Estimation of origin-destination flows for dynamic traffic assignment

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.Includes bibliographical references (p. 107-112).This thesis proposes a framework and method for dynamic origin-destination demand estimation. OD estimation is a critical component of a Dynamic Traffic Assignment system in that it determines the frequencies of drivers' trips through a network. The OD estimation method presented here allows for tunable optimization to three classes of objectives: Assigned traffic flows, deviation from historical data, and relative proportions in historical data. The method can be easily extended to make use of other sources of information such as direct measurements of OD flows from probe vehicles. The framework is extended to allow for nonnegativity and capacity constraints on the OD flows. As OD estimation is intended for use in a real-time setting, computational issues are critical, and several simplifications to increase computational efficiency are propsed and evaluted, called the Exact-Match estimator and the Large-Flow estimator. The algorithms presented are implemented as part of the DynaMIT (Dynamic Network Assignment for the Management of Information to Travelers) traffic estimation and prediction software, which incorporates models for driver route choice and traffic movement simulation.by Josef Joshua Brandriss.S.M

Experimental strategies for the investigation of low temperature properties in granitic and pegmatitic melts

The physical behavior of silicate melts during the final stages of intrusion in the earth's crust are poorly understood. In particular, the low temperature limit of igneous petrogenesis is poorly constrained. The extreme differentiates of granitic magmatism that lead to pegmatite genesis span a very large range of composition not normally considered to be within the domain of igneous melt compositions. This combination of very low petrogenetic temperatures and extreme chemistries requires a concentrated effort for the determination of melt properties under conditions of pressure, temperature and composition appropriate to these systems. An experimental strategy for the determination of melt properties under appropriate conditions is presented. The determination of individual melt properties at very low temperatures is described with the aid of three examples, heat capacity, volume and viscosity. In this way the physical behavior of an important component of the earth's crust will become accessible

A Comparative Analysis of Influenza Vaccination Programs

The threat of avian influenza and the 2004-2005 influenza vaccine supply shortage in the United States has sparked a debate about optimal vaccination strategies to reduce the burden of morbidity and mortality caused by the influenza virus. We present a comparative analysis of two classes of suggested vaccination strategies: mortality-based strategies that target high risk populations and morbidity-based that target high prevalence populations. Applying the methods of contact network epidemiology to a model of disease transmission in a large urban population, we evaluate the efficacy of these strategies across a wide range of viral transmission rates and for two different age-specific mortality distributions. We find that the optimal strategy depends critically on the viral transmission level (reproductive rate) of the virus: morbidity-based strategies outperform mortality-based strategies for moderately transmissible strains, while the reverse is true for highly transmissible strains. These results hold for a range of mortality rates reported for prior influenza epidemics and pandemics. Furthermore, we show that vaccination delays and multiple introductions of disease into the community have a more detrimental impact on morbidity-based strategies than mortality-based strategies. If public health officials have reasonable estimates of the viral transmission rate and the frequency of new introductions into the community prior to an outbreak, then these methods can guide the design of optimal vaccination priorities. When such information is unreliable or not available, as is often the case, this study recommends mortality-based vaccination priorities

An experiment to assess the effects of diatom dissolution on oxygen isotope ratios

Rationale: Current studies which use the oxygen isotope composition from diatom silica (δ18Odiatom) as a palaeoclimate proxy assume that the δ18Odiatom value reflects the isotopic composition of the water in which the diatom formed. However, diatoms dissolve post mortem, preferentially losing less silicified structures in the water column and during/after burial into sediments. The impact of dissolution on δ18Odiatom values and potential misinterpretation of the palaeoclimate record are evaluated. Methods: Diatom frustules covering a range of ages (6 samples from the Miocene to the Holocene), environments and species were exposed to a weak alkaline solution for 48 days at two temperatures (20 °C and 4 °C), mimicking natural dissolution post mucilage removal. Following treatment, dissolution was assessed using scanning electron microscope images and a qualitative diatom dissolution index. The diatoms were subsequently analysed for their δ18O values using step-wise fluorination and isotope ratio mass spectrometry. Results: Variable levels of diatom dissolution were observed between the six samples; in all cases higher temperatures resulted in more frustule degradation. Dissolution was most evident in younger samples, probably as a result of the more porous nature of the silica. The degree of diatom dissolution does not directly equate to changes in the isotope ratios; the δ18Odiatom value was, however, lower after dissolution, but in only half the samples was this reduction outside the analytical error (2σ analytical error = 0.46‰). Conclusions: We have shown that dissolution can have a small negative impact on δ18Odiatom values, causing reductions of up to 0.59‰ beyond analytical error (0.46‰) at natural environmental temperatures. These findings need to be considered in palaeoenvironmental reconstructions using δ18Odiatom values, especially when interpreting variations in these values of <1‰

The use of multivariate statistics to resolve multiple contamination signals in the oxygen isotope analysis of biogenic silica

Analysis of the oxygen isotope composition (δ18O) of diatom silica is a commonly used tool for palaeoclimate reconstruction that recent studies have demonstrated may be complicated by the presence of non-diatom detrital material. Such contamination can mask any true climate-driven signal, leading to spurious results. Analysis of the 2.6-Ma Barsemoi diatomites from the East African Rift Valley highlights the presence of both tephra and clay in purified samples. Here we present a new method for assessing the relative contribution and geochemical composition of contamination components where sedimentary samples may be affected by more than one type of contamination. This approach shows that the incorporation of analytical techniques, such as X-ray fluorescence spectrometry, coupled with statistical modelling, can be used to develop a three end-member model to successfully resolve climate-driven changes in δ18Odiatom. Mass-balance corrections made to δ18Odiatom data demonstrate the importance of adopting quantitative geochemical analysis in tandem with the δ18O analysis of biogenic silica, to obtain accurate and meaningful results for palaeoclimate reconstruction

Differential Flo8p-dependent regulation of FLO1 and FLO11 for cell–cell and cell–substrate adherence of S. cerevisiae S288c

Cell–cell and cell–surface adherence represents initial steps in forming multicellular aggregates or in establishing cell–surface interactions. The commonly used Saccharomyces cerevisiae laboratory strain S288c carries a flo8 mutation, and is only able to express the flocculin-encoding genes FLO1 and FLO11, when FLO8 is restored. We show here that the two flocculin genes exhibit differences in regulation to execute distinct functions under various environmental conditions. In contrast to the laboratory strain Σ1278b, haploids of the S288c genetic background require FLO1 for cell–cell and cell–substrate adhesion, whereas FLO11 is required for pseudohyphae formation of diploids. In contrast to FLO11, FLO1 repression requires the Sin4p mediator tail component, but is independent of the repressor Sfl1p. FLO1 regulation also differs from FLO11, because it requires neither the KSS1 MAP kinase cascade nor the pathways which lead to the transcription factors Gcn4p or Msn1p. The protein kinase A pathway and the transcription factors Flo8p and Mss11p are the major regulators for FLO1 expression. Therefore, S. cerevisiae is prepared to simultaneously express two genes of its otherwise silenced FLO reservoir resulting in an appropriate cellular surface for different environments

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance

The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein–DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 complexes from the protein–DNA docking benchmark. We show that HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s). Our DNA analysis and modelling procedure captures the bend and twist motions occurring upon complex formation and uses these to generate custom-built DNA structural models, more closely resembling the bound form, for use in a second docking round. We achieve throughout the benchmark an overall success rate of 94% of one-star solutions or higher (interface root mean square deviation ≤4 Å and fraction of native contacts >10%) according to CAPRI criteria. Our improved protocol successfully predicts even the challenging protein–DNA complexes in the benchmark. Finally, our method is the first to readily dock multiple molecules (N > 2) simultaneously, pushing the limits of what is currently achievable in the field of protein–DNA docking