A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations

There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video system to estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” were captured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using image analysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacoustic survey and from direct measures of fish size using visual census techniques. We discovered a possible bias in length measures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations.

Quantifying chaos: practical estimation of the correlation dimension

Be it a physical object or a mathematical model, a nonlinear dynamical system can display complicated aperiodic behavior, or "chaos." In many cases, this chaos is associated with motion on a strange attractor in the system's phase space. And the dimension of the strange attractor indicates the effective number of degrees of freedom in the dynamical system.

In this thesis, we investigate numerical issues involved with estimating the dimension of a strange attractor from a finite time series of measurements on the dynamical system.

Of the various definitions of dimension, we argue that the correlation dimension is the most efficiently calculable and we remark further that it is the most commonly calculated. We are concerned with the practical problems that arise in attempting to compute the correlation dimension. We deal with geometrical effects (due to the inexact self-similarity of the attractor), dynamical effects (due to the nonindependence of points generated by the dynamical system that defines the attractor), and statistical effects (due to the finite number of points that sample the attractor). We propose a modification of the standard algorithm, which eliminates a specific effect due to autocorrelation, and a new implementation of the correlation algorithm, which is computationally efficient.

Finally, we apply the algorithm to chaotic data from the Caltech tokamak and the Texas tokamak (TEXT); we conclude that plasma turbulence is not a low- dimensional phenomenon.

Quantifying synergistic information

Within the microcosm of information theory, I explore what it means for a system to be functionally irreducible. This is operationalized as quantifying the extent to which cooperative or “synergistic” effects enable random variables X₁, ... , X_n to predict (have mutual information about) a single target random variable Y . In Chapter 1, we introduce the problem with some emblematic examples. In Chapter 2, we show how six different measures from the existing literature fail to quantify this notion of synergistic mutual information. In Chapter 3 we take a step towards a measure of synergy which yields the first nontrivial lowerbound on synergistic mutual information. In Chapter 4, we find that synergy is but the weakest notion of a broader concept of irreducibility. In Chapter 5, we apply our results from Chapters 3 and 4 towards grounding Giulio Tononi’s ambitious φ measure which attempts to quantify the magnitude of consciousness experience.

Future of earthquake early warning : quantifying uncertainty and making fast automated decisions for applications

Earthquake early warning (EEW) systems have been rapidly developing over the past decade. Japan Meteorological Agency (JMA) has an EEW system that was operating during the 2011 M9 Tohoku earthquake in Japan, and this increased the awareness of EEW systems around the world. While longer-time earthquake prediction still faces many challenges to be practical, the availability of shorter-time EEW opens up a new door for earthquake loss mitigation. After an earthquake fault begins rupturing, an EEW system utilizes the first few seconds of recorded seismic waveform data to quickly predict the hypocenter location, magnitude, origin time and the expected shaking intensity level around the region. This early warning information is broadcast to different sites before the strong shaking arrives. The warning lead time of such a system is short, typically a few seconds to a minute or so, and the information is uncertain. These factors limit human intervention to activate mitigation actions and this must be addressed for engineering applications of EEW. This study applies a Bayesian probabilistic approach along with machine learning techniques and decision theories from economics to improve different aspects of EEW operation, including extending it to engineering applications.

Existing EEW systems are often based on a deterministic approach. Often, they assume that only a single event occurs within a short period of time, which led to many false alarms after the Tohoku earthquake in Japan. This study develops a probability-based EEW algorithm based on an existing deterministic model to extend the EEW system to the case of concurrent events, which are often observed during the aftershock sequence after a large earthquake.

To overcome the challenge of uncertain information and short lead time of EEW, this study also develops an earthquake probability-based automated decision-making (ePAD) framework to make robust decision for EEW mitigation applications. A cost-benefit model that can capture the uncertainties in EEW information and the decision process is used. This approach is called the Performance-Based Earthquake Early Warning, which is based on the PEER Performance-Based Earthquake Engineering method. Use of surrogate models is suggested to improve computational efficiency. Also, new models are proposed to add the influence of lead time into the cost-benefit analysis. For example, a value of information model is used to quantify the potential value of delaying the activation of a mitigation action for a possible reduction of the uncertainty of EEW information in the next update. Two practical examples, evacuation alert and elevator control, are studied to illustrate the ePAD framework. Potential advanced EEW applications, such as the case of multiple-action decisions and the synergy of EEW and structural health monitoring systems, are also discussed.

Towards a Comprehensive Approach to Quantifying and Mapping Ecosystem Services Flows

25 p.

Quantifying Earthquake Collapse Risk of Tall Steel Braced Frame Buildings Using Rupture-to-Rafters Simulations

This thesis examines collapse risk of tall steel braced frame buildings using rupture-to-rafters simulations due to suite of San Andreas earthquakes. Two key advancements in this work are the development of (i) a rational methodology for assigning scenario earthquake probabilities and (ii) an artificial correction-free approach to broadband ground motion simulation. The work can be divided into the following sections: earthquake source modeling, earthquake probability calculations, ground motion simulations, building response, and performance analysis.

As a first step the kinematic source inversions of past earthquakes in the magnitude range of 6-8 are used to simulate 60 scenario earthquakes on the San Andreas fault. For each scenario earthquake a 30-year occurrence probability is calculated and we present a rational method to redistribute the forecast earthquake probabilities from UCERF to the simulated scenario earthquake. We illustrate the inner workings of the method through an example involving earthquakes on the San Andreas fault in southern California.

Next, three-component broadband ground motion histories are computed at 636 sites in the greater Los Angeles metropolitan area by superposing short-period (0.2~s-2.0~s) empirical Green's function synthetics on top of long-period ($>$ 2.0~s) spectral element synthetics. We superimpose these seismograms on low-frequency seismograms, computed from kinematic source models using the spectral element method, to produce broadband seismograms.

Using the ground motions at 636 sites for the 60 scenario earthquakes, 3-D nonlinear analysis of several variants of an 18-story steel braced frame building, designed for three soil types using the 1994 and 1997 Uniform Building Code provisions and subjected to these ground motions, are conducted. Model performance is classified into one of five performance levels: Immediate Occupancy, Life Safety, Collapse Prevention, Red-Tagged, and Model Collapse. The results are combined with the 30-year probability of occurrence of the San Andreas scenario earthquakes using the PEER performance based earthquake engineering framework to determine the probability of exceedance of these limit states over the next 30 years.

Quantifying Earthquake Collapse Risk of Tall Steel Moment Frame Buildings Using Rupture-to-Rafters Simulations

There is a sparse number of credible source models available from large-magnitude past earthquakes. A stochastic source model generation algorithm thus becomes necessary for robust risk quantification using scenario earthquakes. We present an algorithm that combines the physics of fault ruptures as imaged in laboratory earthquakes with stress estimates on the fault constrained by field observations to generate stochastic source models for large-magnitude (Mw 6.0-8.0) strike-slip earthquakes. The algorithm is validated through a statistical comparison of synthetic ground motion histories from a stochastically generated source model for a magnitude 7.90 earthquake and a kinematic finite-source inversion of an equivalent magnitude past earthquake on a geometrically similar fault. The synthetic dataset comprises of three-component ground motion waveforms, computed at 636 sites in southern California, for ten hypothetical rupture scenarios (five hypocenters, each with two rupture directions) on the southern San Andreas fault. A similar validation exercise is conducted for a magnitude 6.0 earthquake, the lower magnitude limit for the algorithm. Additionally, ground motions from the Mw7.9 earthquake simulations are compared against predictions by the Campbell-Bozorgnia NGA relation as well as the ShakeOut scenario earthquake. The algorithm is then applied to generate fifty source models for a hypothetical magnitude 7.9 earthquake originating at Parkfield, with rupture propagating from north to south (towards Wrightwood), similar to the 1857 Fort Tejon earthquake. Using the spectral element method, three-component ground motion waveforms are computed in the Los Angeles basin for each scenario earthquake and the sensitivity of ground shaking intensity to seismic source parameters (such as the percentage of asperity area relative to the fault area, rupture speed, and risetime) is studied.

Under plausible San Andreas fault earthquakes in the next 30 years, modeled using the stochastic source algorithm, the performance of two 18-story steel moment frame buildings (UBC 1982 and 1997 designs) in southern California is quantified. The approach integrates rupture-to-rafters simulations into the PEER performance based earthquake engineering (PBEE) framework. Using stochastic sources and computational seismic wave propagation, three-component ground motion histories at 636 sites in southern California are generated for sixty scenario earthquakes on the San Andreas fault. The ruptures, with moment magnitudes in the range of 6.0-8.0, are assumed to occur at five locations on the southern section of the fault. Two unilateral rupture propagation directions are considered. The 30-year probabilities of all plausible ruptures in this magnitude range and in that section of the fault, as forecast by the United States Geological Survey, are distributed among these 60 earthquakes based on proximity and moment release. The response of the two 18-story buildings hypothetically located at each of the 636 sites under 3-component shaking from all 60 events is computed using 3-D nonlinear time-history analysis. Using these results, the probability of the structural response exceeding Immediate Occupancy (IO), Life-Safety (LS), and Collapse Prevention (CP) performance levels under San Andreas fault earthquakes over the next thirty years is evaluated.

Furthermore, the conditional and marginal probability distributions of peak ground velocity (PGV) and displacement (PGD) in Los Angeles and surrounding basins due to earthquakes occurring primarily on the mid-section of southern San Andreas fault are determined using Bayesian model class identification. Simulated ground motions at sites within 55-75km from the source from a suite of 60 earthquakes (Mw 6.0 − 8.0) primarily rupturing mid-section of San Andreas fault are considered for PGV and PGD data.

A atividade da pterocarpanoquinona LQB 118 in vitro e in vivo em Leishmania braziliensis

As leishmanioses estão entre as mais importantes endemias brasileiras e encontram-se entre as doenças mais negligenciadas no mundo. O arsenal terapêutico disponível é restrito, tóxico, caro e em algumas situações ineficazes, devido ao surgimento de cepas resistentes do parasito. No Brasil são registrados anualmente mais de 20 mil casos de leishmaniose tegumentar e a Leishmania braziliensis é a principal espécie causadora das formas clínicas cutânea e mucosa. Portanto tornam-se importantes estudos que conduzam ao desenvolvimento de novas alternativas terapêuticas. O objetivo do presente estudo foi avaliar a atividade da pterocarpanoquinona denominada LQB118 sobre Leishmania braziliensis in vitro e in vivo usando hamsters como modelo experimental. O efeito antiparasitário foi avaliado sobre o crescimento in vitro das formas promastigotas e sobre amastigotas intracelulares em macrófagos peritoneais de camundongos. Para avaliar o modo ação in vitro foi investigada a indução de apoptose usando marcação por TUNEL e Anexina V-FITC. O efeito sobre a modulação da ativação de macrófagos murinos foi analisada pela dosagem de óxido nítrico (reagente de Griess) e de citocinas IL-12, TNF-alfa e IL-10 (por ELISA) nos sobrenadantes de macrófagos. In vivo a atividade terapêutica da LQB 118 foi estudada em grupos de hamsters infectados com L.braziliensis na pata, tratados com a LQB118 pelas vias intralesional (100M/3x/semana) ou oral (0,5mg/5x/semana) após 7 dias de infecção durante oito semanas. A ação terapêutica foi analisada através do tamanho da lesão. A resposta imune foi avaliada durante o tratamento, pela resposta de hipersensibilidade tardia (DTH) ao antígeno total de L. braziliensis. A ação da LQB118 in vitro foi dose-dependente tanto na forma promastigota inibindo 45%, 64,7% e 99,95%, quanto nas amastigotas intracelulares 22%, 72% e 81% nas concentrações de 5M, 10M e 20M, respectivamente para ambas as formas evolutivas. A LQB118 foi capaz de induzir a externalização de fosfatidilserina em promastigotas (18,57% das células incubadas por 24 h e em 25,79% de células tratadas por 48h) e também promoveu aumento da fluorescência nas duas formas evolutivas da Leishmania quando comparadas aos controles, demonstrando a indução de fragmentação do DNA do parasito. Esta substância também foi capaz de modular a resposta dos macrófagos infectados por 24 horas aumentando de forma dose-dependente a IL-12 e NO, mantendo constante TNF-α. In vivo, na sétima semana de tratamento, observamos uma redução significativa do tamanho das lesões nos animais tratados com LQB 118 intralesional (p<0, 001) e no grupo tratado pela via oral (p<0,05) quando comparado com o controle. Estes resultados demonstram que a atividade anti-Leishmania da LQB118 é direta sobre o parasito pela indução de morte por apoptose, apresentando também uma ação moduladora da resposta dos macrófagos contribuindo para ação leishmanicida, sem alterar a morfologia da célula hospedeira e que a LQB 118 apresenta uma atividade terapêutica no modelo hamster e pode ser uma importante molécula para o desenvolvimento de um novo fármaco.

Efeito da 1,10-fenantrolina e seus derivados complexados em metal na atividade proteolítica de Leishmania braziliensis

Leishmanioses são um grupo de doenças com um largo espectro de manifestações clínicas, as quais variam desde lesões cutâneas até o envolvimento visceral severo, podendo levar ao óbito. A leishmaniose é, ainda hoje, uma doença negligenciada, estando entre os agravos prioritários do programa de pesquisa sobre doenças da pobreza da Organização Mundial da Saúde (OMS). Além de não haver vacinas disponíveis, a terapia é baseada em medicamentos injetáveis que causam sérios efeitos colaterais, tornando o tratamento inviável para muitos países endêmicos. Drogas derivadas de metal representam um novo arsenal terapêutico antimicrobiano e anti-câncer. Os inibidores de peptidase/agentes quelantes tais como 1,10-fenantrolina e seus derivados, no estado livre de metal ou como ligantes com metais de transição, interferem com a função de vários sistemas biológicos. Em trabalhos anteriores, nosso grupo descreveu que o parasito L. braziliensis produziu moléculas gp63 sensíveis a 1,10-fenantrolina. No presente trabalho, demonstramos a distribuição celular da molécula gp63 em uma cepa virulenta de L. braziliensis por meio de análises bioquímicas e imuno-histoquímica. Depois disso, relatamos os efeitos inibitórios de três compostos derivados da 1,10-fenantrolina, 1,10-fenantrolina-5,6-diona (phendio), [Cu(phendio)2] e [Ag(phendio)2], nas atividades metalopeptidases celulares e extracelulares produzidas por promastigotas de L. braziliensis, bem como as suas ações sobre a viabilidade do parasita e na interação com as células de macrófagos murinos. As moléculas gp63 foram detectadas em compartimentos de parasitos, incluindo membrana citoplasmatica e bolsa flagelar. O tratamento de promastigotas de L. braziliensis durante 1 hora com 1,10-fenantrolina e seus derivados resultou numa inibição significativa da viabilidade celular e mostrou um mecanismo de ação irreversível. Estes inibidores de metalopeptidases induziram apoptose em promastigotas de L. braziliensis, demonstrada através da marcação com anexina/iodeto de propídio e ensaio TUNEL. O pré-tratamento de promastigotas com os inibidores de metalopeptidases induziram uma diminuição na expressão de moléculas de superfície gp63, assim como uma redução significativa no índice de associação com macrófagos. Em paralelo, macrófagos infectados com L. braziliensis e tratados com 1,10-fenantrolina e seus derivados promoveram uma potente redução sobre o número de amastigotas intracelulares. O tratamento de macrófagos com 1,10-fenantrolina e seus derivados não induziram o aumento de óxido nítrico. A ação combinatória sobre a capacidade de crescimento entre os compostos derivados da 1,10-fenantrolina e Glucantime, quando ambos foram utilizados em concentracões sub-inibidoras, também foi observada. In vivo os compostos derivados da 1,10-fenantrolina e seus drivados foram capazes de controlar o tamanho das lesões a partir da terceira semana de tratamento em relação ao controle não tratado em hamsters infectados quando administrado por via intraperitoneal. Os animais tratados com os compostos apresentaram maior resposta intradérmica (DTH) aos antígenos de L. braziliensis. Coletivamente, a 1,10-fenantrolina e seus derivados metálicos apresentam uma nova perspectiva de estudos para o desenvolvimento de novos fármacos anti-L. braziliensis