photosystems (PSII and PSI) of photosynthesis is regulated by the light state transition. Three models have been proposed for the mechanism of the state transition in phycobilisome (PBS) containing organisms, two involving protein phosphorylation. A procedure for the rapid isolation of thylakoid membranes and PBS fractions from the cyanobacterium Synechococcus m. PCC 6301 in light state 1 and light state 2 was developed. The phosphorylation of thylakoid and soluble proteins rapidly isolated from intact cells in state 1 and state 2 was investigated. 77 K fluorescence emission spectra revealed that rapidly isolated thylakoid membranes retained the excitation energy distribution characteristic of intact cells in state 1 and state 2. Phosphoproteins were identified by gel electrophoresis of both thylakoid membrane and phycobilisome fractions isolated from cells labelled with 32p orthophosphate. The results showed very close phosphoprotein patterns for either thylakoid membrane or PBS fractions in state 1 and state 2. These results do not support proposed models for the state transition which required phosphorylation of PBS or thylakoid membrane proteins.

Characterization of the state transition in the cyanobacterium synechococcus sp. 7002 and a phycobilisome-less Mutant

ABSTRACT Photosynthetic state transitions were investigated in the cyanobacterium Synechococcus sp. PCC 7002 in both wild-type cells and mutant cells lacking phycobilisomes. Preillumination in the presence of DCMU (3(3,4 dichlorophenyl) 1,1 dimethyl urea) induced state 1 and dark adaptation induced state 2 in both wild-type and mutant cells as determined by 77K fluorescence emission spectroscopy. Light-induced transitions were observed in the wildtype after preferential excitation of phycocyanin (state 2) or preferential excitation of chlorophyll .a. (state 1). The state 1 and 2 transitions in the wild-type had half-times of approximately 10 seconds. Cytochrome f and P-700 oxidation kinetics could not be correlated with any current state transition model as cells in state 1 showed faster oxidation kinetics regardless of excitation wavelength. Light-induced transitions were also observed in the phycobilisomeless mutant after preferential excitation of short wavelength chlorophyll !l. (state 2) or carotenoids and long wavelength chlorophyll it (state 1). One-dimensional electrophoresis revealed no significant differences in phosphorylation patterns of resolved proteins between wild-type cells in state 1 and state 2. It is concluded that the mechanism of the light state transition in cyanobacteria does not require the presence of the phycobilisome. The results contradict proposed models for the state transition which require an active role for the phycobilisome.

Investigating the effects of arousal state on cognitive performance in individuals with and without mild head injury

We examined the cognitive and emotional sequelae following mild head injury (MHI; e.g., concussion) in high-functioning individuals and whether persons with MHI pre~ent, both physiologically and via self-report, in a manner different from (i.e., underaroused) that of persons who have no history of head injury. We also investigated the effect arousal state ~as on the cognitive performance of this population. Using a quasiexperimental research design (N = 91), we examined changes in attention, working memory, and cognitive flexibility (subtests ofthe WAIS-III, 1997,WMS-III, 1997, & DKEFS, 2002) as a function of manipulated arousal (i.e., induced psychosocial stress/activation; reduced activation/relaxation). In addition to self-reported arousal and state anxiety (State-Trait Anxiety Inventory; Speilberger, 1983a) measures, physiological indices of arousal state (i.e., electrodermal responsivity, heart rate, and respiration activity) were recorded (via Polygraph Professional Suite, 2008) across a 2.5 hour interval while completing various cognitive tasks. Students also completed the Post-concussive Symptom Checklist (Gouvier et aI., 1992). The results demonstrate that university students who report a history ofMHI (i.e., "altered state of consciousness") experience significantly lower levels of anxiety, were physiologically underaroused, and were less responsive to stressors in their environment, compared to their non-~HI cohorts. As expected, cognitive flexibility (but not other neuropsychological measures of cognition) was advantaged with increased stress, and disadvantaged with reduced stress, in persons with reported MHI, but not for those without reported MHI which provided limited support for our hypothesis. Further, university students who had no complaints related to their previous MHI endorsed a greater number of traditional post-concussive symptoms in terms of intensity, duration and frequency as compared to students who did not report a MHI. The underarousal in traumatic brain injury has been associated with (ventromedial prefrontal cortex) VMPFC disruption and may be implicated in MHI generally. Students who report sustaining a previous MHI may be less able to physiologically respond and/or cognitively appraise, stressful experiences as compared to their no-MHI cohort and experience persistent, long-lasting consequences despite the subtle nature of a history of head injury.

Higher Education Governance in Vietnam: University Action, the State and Changing Relationships

Diese Dissertation stellt eine Studie da, welche sich mit den Änderungen in der Governance der Hochschulbildung in Vietnam beschäftigt. Das zentrale Ziel dieser Forschungsarbeit ist die Untersuchung der Herkunft und Änderung in der Beziehung der Mächte zwischen dem vietnamesischen Staat und den Hochschulbildungsinstituten (HI), welche hauptsächlich aus der Interaktion dieser beiden Akteure resultiert. Die Macht dieser beiden Akteure wurde im sozialen Bereich konstruiert und ist hauptsächlich durch ihre Nützlichkeit und Beiträge für die Hochschulbildung bestimmt. Diese Arbeit beschäftigt sich dabei besonders mit dem Aspekt der Lehrqualität. Diese Studie nimmt dabei die Perspektive einer allgemeinen Governance ein, um die Beziehung zwischen Staat und HI zu erforschen. Zudem verwendet sie die „Resource Dependence Theory“ (RDT), um das Verhalten der HI in Bezug auf die sich verändernde Umgebung zu untersuchen, welche durch die Politik und eine abnehmende Finanzierung charakterisiert ist. Durch eine empirische Untersuchung der Regierungspolitik sowie der internen Steuerung und den Praktiken der vier führenden Universitäten kommt die Studie zu dem Schluss, dass unter Berücksichtigung des Drucks der Schaffung von Einkommen die vietnamesischen Universitäten sowohl Strategien als auch Taktiken entwickelt haben, um Ressourcenflüsse und Legitimität zu kontrollieren. Die Entscheidungs- und Zielfindung der Komitees, die aus einer Mehrheit von Akademikern bestehen, sind dabei mächtiger als die der Manager. Daher werden bei initiativen Handlungen der Universitäten größtenteils Akademiker mit einbezogen. Gestützt auf die sich entwickelnden Muster der Ressourcenbeiträge von Akademikern und Studierenden für die Hochschulbildung prognostiziert die Studie eine aufstrebende Governance Konfiguration, bei der die Dimensionen der akademischen Selbstverwaltung und des Wettbewerbsmarktes stärker werden und die Regulation des Staates rational zunimmt. Das derzeitige institutionelle Design und administrative System des Landes, die spezifische Gewichtung und die Koordinationsmechanismen, auch als sogenanntes effektives Aufsichtssystem zwischen den drei Schlüsselakteuren - der Staat, die HI/Akademiker und die Studierenden – bezeichnet, brauchen eine lange Zeit zur Detektion und Etablierung. In der aktuellen Phase der Suche nach einem solchen System sollte die Regierung Management-Tools stärken, wie zum Beispiel die Akkreditierung, belohnende und marktbasierte Instrumente und das Treffen informations-basierter Entscheidungen. Darüber hinaus ist es notwendig die Transparenz der Politik zu erhöhen und mehr Informationen offenzulegen.

Human amygdala responses during presentation of happy and neutral faces: correlations with state anxiety

BACKGROUND: Previous functional imaging studies demonstrating amygdala response to happy facial expressions have all included the presentation of negatively valenced primary comparison expressions within the experimental context. This study assessed amygdala response to happy and neutral facial expressions in an experimental paradigm devoid of primary negatively valenced comparison expressions. METHODS: Sixteen human subjects (eight female) viewed 16-sec blocks of alternating happy and neutral faces interleaved with a baseline fixation condition during two functional magnetic resonance imaging scans. RESULTS: Within the ventral amygdala, a negative correlation between happy versus neutral signal changes and state anxiety was observed. The majority of the variability associated with this effect was explained by a positive relationship between state anxiety and signal change to neutral faces. CONCLUSIONS: Interpretation of amygdala responses to facial expressions of emotion will be influenced by considering the contribution of each constituent condition within a greater subtractive finding, as well as 1) their spatial location within the amygdaloid complex; and 2) the experimental context in which they were observed. Here, an observed relationship between state anxiety and ventral amygdala response to happy versus neutral faces was explained by response to neutral faces.

Development and application of a novel algorithm for steady-state optimising control using dynamic information

A novel optimising controller is designed that leads a slow process from a sub-optimal operational condition to the steady-state optimum in a continuous way based on dynamic information. Using standard results from optimisation theory and discrete optimal control, the solution of a steady-state optimisation problem is achieved by solving a receding-horizon optimal control problem which uses derivative and state information from the plant via a shadow model and a state-space identifier. The paper analyzes the steady-state optimality of the procedure, develops algorithms with and without control rate constraints and applies the procedure to a high fidelity simulation study of a distillation column optimisation.

Spinal cord injury: assessment of autonomic state-dependent control of cardiovascular system and body core temperature

Spinal cord injury (SCI) results not only in paralysis; but it is also associated with a range of autonomic dysregulation that can interfere with cardiovascular, bladder, bowel, temperature, and sexual function. The entity of the autonomic dysfunction is related to the level and severity of injury to descending autonomic (sympathetic) pathways. For many years there was limited awareness of these issues and the attention given to them by the scientific and medical community was scarce. Yet, even if a new system to document the impact of SCI on autonomic function has recently been proposed, the current standard of assessment of SCI (American Spinal Injury Association (ASIA) examination) evaluates motor and sensory pathways, but not severity of injury to autonomic pathways. Beside the severe impact on quality of life, autonomic dysfunction in persons with SCI is associated with increased risk of cardiovascular disease and mortality. Therefore, obtaining information regarding autonomic function in persons with SCI is pivotal and clinical examinations and laboratory evaluations to detect the presence of autonomic dysfunction and quantitate its severity are mandatory. Furthermore, previous studies demonstrated that there is an intimate relationship between the autonomic nervous system and sleep from anatomical, physiological, and neurochemical points of view. Although, even if previous epidemiological studies demonstrated that sleep problems are common in spinal cord injury (SCI), so far only limited polysomnographic (PSG) data are available. Finally, until now, circadian and state dependent autonomic regulation of blood pressure (BP), heart rate (HR) and body core temperature (BcT) were never assessed in SCI patients. Aim of the current study was to establish the association between the autonomic control of the cardiovascular function and thermoregulation, sleep parameters and increased cardiovascular risk in SCI patients.

State Pharmaceutical Assisstance for the Elderly and Disabled: Planning Issues for Program and Non-Program States

The Medicare Catastrophic Coverage Act (MCCA) would have mandated federal assistance for Medicare beneficiaries who have high annual prescription medication costs, High national expenditures for such drugs have encouraged the development of private and state insurance programs to help with these costs. Ten state pharmaceutical assistance programs (SPAPs), designed to help certain elderly, low income, or disabled people, exist for those ineligible for Medicaid or unable to purchase coverage privately. Coordination of state and federal benefits was a consideration for established programs, and programs being planned needed to determine the feasibity of integration of federal assistance. But the enactment and subsequent appeal of the Act affected both planning and policy implications for these SPAPs. All U.S. states and territories were surveyed before the bill's repeal to collect data on the effects of MCCA for those with prescription drug programs and those without. The repeal of the federal program places pressure on the nonprogram states to proceed, perhaps more cautiously, to initiate program; for their own residents, given increasing out-of-pocket and insurance costs, and no federal program.

"The State Starts from the Family": Peace and Harmony in Tajikistan's Eastern Pamirs

Based on anthropological fieldwork between 2008 and 2011, this article focuses on how people in Tajikistan's eastern Pamirs conceptualize well-being through the establishment of peace and harmony. An exploration of the interactional use of the terms ‘peace’ and ‘harmony’ in Kyrgyz and Tajik (tynchtyk, yntymak, tinji, and vahdat) makes manifest that the meanings of these terms are connected to the fields of ‘family’, ‘leadership’, and ‘state���. Basing their reasoning on the officially promoted analogy between family and state, people in the eastern Pamirs distinguish between social spaces that are related to well-being and those that are not. As a factor of distinction, and crucial to the establishment of peace and harmony, the moral quality of leadership plays an important role. Positive experiences of such leadership as balanced and morally pure are mainly identified and witnessed within families and neighbourhoods and only occasionally in state institutions. This discrepancy raises the question of where to locate boundaries between good and bad, moral and immoral, harmonious and conflictual. Thus, this article contributes not only to the study of local concepts of well-being in Central Asia but also to the study of local concepts of ‘ill-being’ which challenge them.

Firearm legislation and firearm mortality in the USA: a cross-sectional, state-level study.

BACKGROUND In an effort to reduce firearm mortality rates in the USA, US states have enacted a range of firearm laws to either strengthen or deregulate the existing main federal gun control law, the Brady Law. We set out to determine the independent association of different firearm laws with overall firearm mortality, homicide firearm mortality, and suicide firearm mortality across all US states. We also projected the potential reduction of firearm mortality if the three most strongly associated firearm laws were enacted at the federal level. METHODS We constructed a cross-sectional, state-level dataset from Nov 1, 2014, to May 15, 2015, using counts of firearm-related deaths in each US state for the years 2008-10 (stratified by intent [homicide and suicide]) from the US Centers for Disease Control and Prevention's Web-based Injury Statistics Query and Reporting System, data about 25 firearm state laws implemented in 2009, and state-specific characteristics such as firearm ownership for 2013, firearm export rates, and non-firearm homicide rates for 2009, and unemployment rates for 2010. Our primary outcome measure was overall firearm-related mortality per 100 000 people in the USA in 2010. We used Poisson regression with robust variances to derive incidence rate ratios (IRRs) and 95% CIs. FINDINGS 31 672 firearm-related deaths occurred in 2010 in the USA (10·1 per 100 000 people; mean state-specific count 631·5 [SD 629·1]). Of 25 firearm laws, nine were associated with reduced firearm mortality, nine were associated with increased firearm mortality, and seven had an inconclusive association. After adjustment for relevant covariates, the three state laws most strongly associated with reduced overall firearm mortality were universal background checks for firearm purchase (multivariable IRR 0·39 [95% CI 0·23-0·67]; p=0·001), ammunition background checks (0·18 [0·09-0·36]; p<0·0001), and identification requirement for firearms (0·16 [0·09-0·29]; p<0·0001). Projected federal-level implementation of universal background checks for firearm purchase could reduce national firearm mortality from 10·35 to 4·46 deaths per 100 000 people, background checks for ammunition purchase could reduce it to 1·99 per 100 000, and firearm identification to 1·81 per 100 000. INTERPRETATION Very few of the existing state-specific firearm laws are associated with reduced firearm mortality, and this evidence underscores the importance of focusing on relevant and effective firearms legislation. Implementation of universal background checks for the purchase of firearms or ammunition, and firearm identification nationally could substantially reduce firearm mortality in the USA. FUNDING None.

The Secular State Under Siege: Religion and Politics in Europe and America

Throughout human history, religion and politics have entertained the most intimate of connections as systems of authority regulating individuals and society. While the two have come apart through the process of secularization, secularism is challenged today by the return of public religion. This cogent analysis unravels the nature of the connection, disconnection, and attempted reconnection between religion and politics in the West. In a comparison of Western Europe and North America, Christianity and Islam, Joppke advances far-reaching theoretical, historical, and comparative-political arguments. With respect to theory, it is argued that only a “substantive” concept of religion, as pertaining to the existence of supra-human powers, opens up the possibility of a historical-comparative perspective on religion. At the level of history, secularization is shown to be the distinct outcome of Latin Christianity itself. And at the level of comparative politics, the Christian Right in America which has attacked the “wall of separation” between religion and state and Islam in Europe with the controversial insistence on sharia law and other “illiberal” claims from some quarters are taken to be counterpart incarnations of public religion and challenges to the secular state. This clearly argued, sweeping book will provide an invaluable framework for approaching an array of critical issues at the intersection of religion, law and politics for advanced students and researchers across the social sciences and legal studies, as well as for the interested public.

New England Railroads, 1838 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Sketch of the states of Massachusetts, Connecticut, and Rhode Island, and parts of New Hampshire & New York exhibiting the several rail road routes completed, constructing, chartered & contemplated : published by order of the Legislature of Massachusetts, drawn by A. Kennedy ; engraved by Morse & Tuttle. It was published in 1838. Scale [ca. 1:700,000]. The image inside the map neatline is georeferenced to the surface of the earth and fit to the USA Contiguous Albers Equal Area Conic projection (Meters). All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, or other information associated with the principal map. This map shows features such as roads, completed, chartered, and contemplated railroads, drainage, state and county boundaries, and more. This layer is part of a selection of digitally scanned and georeferenced historic maps of New England from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of regions, originators, ground condition dates, scales, and purposes.

Connecticut, Massachusetts, and Rhode Island, 1837 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Map of Massachusetts, Rhode-Island & Connecticut : compiled from the latest authorities, engraved by J. Wells. It was published by A.F. Wilcox & Co. in 1837. Scale [ca. 1:442,000].The image inside the map neatline is georeferenced to the surface of the earth and fit to the USA Contiguous Albers Equal Area Conic projection (Meters). All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as cities and towns, roads, railroads, drainage, churches, academies, banks, court houses, industry locations (e.g. mills, factories, mines, etc.), town, county, and state boundaries, and more. It also includes many inset maps of the major cities of New England.This layer is part of a selection of digitally scanned and georeferenced historic maps of New England from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of regions, originators, ground condition dates, scales, and map purposes.