Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / Includes bibliographical references (leaves 81-83). / Although embryonic stem (ES) cells and their pluripotent capability have been elucidated for decades, little study has been done on obtaining the pluripotency profile of ES cells in the incipient stages of differentiation. In this research, an ES cell line with transfected green fluorescent protein (GFP) co-expressed by an Oct-4 promoter was analyzed by fluorescence-activated cell sorter (FACS) to obtain such profile. As Oct-4 is an ES cell differentiation marker whose expression varies with pluripotency, GFP expression could simply be measured in these cells to determine how pluripotent they are as a population. The differentiation characterization of ES cells was also conducted with different culture conditions of reduced serum and glucose concentrations both in the presence and absence of leukemia inhibitory factor (LIF) which prevents spontaneous differentiation, as well as at varied LIF concentrations and seeding densities. In addition, fundamental growth kinetic and metabolic profiles were obtained to get a more complete picture of how ES cells behave under these varied culturing conditions. The doubling time (t[sub]d) of R1 Oct4-GFP cell line was found to be 13 hours in LIF⁺ culture and 8 hours in culture with LIF addition after 7 days of LIF withdrawal, implying that cell proliferation rate is higher for cells receiving a sudden upregulation of genes controlling cell division through LIF addition. Although the upregulation of the genes is rapid, the downregulation of these genes through LIF withdrawal was found to take 6-7 days, while 3-4 days were required to downregulate the pou5f gene (which controls Oct4 expression). Higher concentration of LIF resulted in higher ES cell proliferation rate, but GFP⁺ expression was unaffected by / (cont.) concentration. Higher seeding density resulted in greater improvement in GFP⁺ expression for LIF⁺ culture but lower non significant reduction in GFP⁺ expression in LIF⁻ culture. Low level of glucose in medium led to reduction in the rate of ES cellular mechanisms and lower Y[sub]lac/gluc (8-49 % versus 40-60 % in high glucose), but metabolic rates were consistent with cells grown in high glucose medium, implying more efficient glucose metabolism through oxidative phosphorylation. The level of serum in medium had no effect on GFP⁺ expression or cell proliferation rate in LIF⁺ cultures, but reduction in GFP⁺ expression level was higher and t[sub]d was longer in low-serum culture (71 [plus-minus] 33 hours versus 35 [plus-minus] 9 hours) in the absence of LIF. / by Yasunori Hashimura. / M.Eng.

Thesis (M. Eng. in Logistics)--Massachusetts Institute of Technology, Engineering Systems Division, 2007. / Includes bibliographical references (p. 74-75). / Increasing supply chain velocity has adverse consequences for consumer product goods manufacturers, but creates value and flexibility for retail stores. This thesis outlines a case study of a rapid replenishment pilot project between the food manufacturer General Mills, Inc. and their retail customer Giant Eagle. We outline constraints that General Mills had to impose upon their customer so it could remain profitable and retain its efficient operating strategy. We offer recommendations to General Mills on how to grow and sustain their rapid replenishment business. / by Deborah Eugenia Becker and Roman Viktorovich Korchagin. / M.Eng.in Logistics

Thesis (M. Eng. in Logistics)--Massachusetts Institute of Technology, Engineering Systems Division, 2005. / Includes bibliographical references (leaves 51-52). / This thesis determines how to design the supply chain policies in a hospital for the wide array of products that exist there. This research was done through interviewing staff and analyzing data of two hospitals implementing automated point of use systems. This thesis argues that a hospital needs to implement more than one supply chain policy in order to achieve its objective of maximizing patient care while avoiding prohibitive costs. The research further proposes that a hospital should develop its supply chain for a specific product based on that product's unit cost, demand, variability, physical size, and criticality. The research analyzes demand data from two hospitals and demonstrates that hospital demand can be modeled using a variation of Croston's method for intermittent demand. This fact was used to generate an appropriate s, Q inventory policy that can be adjusted to fit any product and supply chain policy implemented within the hospital. Under simulation, the proposed inventory policy outperformed existing policies by over 50%. This research further argues current aggregate and "one-size-fits-all" strategies are inappropriate in a hospital and discusses the importance for hospitals to add physical size and criticality attributes to their product master files as these will enable further supply chain enhancements. / by Derek T. DeScioli. / M.Eng.in Logistics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / Includes bibliographical references. / The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) in its wake. While the structural and physiological consequences of negative supercoiling have been well studied, technical challenges have prevented extensive examination of positively supercoiled DNA. Studies suggest that at sufficiently high levels of overwinding, DNA relieves strain by adopting an elongated structure, where the bases are positioned extrahelically and the backbones occupy the center of the helix. This transition has only been identified, however, at a degree of supercoiling substantially higher than is generated physiologically. To examine the structural changes resulting from physiological levels of positive DNA supercoiling, I have developed a method for preparing highly purified positively supercoiled plasmid substrates. Based on a method previously developed in this laboratory, this allows for preparation of large quantities of very pure, highly positively supercoiled plasmid. It also expands on earlier methods by exploiting ionic strength to modulate the direction of supercoiling introduced, allowing preparation of either positively or negatively supercoiled substrates. / (cont.) A combination of approaches has been used to elucidate changes to DNA structure that result from physiological levels of positive supercoiling. Enzymatic probes for regions of single-stranded character are not reactive with positively supercoiled plasmid, indicating that stably unpaired regions are not present. Additionally, the effect of supercoiling on the activity of restriction enzymes has been examined. With the enzymes tested, no substantial differences in cleavage rates were observed with either positively or negatively supercoiled substrates. To examine structural changes at a wider range of superhelical densities, design and preparation was undertaken on 2-aminopurine-containing DNA substrates for use in fluorescence studies with a magnetic micromanipulator. Technical limitations rendered these experiments infeasible with current instrumentation, but important insights were gained for future fluorescence-based A destabilizing effect on the base pairs, however, can be seen using Raman difference spectroscopy, suggesting a subtle shift toward the more extreme extrahelical state. / (cont.) The Raman data suggest that structural adjustments due to positive supercoiling are small but significant, and in addition to the base-pairing effects, alterations are observed in phosphodiester torsion and the minor groove environment, as well as a slight shift in sugar pucker conformation to accommodate lengthening of the DNA backbone. These results point to subtle changes in DNA structure caused by biologically relevant levels of positive superhelical tension and positive supercoiling. All of the changes are consistent with the mechanical effects of helical overwinding and suggest a model in which base pair destabilization in overwound DNA could affect the search mechanisms used by DNA repair enzymes and the binding of other proteins to DNA. / by Marita Christine Barth. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, February 2007. / Includes bibliographical references. / Ligand binding to cell surface receptors initiates a cascade of signaling events regulated by dynamic phosphorylation on a multitude of pathway proteins. Quantitative features, including intensity, timing, and duration of phosphorylation of particular residues play a role in determining cellular response. Mass spectrometry has been previously used to identify and catalog phosphorylation sites or quantify the phosphorylation dynamics of proteins in cell signaling networks. However, identification of phosphorylation sites presents little insight on cellular processes and quantification of phosphorylation dynamics of whole proteins masks the different roles that several phosphorylation sites within one protein have in the network. We have designed a mass spectrometry technique allowing site-specific quantification of dynamic phosphorylation in the cell. We have applied this technique to study signaling events triggered by different members of the epidermal growth factor receptor (EGFR) family. Self organizing maps (SOMs) analysis of our data has highlighted potential biological functions for phosphorylation sites previously unrelated to EGFR signaling and identified network modules regulated by different combinations of EGFR family members. Partial least square regression (PLSR) analysis of our data identified combination of signals strongly correlating with cellular proliferation and migration. / (cont.) Because our method was based on information dependent acquisition (IDA) the reproducibility of peptides identified across multiple analyses was low. To improve our methodology to permit both discovery of new phosphorylation sites and robust quantification of hundreds of nodes within a signaling network we combined IDA-analysis with multiple reaction monitoring (MRM) of selected precursor ions. MRM quantification of high resolution temporal profiles of the EGFR network provided 88% reproducibility across four different samples, as compared to 34% reproducibility by IDA only. In summary, we have developed a new robust mass spectrometry technique allowing site specific identification, quantification and monitoring of dynamic phosphorylation in the cell with high temporal resolution and under any number of biological conditions. Because the data obtained with this method is not sparse it is especially well suited to mathematical and computational analyses. The methodology is also broadly applicable to multiple signaling networks and to a variety of samples, including quantitative analysis of signaling networks in clinical samples. / by Alejandro Wolf Yadlin. / Ph.D.

Thesis (M. Eng. in Logistics)--Massachusetts Institute of Technology, Engineering Systems Division, 2007. / Includes bibliographical references (leaves 54-55). / The objective of this thesis is to analyze the trade-offs of two retail replenishment strategies, DSD (Direct Store Delivery) model and Traditional model. Conceptual and cost models are set up to analyze the trade-offs, and numerous interviews were conducted to obtain insights from academic scholars and industry practitioners. Retail products, retailers and suppliers are categorized according to their synthesized attributes. Based on such categories, retail replenishment strategies are tested to determine which categories are more suitable for DSD or traditional strategies. Besides qualitative analysis on tradeoffs of alternatives, quantitative cost models are built to quantify the tradeoffs between alternatives. / by Jiaqi (Philip) Kuai / M.Eng.in Logistics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Engineering Systems Division, 2011. / 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. 109-121). / The Energy Box is an always-on background processor automating the temporal management of one's home or small business electrical energy usage. Cost savings are achieved in a variety of environments, ranging from at pricing of electricity to real-time demand-sensitive pricing. Further cost savings derive from utilizing weather forecasts to manage local rooftop wind turbines or solar photovoltaics and/or to anticipate price swings from central utilities. The main motivation of this research is to design, construct and test a prototype software architecture for the Energy Box that can accommodate a wide variety of local energy management environments and user preferences. Under some scenarios, appliances can be optimally controlled one at a time, independent of each other. In other scenarios, coordinated control of appliances, either simultaneous or time-sequenced, provide better outcomes. Stochastic dynamic programming is the primary optimization engine. The optimization goal is to balance cost minimization with thermal comfort as specified by consumer preferences. The results demonstrate that the desired general energy management platform is feasible as well as desirable for saving money on electricity while maintaining comfort preferences. Scaling up to neighborhoods, towns and cities, a key contribution is improved understanding of single-home electricity demand dynamics induced by automated decisions. Further research will determine how such local automated decisions affect the broader smart grid with regard to resilience, stability and pricing. / by Daniel James Livengood. / Ph.D.

Thesis (M. Eng. in Logistics)--Massachusetts Institute of Technology, Engineering Systems Division, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 60-62). / The chemical industry is a highly competitive and low margin industry. Chemical transportation faces stringent safety regulations meaning that Cost-To-Serve (C2S), costs associated with products net flow from manufacturers to customers, consists of a big percentage of the delivered product cost. Supply chain practitioners in this industry need to make key logistics decisions to minimize C2S for profitability and business sustainability. In this thesis, we present a network optimization model to minimize the total C2S for SKU-1, a low volume and low margin industrial chemical with a customer base spread across North and South America. We use a mathematical linear program to investigate the effects on total C2S when available production capacities and sources are shifted. We develop the model as a minimum cost flow problem, and more specifically, as a production and transportation problem (PTP). We analyze the total C2S under three scenarios. In the baseline scenario there are three manufacturing facilities in the Midwest, South East, and Europe. In the second scenario, where the Midwest supplier is excluded from the network, the C2S increases by 3%. In the third scenario, where both the Midwest and South East facilities are excluded, the C2S increases by 13%. Under each scenario we calculate the C2S for each individual customer and identify the customers most impacted by the change in supply. Our results provide insight regarding the changes expected to the supply network under capacity constraints and how those changes may affect the profitability of individual customers. / by Fred Dacha and Li Jin. / M.Eng.in Logistics

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / Includes bibliographical references. / Epidermal growth factor (EGF) receptor autocrine and/or paracrine signaling plays an important role in normal epithelial cell proliferation, survival, adhesion and migration. Aberrant expression of the EGF receptor and its cognate ligands have been implicated in various types of cancers, hence EGF receptor autocrine activation is thought to also be involved in tumorigenesis. EGF family ligands are synthesized as membrane-anchored proteins requiring proteolytic release to form the mature soluble, receptor-binding factor. Despite the pathophysiological importance of autocrine systems, how protease-mediated ligand release quantitatively influences receptor-mediated signaling and consequent cell behavior is poorly understood. Therefore, we explored the relationship between autocrine EGF release rate and receptor-mediated ERK activation and migration in human mammary epithelial cells. A quantitative spectrum of EGF release rates was achieved using chimeric EGF ligand precursors modulated by the addition of the metalloprotease inhibitor batimastat. We found that ERK activation increased with increasing ligand release rates despite concomitant EGF receptor downregulation. / (cont.) Cell migration speed depended linearly on the steady-state phospho-ERK level, but was much greater for autocrine compared to exogenous stimulation. In contrast, cell proliferation rates were constant across the various treatment conditions. In addition, we investigated an EGFR-mediated positive feedback through ERK that stimulated a 4-fold increase in release rate of our TGFa based construct. Thus, in these cells, ERK-mediated migration stimulated by EGF receptor signaling is most sensitively regulated by autocrine ligand control mechanisms. / by Elizabeth Jane Joslin. / Ph.D.

Thesis: M. Eng. in Logistics, Massachusetts Institute of Technology, Engineering Systems Division, 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (page 57). / The concept of using different supply chain strategies for different products or product families is a fairly simple component of supply chain management. This practice, known as SKU segmentation, is widely used by many companies. However, most research and success stories involve a relatively stable portfolio of brands and products, and products with easily identifiable attributes such as profit margins and demand. This thesis attempts to determine if and how a SKU segmentation can be conducted when product mix is constantly changing and many key variables used in traditional segmentations are not known in advance. To explore this problem, we analyze one year of purchase order data and shipment data provided by our sponsor company. The objective is to use data from purchase orders to predict which items are candidates for different supply chain configurations (i.e. an expedited supply chain for time-sensitive products or an efficient supply chain if there is opportunity to reduce cost and still meet demand). We start by mapping the current supply chain process using historical data and interviews with employees. The key piece of the process we want to understand is how early or late products arrive at destination in relation to when those goods are expected in retail stores (a metric we refer to as "destination dwell time"). We then use visualization and statistical analysis to determine what PO information is related to the destination dwell time. After testing various multi-factor regression models to predict the length of this dwell time, we conclude that a neural network regression model predicts this time most accurately. We then assess whether or not it is feasible for the sponsor company to use this model to "speed up" or "slow down" the supply chain for different products as needed. / by Huiping Jin and Brad Gilligan. / M. Eng. in Logistics