Advances in sequential data assimilation and numerical weather forecasting: an Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic Ensemble Square Root Filters, and a test of a new time stepping scheme in an atmospheric model

This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn’t represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion in the mean value of the function. Using statistical significance tests both at the local and field level, it is shown that the climatology of the SPEEDY model is not modified by the changed time stepping scheme; hence, no retuning of the parameterizations is required. It is found the accuracy of the medium-term forecasts is increased by using the RAW filter.

Do phytoplankton communities evolve through a self-regulatory abundance-diversity relationship?

A small group of phytoplankton species that produce toxic or allelopathic chemicals has a significant effect on plankton dynamics in marine ecosystems. The species of non-toxic phytoplankton, which are large in number, are affected by the toxin-allelopathy of those species. By analysis of the abundance data of marine phytoplankton collected from the North-West coast of the Bay of Bengal, an empirical relationship between the abundance of the potential toxin-producing species and the species diversity of the non-toxic phytoplankton is formulated. A change-point analysis demonstrates that the diversity of non-toxic phytoplankton increases with the increase of toxic species up to a certain level. However, for a massive increase of the toxin-producing species the diversity of phytoplankton at species level reduces gradually. Following the results, a deterministic relationship between the abundance of toxic phytoplankton and the diversity of non-toxic phytoplankton is developed. The abundance–diversity relationship develops a unimodal pathway through which the abundance of toxic species regulates the diversity of phytoplankton. These results contribute to the current understanding of the coexistence and biodiversity of phytoplankton, the top-down vs. bottom-up debate, and to that of abundance–diversity relationship in marine ecosystems.

A longitudinal analysis of self‐regulation and well-being: avoidance personal goals, avoidance coping, stress generation, and subjective well-being

We conducted 2 longitudinal meditational studies to test an integrative model of goals, stress and coping, and well‐being. Study 1 documented avoidance personal goals as an antecedent of life stressors and life stressors as a partial mediator of the relation between avoidance goals and longitudinal change in subjective well‐being (SWB). Study 2 fully replicated Study 1 and likewise validated avoidance goals as an antecedent of avoidance coping and avoidance coping as a partial mediator of the relation between avoidance goals and longitudinal change in SWB. It also showed that avoidance coping partially mediates the link between avoidance goals and life stressors and validated a sequential meditational model involving both avoidance coping and life stressors. The aforementioned results held when controlling for social desirability, basic traits, and general motivational dispositions. The findings are discussed with regard to the integration of various strands of research on self‐regulation. (PsycINFO Database Record (c) 2012 APA, all rights reserved)(journal abstract)

Bioactive films produced from self-assembling peptide amphiphiles as versatile substrates for tuning cell adhesion and tissue architecture in serum-free conditions

The development of versatile bioactive surfaces able to emulate in vivo conditions is of enormous importance to the future of cell and tissue therapy. Tuning cell behaviour on two-dimensional surfaces so that the cells perform as if they were in a natural three-dimensional tissue represents a significant challenge, but one that must be met if the early promise of cell and tissue therapy is to be fully realised. Due to the inherent complexities involved in the manufacture of biomimetic three-dimensional substrates, the scaling up of engineered tissue-based therapies may be simpler if based upon proven two-dimensional culture systems. In this work, we developed new coating materials composed of the self-assembling peptide amphiphiles (PAs) C16G3RGD (RGD) and C16G3RGDS (RGDS) shown to control cell adhesion and tissue architecture while avoiding the use of serum. When mixed with the C16ETTES diluent PA at 13 : 87 (mol mol-1) ratio at 1.25 times 10-3 M, the bioactive {PAs} were shown to support optimal adhesion, maximal proliferation, and prolonged viability of human corneal stromal fibroblasts ({hCSFs)}, while improving the cell phenotype. These {PAs} also provided stable adhesive coatings on highly-hydrophobic surfaces composed of striated polytetrafluoroethylene ({PTFE)}, significantly enhancing proliferation of aligned cells and increasing the complexity of the produced tissue. The thickness and structure of this highly-organised tissue were similar to those observed in vivo, comprising aligned newly-deposited extracellular matrix. As such, the developed coatings can constitute a versatile biomaterial for applications in cell biology, tissue engineering, and regenerative medicine requiring serum-free conditions.

On the spectra and pseudospectra of a class of non-self-adjoint random matrices and operators

In this paper we develop and apply methods for the spectral analysis of non-selfadjoint tridiagonal infinite and finite random matrices, and for the spectral analysis of analogous deterministic matrices which are pseudo-ergodic in the sense of E. B. Davies (Commun. Math. Phys. 216 (2001), 687–704). As a major application to illustrate our methods we focus on the “hopping sign model” introduced by J. Feinberg and A. Zee (Phys. Rev. E 59 (1999), 6433–6443), in which the main objects of study are random tridiagonal matrices which have zeros on the main diagonal and random ±1’s as the other entries. We explore the relationship between spectral sets in the finite and infinite matrix cases, and between the semi-infinite and bi-infinite matrix cases, for example showing that the numerical range and p-norm ε - pseudospectra (ε > 0, p ∈ [1,∞] ) of the random finite matrices converge almost surely to their infinite matrix counterparts, and that the finite matrix spectra are contained in the infinite matrix spectrum Σ. We also propose a sequence of inclusion sets for Σ which we show is convergent to Σ, with the nth element of the sequence computable by calculating smallest singular values of (large numbers of) n×n matrices. We propose similar convergent approximations for the 2-norm ε -pseudospectra of the infinite random matrices, these approximations sandwiching the infinite matrix pseudospectra from above and below.

Should system dynamics be described as a 'hard' or 'deterministic' systems approach?

This paper explores the criticism that system dynamics is a ‘hard’ or ‘deterministic’ systems approach. This criticism is seen to have four interpretations and each is addressed from the perspectives of social theory and systems science. Firstly, system dynamics is shown to offer not prophecies but Popperian predictions. Secondly, it is shown to involve the view that system structure only partially, not fully, determines human behaviour. Thirdly, the field's assumptions are shown not to constitute a grand content theory—though its structural theory and its attachment to the notion of causality in social systems are acknowledged. Finally, system dynamics is shown to be significantly different from systems engineering. The paper concludes that such confusions have arisen partially because of limited communication at the theoretical level from within the system dynamics community but also because of imperfect command of the available literature on the part of external commentators. Improved communication on theoretical issues is encouraged, though it is observed that system dynamics will continue to justify its assumptions primarily from the point of view of practical problem solving. The answer to the question in the paper's title is therefore: on balance, no.

Self-concept clarity and compulsive Internet use: the role of preference for virtual interactions and employment status in British and North-American samples

Background and Aims Compulsive Internet Use (CIU) describes a maladaptive relationship with the Internet characterised by loss of control and conflict. Although also affecting adults, most studies use teenage samples, and theoretical development on risk factors is scarce. According to Davis (2001), the social connectivity function of the Internet is key in identifying traits associated with CIU. Since Self-Concept Clarity (SCC) is strongly related to social anxiety, and virtual interactions allow “self-edition”, we hypothesized that individuals low in SCC could choose virtual interactions as safer alternative to satisfy their social needs. This could in turn increase the risk of CIU. Building on a previous study, we also expected CIU to be more harmful in the unemployed. Methods We collected samples from the UK (N = 532) and US (N = 502) with equal distribution of employed and unemployed individuals. We ran Measurement Invariance tests to confirm that the constructs were equivalent across countries. Subsequently, we conducted mediation and moderation analysis to test our hypothesis with Multigroup Confirmatory Factor Analysis. Results Measurement Invariance was confirmed. The relationship between SCC and CIU was partially mediated by preference of virtual interactions in both countries. This preference was significantly related to lower social support. Short term unemployment seemed to accentuate the negative impact of CIU on life satisfaction in both countries, although only marginally significantly in the US. The unemployed reported significantly lower levels of life satisfaction. Conclusion We demonstrated that SCC is a key vulnerability factor to CIU in adults, and confirmed the additional risks for the unemployed.

Microgranitic Enclaves as Products of Self-mixing Events: a Study of Open-system Processes in the Maua Granite, Sao Paulo, Brazil, Based on in situ Isotopic and Trace Elements in Plagioclase

Felsic microgranular enclaves with structures indicating that they interacted in a plastic state with their chemically similar host granite are abundant in the Maua Pluton, SE Brazil. Larger plagioclase xenocrysts are in textural disequilibrium with the enclave groundmass and show complex zoning patterns with partially resorbed An-rich cores (locally with patchy textures) surrounded by more sodic rims. In situ laser ablation-(multi-collector) inductively coupled plasma mass spectrometry trace element and Sr isotopic analyses performed on the plagioclase xenocrysts indicate open-system crystallization; however, no evidence of derivation from more primitive basic melts is observed. The An-rich cores have more radiogenic initial Sr isotopic ratios that decrease towards the outermost part of the rims, which are in isotopic equilibrium with the matrix plagioclase. These profiles may have been produced by either (1) diffusional re-equilibration after rim crystallization from the enclave-forming magma, as indicated by relatively short calculated residence times, or (2) episodic contamination with a decrease of the contaminant ratio proportional to the extent to which the country rocks were isolated by the crystallization front. Profiles of trace elements with high diffusion coefficients would require unrealistically long residence times, and can be modeled in terms of fractional crystallization. A combination of trace element and Sr isotope data suggests that the felsic microgranular enclaves from the Maua Pluton are the products of interaction between end-member magmas that had similar compositions, thus recording `self-mixing` events.

Estudo exploratório da deposição de filmes de diamante em alguns substratos cerâmicos

o presente trabalho é um estudo exploratório a respeito da síntese de filmes de diamante via deposiçãoquímica a vapor (CVD) sobre alguns substratos cerâmicos: diboreto de titânio (TiB2), ítria (Y20a), zircão (ZrSi04), zircônia parcialmente e totalmente estabilizada com ítria (Zr02), pirofilita ( Al2Si4OlO(OHh), .alumina (Al2Oa) e nitreto de boro hexagonal (h-BN). Estes substratos foram produzidos, em sua maioria, a partir da sinterização de pós micrométricos em altas temperaturas. Além do estudo em relação a possíveis candidatos alternativos ao tradicional silício para o crescimento de filmes auto-sustentáveis, procuramos encontrar substratos onde o filme aderisse bem e cujas propriedades tribológicas pudessem ser melhoradas com o recobrimento com filme de diamante.Dentre os materiais selecionados, constatamos que a topografia da superfície relacionada à densidade de contornos de grão, desempenha um papel relevante na nucleação do diamante. Além disso, os materiais que favorecem a formação de carbonetos conduziram a melhores resultados na nucleação e crescimento do filme, indicando que a ação da atmosfera reativa do CVD com o substrato também contribui decisivamente para o processo de nucleação. A partir dos resultados obtidos, concluímos que a aderência do filme de diamante ao zircão é excelente, assim como a qualidade do filme, o que pode serexplorado convenientemente caso as propriedades mecânicas do sinterizado de zircão sejam adequadas. No caso da zircônia parcialmente estabilizada, os resultados obtidos foram surpreendentes e este material poderia substituir o convencional substrato de silício para a deposição de filmes auto-sustentados de diamante, com inúmeras vantagens, dentre elas o fato de ser reutilizável e de não ser necessário ataque com ácidos para remoção do substrato, o que evita a geração de resíduos químicos.

Effect of partially demineralized dentin beneath the hybrid layer on dentin-adhesive interface micromechanics

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Self-Organizing Maps of Molecular Descriptors for Sesquiterpene Lactones and Their Application to the Chemotaxonomy of the Asteraceae Family

The Asteraceae, one of the largest families among angiosperms, is chemically characterised by the production of sesquiterpene lactones (SLs). A total of 1,111 SLs, which were extracted from 658 species, 161 genera, 63 subtribes and 15 tribes of Asteraceae, were represented and registered in two dimensions in the SISTEMATX, an in-house software system, and were associated with their botanical sources. The respective 11 block of descriptors: Constitutional, Functional groups, BCUT, Atom-centred, 2D autocorrelations, Topological, Geometrical, RDF, 3D-MoRSE, GETAWAY and WHIM were used as input data to separate the botanical occurrences through self-organising maps. Maps that were generated with each descriptor divided the Asteraceae tribes, with total index values between 66.7% and 83.6%. The analysis of the results shows evident similarities among the Heliantheae, Helenieae and Eupatorieae tribes as well as between the Anthemideae and Inuleae tribes. Those observations are in agreement with systematic classifications that were proposed by Bremer, which use mainly morphological and molecular data, therefore chemical markers partially corroborate with these classifications. The results demonstrate that the atom-centred and RDF descriptors can be used as a tool for taxonomic classification in low hierarchical levels, such as tribes. Descriptors obtained through fragments or by the two-dimensional representation of the SL structures were sufficient to obtain significant results, and better results were not achieved by using descriptors derived from three-dimensional representations of SLs. Such models based on physico-chemical properties can project new design SLs, similar structures from literature or even unreported structures in two-dimensional chemical space. Therefore, the generated SOMs can predict the most probable tribe where a biologically active molecule can be found according Bremer classification.

Nanotechnology control of self organized biomolecules and biomaterials for medical research

Nanotechnology entails the manufacturing and manipulation of matter at length scales ranging from single atoms to micron-sized objects. The ability to address properties on the biologically-relevant nanometer scale has made nanotechnology attractive for Nanomedicine. This is perceived as a great opportunity in healthcare especially in diagnostics, therapeutics and more in general to develop personalized medicine. Nanomedicine has the potential to enable early detection and prevention, and to improve diagnosis, mass screening, treatment and follow-up of many diseases. From the biological standpoint, nanomaterials match the typical size of naturally occurring functional units or components of living organisms and, for this reason, enable more effective interaction with biological systems. Nanomaterials have the potential to influence the functionality and cell fate in the regeneration of organs and tissues. To this aim, nanotechnology provides an arsenal of techniques for intervening, fabricate, and modulate the environment where cells live and function. Unconventional micro- and nano-fabrication techniques allow patterning biomolecules and biocompatible materials down to the level of a few nanometer feature size. Patterning is not simply a deterministic placement of a material; in a more extended acception it allows a controlled fabrication of structures and gradients of different nature. Gradients are emerging as one of the key factors guiding cell adhesion, proliferation, migration and even differentiation in the case of stem cells. The main goal of this thesis has been to devise a nanotechnology-based strategy and tools to spatially and temporally control biologically-relevant phenomena in-vitro which are important in some fields of medical research.

Fluctuation properties in random walks on networks and simple integrate and fire models

In questa tesi si è studiato l’insorgere di eventi critici in un semplice modello neurale del tipo Integrate and Fire, basato su processi dinamici stocastici markoviani definiti su una rete. Il segnale neurale elettrico è stato modellato da un flusso di particelle. Si è concentrata l’attenzione sulla fase transiente del sistema, cercando di identificare fenomeni simili alla sincronizzazione neurale, la quale può essere considerata un evento critico. Sono state studiate reti particolarmente semplici, trovando che il modello proposto ha la capacità di produrre effetti "a cascata" nell’attività neurale, dovuti a Self Organized Criticality (auto organizzazione del sistema in stati instabili); questi effetti non vengono invece osservati in Random Walks sulle stesse reti. Si è visto che un piccolo stimolo random è capace di generare nell’attività della rete delle fluttuazioni notevoli, in particolar modo se il sistema si trova in una fase al limite dell’equilibrio. I picchi di attività così rilevati sono stati interpretati come valanghe di segnale neurale, fenomeno riconducibile alla sincronizzazione.

Brown Capuchins (Cebus apella) Exhibit Self-Control on a Delay of Gratification Food Exchange Task When Food Options Differ Qualitatively

Self-control allows an individual to obtain a more preferred outcome by forgoing an immediate interest. Self-control is an advanced cognitive process because it involves the ability to weigh the costs and benefits of impulsive versus restrained behavior, determine the consequences of such behavior, and make decisions based on the most advantageous course of action. Self-control has been thoroughly explored in Old World primates, but less so in New World monkeys. There are many ways to test self-control abilities in non-human primates, including exchange tasks in which an animal must forgo an immediate, less preferred reward to receive a delayed, more preferred reward. I examined the self-control abilities of six capuchin monkeys using a task in which a monkey was given a less preferred food and was required to wait a delay interval to trade the fully intact less preferred food for a qualitatively higher, more preferred food. Partially eaten pieces of the less preferred food were not rewarded, and delay intervals increased on an individual basis based on performance. All six monkeys were successful in inhibiting impulsivity and trading a less preferred food for a more preferred food at the end of a delay interval. The maximum duration each subject postponed gratification instead of responding impulsively was considered their delay tolerance. This study was the first to show that monkeys could inhibit impulsivity in a delay of gratification food exchange task in which the immediate and delayed food options differed qualitatively and a partially eaten less preferred food was not rewarded with the more preferred food at the end of a delay interval. These results show that New World monkeys possess advanced cognitive abilities similar to those of Old World primates.

Avoidant coping partially mediates the relationship between patient problem behaviors and depressive symptoms in spousal Alzheimer caregivers

OBJECTIVE: Caring for a loved one with Alzheimer disease is a highly stressful experience that is associated with significant depressive symptoms. Previous studies indicate a positive association between problem behaviors in patients with Alzheimer disease (e.g., repeating questions, restlessness, and agitation) and depressive symptoms in their caregivers. Moreover, the extant literature indicates a robust negative relationship between escape-avoidance coping (i.e., avoiding people, wishing the situation would go away) and psychiatric well-being. The purpose of this study was to test a mediational model of the associations between patient problem behaviors, escape-avoidance coping, and depressive symptoms in Alzheimer caregivers. METHODS: Ninety-five spousal caregivers (mean age: 72 years) completed measures assessing their loved ones' frequency of problem behaviors, escape-avoidance coping, and depressive symptoms. A mediational model was tested to determine if escape-avoidant coping partially mediated the relationship between patient problem behaviors and caregiver depressive symptoms. RESULTS: Patient problem behaviors were positively associated with escape-avoidance coping (beta = 0.38, p < 0.01) and depressive symptoms (beta = 0.26, p < 0.05). Escape-avoidance coping was positively associated with depressive symptoms (beta = 0.33, p < 0.01). In a final regression analysis, the impact of problem behaviors on depressive symptoms was less after controlling for escape-avoidance coping. Sobel's test confirmed that escape-avoidance coping significantly mediated the relationship between problem behaviors and depressive symptoms (z = 2.07, p < 0.05). CONCLUSION: Escape-avoidance coping partially mediates the association between patient problem behaviors and depressive symptoms among elderly caregivers of spouses with dementia. This finding provides a specific target for psychosocial interventions for caregivers.