Scheduling of biological samples for DNA sequencing

Thesis (S.M.)--Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 95-97).In a DNA sequencing workflow, a biological sample has to pass through multiple process steps. Two consecutive steps are hydroshearing and library construction. Samples arrive randomly into the inventory and are to complete both processes before their due dates. The research project is to decide the optimal sequence of samples to go through these two processes subject to operational constraints. Two approaches, namely, heuristic and integer programming have been pursued in this thesis. A heuristic algorithm is proposed to solve the scheduling problem. A variant of the problem involving deterministic arrivals of samples is also considered for comparison purposes. Comparison tests between the two approaches are carried out to investigate the performance of the proposed heuristic for the original problem and its variant. Sensitivity analysis of the schedule to parameters of the problem is also conducted when using both approaches.by Yuwei Hu and Chin Soon Lim.S.M

A study on real estate derivatives

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Architecture, 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (leaves 85-86).All major asset classes including stocks and bonds have a well developed derivative market. Derivatives enable counterparties to reflect a view on a particular market, without having to trade the underlying asset. This seems to be a particularly appealing feature for real estate, an industry characterized by high transaction cost, long lead transaction time and lack of short-selling mechanism. Still, real estate remains the last major asset class without a liquid derivative market until recently when Credit Suisse began to offer swaps on the NCREIF Property Index (NPI) in the U.S. early this year following the UK's ten-year endeavor in developing real estate derivative market. The purpose of this thesis is two fold. First, in chapter one and two, we would like to explain what real estate derivatives are, how they work and why they can be beneficial to investors. Second, we are introducing some practical tools investors may use in evaluating and trading real estate derivatives. In chapter three, we are introducing three forecasting models on the NCREIF Property Index. In chapter four, we are expanding Prof. David Geltner's pricing methods on real estate index capital return swap to the NPI total return swap and property type total return swap.(cont.) These pricing methods present a basic foundation for investors to price all three types of swap currently being offered by Credit Suisse. In our study, we find that derivatives can provide numerous benefits to real estate investors including low transaction cost, quick execution and short-selling mechanism. These benefits in turn can help investors implement various strategies including hedging against market risk, asset allocation, sector rebalancing, international diversification and portable Alpha. Our research on UK's experience in real estate derivatives as well as our investor survey results in the U.S. and the UK lead us to believe that further initiative and pioneering efforts are critical for the development of the real estate derivatives market. By presenting this study on index forecasting models and pricing methodologies, we hope to increase the awareness and comfort level of investors and thus encourage the proliferation of real estate derivatives.by Jong Yoon Lim and Yi Zhang.S.M

The Solar--Stellar Connection

Stars have proven to be surprisingly prolific radio sources and the added sensitivity of the Square Kilometer Array will lead to advances in many directions. This chapter discusses prospects for studying the physics of stellar atmospheres and stellar winds across the HR diagram.Comment: to appear in "Science with the Square Kilometer Array," eds. C. Carilli and S. Rawlings, New Astronomy Reviews (Elsevier: Amsterdam

Lactobacillus fermentum LAB 9-fermented soymilk with enriched isoflavones and antioxidants improved memory In vivo

This study examined lactic acid bacteria (LAB)-fermented soymilk for their ability in hydrolyzing glucosides to aglycones and corresponding antioxidant capacity and memory enhancing effect. Twelve LAB isolated from Malaysian fermented food and milk products were incubated in commercially available soymilk for 48 h. Generally, soymilk supported LAB growth and significantly increased (p<0.05) conversion to bioactive aglycone by 2.1-6.5 fold when compared to unfermented soymilk. Lactobacillus fermentum LAB 9- fermented soymilk, in particular, was presented with increased total phenolic content (+10%) as opposed to unfermented soymilk. Lactobacilli (LAB 10-12)- and pediococci (LAB 5)-fermented soymilk elicited maximal DPPH radical-scavenging activity. LAB 1, 7, 8, 9 and 12 exhibited significantly higher (p<0.05) ferrous ion chelating activity when compared to control. Interestingly, LAB 9 had significantly improved memory deficit (p<0.05) in LPS-challenged mice. LAB-enriched nutritional value of soymilk could be useful against oxidative stress and memory deficit

Optical system for high-speed AFM

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 191-192).This thesis presents the design and development of an optical cantilever deflection sensor for a high speed Atomic Force Microscope (AFM). This optical sensing system is able to track a small cantilever while the X-Y scanner moves in the X-Y plane at 1KHz over a large range of 50x50 microns. To achieve these requirements, we evaluated a number of design concepts among which the lever method and the fiber collimator method were selected. Experiments were performed to characterize the performance of the integrated AFM and to show that the cantilever tracking while the scanner is in operation was accomplished. A triangular grating was imaged with the lever method optical subassembly integrated with the scanner to demonstrate the effectiveness of the approach.by Kwang Yong Lim.S.M

Are there nu_mu or nu_tau in the flux of solar neutrinos on earth?

Using the model independent method of Villante, Fiorentini, Lisi, Fogli, Palazzo, and the rates measured in the SNO and Super-Kamiokande solar neutrino experiment, we calculate the amount of active nu_mu or nu_tau present in the flux of solar neutrinos on Earth. We show that the probability of nu_e->nu_{mu,tau} transitions is larger than zero at 99.89% CL. We find that the averaged flux of nu_{mu,tau} on Earth is larger than 0.17 times the 8B nu_e flux predicted by the BP2000 Standard Solar Model at 99% CL. We discuss also the consequences of possible nu_e->anti-nu_{mu,tau} or nu_e->anti-nu_e transitions of solar neutrinos. We derive a model-independent lower limit of 0.52 at 99% CL for the ratio of the 8B nu_e flux produced in the Sun and its value in the BP2000 Standard Solar Model.Comment: 5 pages. Added discussion on possible nu_e->anti-nu_{mu,tau} or nu_e->anti-nu_e transition

Entanglement preparation using symmetric multiports

We investigate the entanglement produced by a multi-path interferometer that is composed of two symmetric multiports, with phase shifts applied to the output of the first multiport. Particular attention is paid to the case when we have a single photon entering the interferometer. For this situation we derive a simple condition that characterize the types of entanglement that one can generate. We then show how one can use the results from the single photon case to determine what kinds of multi-photon entangled states one can prepare using the interferometer.Comment: 6 pages, 2 figures, accepted for publication in European Journal of Physics

Zika Virus Outbreak on Curaçao and Bonaire, a Report Based on Laboratory Diagnostics Data

Background: Zika virus (ZIKV) emerged in May 2015 in Brazil, from which it spread to many other countries in Latin America. Cases of ZIKV infection were eventually also reported in Curaçao (January 2016) and Bonaire (February 2016). Methods: In the period of 16 December 2015 until 26 April 2017, serum, EDTA-plasma or urine samples were taken at Medical Laboratory Services (MLS) from patients on Curaçao and tested in qRT-PCR at the Erasmus Medical Centre (EMC) in the Netherlands. Between 17 October 2016 until 26 April 2017 all samples of suspected ZIKV-patients collected on Curaçao, as well as on Bonaire, were tested at MLS. Paired urine and/or serum samples from patients were analyzed for ZIKV shedding kinetics, and compared in terms of sensitivity for ZIKV RNA detection. Furthermore, the age and ge