Improving complex enterprises with system models

Thesis (S.M.)--Massachusetts Institute of Technology, Engineering Systems Division, 2005.Includes bibliographical references (leaves 96-98).Air Force sustainment operations are the focus of an intensive internal effort to improve performance and reduce costs. Past improvement initiatives have often failed to produce the intended results, and have caused performance to decline in some cases. Exploratory research was conducted at an Air Logistics Center to study how improvements are executed. Two conclusions are drawn from this research. The first is that changing sustainment operations is a problem of high dynamic and behavioral complexity. The second conclusion is that system models are well suited to coordinating change at the ALC because they provide insight into how a complicated system can be managed and improved. Three key findings support these conclusions. First, there is significant correlation between categories of unavailable F-16 aircraft such that reductions in one category are associated with increases in another. Second, an analysis of change efforts in two parts of the ALC shows that systemic influences, such as the inability to reinvest in improvements, are hindering change initiatives in one part of the ALC.(cont.) The third finding is that a model of sustainment operations suggests that independent improvement initiatives are outperformed by coordinated efforts driven with an understanding of systemic interactions. Leaders throughout the sustainment community have expressed their desire to understand how sustainment operations function as a system. A hybrid approach to change is offered as a method for understanding and improving sustainment operations. System models are used to quantify and model system interactions; then policies and recommendations are drawn from the models. Recommendations may include process-level improvements utilizing change methods already in use at the ALC.by Justin M. Hemann.S.M

Assessing positive matrix factorization model fit: a new method to estimate uncertainty and bias in factor contributions at the daily time scale

International audienceA Positive Matrix Factorization receptor model for aerosol pollution source apportionment was fit to a synthetic dataset simulating one year of daily measurements of ambient PM2.5 concentrations, comprised of 39 chemical species from nine pollutant sources. A novel method was developed to estimate model fit uncertainty and bias at the daily time scale, as related to factor contributions. A balanced bootstrap is used to create replicate datasets, with the same model then fit to the data. Neural networks are trained to classify factors based upon chemical profiles, as opposed to correlating contribution time series, and this classification is used to align factor orderings across results associated with the replicate datasets. Factor contribution uncertainty is assessed from the distribution of results associated with each factor. Comparing modeled factors with input factors used to create the synthetic data assesses bias. The results indicate that variability in factor contribution estimates does not necessarily encompass model error: contribution estimates can have small associated variability yet also be very biased. These results are likely dependent on characteristics of the data

Assessing positive matrix factorization model fit: a new method to estimate uncertainty and bias in factor contributions at the measurement time scale

A Positive Matrix Factorization receptor model for aerosol pollution source apportionment was fit to a synthetic dataset simulating one year of daily measurements of ambient PM<sub>2.5</sub> concentrations, comprised of 39 chemical species from nine pollutant sources. A novel method was developed to estimate model fit uncertainty and bias at the daily time scale, as related to factor contributions. A circular block bootstrap is used to create replicate datasets, with the same receptor model then fit to the data. Neural networks are trained to classify factors based upon chemical profiles, as opposed to correlating contribution time series, and this classification is used to align factor orderings across the model results associated with the replicate datasets. Factor contribution uncertainty is assessed from the distribution of results associated with each factor. Comparing modeled factors with input factors used to create the synthetic data assesses bias. The results indicate that variability in factor contribution estimates does not necessarily encompass model error: contribution estimates can have small associated variability across results yet also be very biased. These findings are likely dependent on characteristics of the data

Proteasome assembly from 15S precursors involves major conformational changes and recycling of the Pba1-Pba2 chaperone

The chaperones Ump1 and Pba1-Pba2 promote efficient biogenesis of 20S proteasome core particles from its subunits via 15S intermediates containing alpha and beta subunits, except beta7. Here we elucidate the structural role of these chaperones in late steps of core particle biogenesis using biochemical, electron microscopy, cross-linking and mass spectrometry analyses. In 15S precursor complexes, Ump1 is largely unstructured, lining the inner cavity of the complex along the interface between alpha and beta subunits. The alpha and beta subunits form loosely packed rings with a wider alpha ring opening than in the 20S core particle, allowing for the Pba1-Pba2 heterodimer to be partially embedded in the central alpha ring cavity. During biogenesis, the heterodimer is expelled from the alpha ring by a restructuring event that organizes the beta ring and leads to tightening of the alpha ring opening. In this way, the Pba1-Pba2 chaperone is recycled for a new round of proteasome assembly

Stage-specific sensitivity to p53 restoration during lung cancer progression

2011 May 25Tumorigenesis is a multistep process that results from the sequential accumulation of mutations in key oncogene and tumour suppressor pathways. Personalized cancer therapy that is based on targeting these underlying genetic abnormalities presupposes that sustained inactivation of tumour suppressors and activation of oncogenes is essential in advanced cancers. Mutations in the p53 tumour-suppressor pathway are common in human cancer and significant efforts towards pharmaceutical reactivation of defective p53 pathways are underway1, 2, 3. Here we show that restoration of p53 in established murine lung tumours leads to significant but incomplete tumour cell loss specifically in malignant adenocarcinomas, but not in adenomas. We define amplification of MAPK signalling as a critical determinant of malignant progression and also a stimulator of Arf tumour-suppressor expression. The response to p53 restoration in this context is critically dependent on the expression of Arf. We propose that p53 not only limits malignant progression by suppressing the acquisition of alterations that lead to tumour progression, but also, in the context of p53 restoration, responds to increased oncogenic signalling to mediate tumour regression. Our observations also underscore that the p53 pathway is not engaged by low levels of oncogene activity that are sufficient for early stages of lung tumour development. These data suggest that restoration of pathways important in tumour progression, as opposed to initiation, may lead to incomplete tumour regression due to the stage-heterogeneity of tumour cell populations.National Cancer Institute (U.S.) (Cancer Center Support Grant P30-CA14051)American Cancer Society (New England Area Fellow)Leukemia & Lymphoma Society of America (Fellow)Massachusetts Institute of Technology. Undergraduate Research Program (John Reed Fund)Damon Runyon Cancer Research Foundation (Merck Fellow)Genentech, Inc. (Postdoctoral Fellow)Howard Hughes Medical Institut

In Vivo RNAi Screening Identifies Regulators of Actin Dynamics as Key Determinants of Lymphoma Progression

April 1, 2010Mouse models have markedly improved our understanding of cancer development and tumor biology. However, these models have shown limited efficacy as tractable systems for unbiased genetic experimentation. Here, we report the adaptation of loss-of-function screening to mouse models of cancer. Specifically, we have been able to introduce a library of shRNAs into individual mice using transplantable Eμ-myc lymphoma cells. This approach has allowed us to screen nearly 1,000 genetic alterations in the context of a single tumor-bearing mouse. These experiments have identified a central role for regulators of actin dynamics and cell motility in lymphoma cell homeostasis in vivo. Validation experiments confirmed that these proteins represent bona fide lymphoma drug targets. Additionally, suppression of two of these targets, Rac2 and twinfilin, potentiated the action of the front-line chemotherapeutic vincristine, suggesting a critical relationship between cell motility and tumor relapse in hematopoietic malignancies.National Institutes of Health (U.S.) (RO1 CA128803-01)Massachusetts Institute of Technology. Dept. of Biology (Training Grant)Massachusetts Institute of Technology. Undergraduate Research Opportunities ProgramNational Cancer Institute (U.S.). Integrative Cancer Biology Program (Grant 1-U54-CA112967

PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes

Developmental and lineage plasticity have been observed in numerous malignancies and have been correlated with tumor progression and drug resistance. However, little is known about the molecular mechanisms that enable such plasticity to occur. Here, we describe the function of the plant homeodomain finger protein 6 (PHF6) in leukemia and define its role in regulating chromatin accessibility to lineage-specific transcription factors. We show that loss of Phf6 in B-cell leukemia results in systematic changes in gene expression via alteration of the chromatin landscape at the transcriptional start sites of B-cell- and T-cell-specific factors. Additionally, Phf6KO cells show significant down-regulation of genes involved in the development and function of normal B cells, show up-regulation of genes involved in T-cell signaling, and give rise to mixed-lineage lymphoma in vivo. Engagement of divergent transcriptional programs results in phenotypic plasticity that leads to altered disease presentation in vivo, tolerance of aberrant oncogenic signaling, and differential sensitivity to frontline and targeted therapies. These findings suggest that active maintenance of a precise chromatin landscape is essential for sustaining proper leukemia cell identity and that loss of a single factor (PHF6) can cause focal changes in chromatin accessibility and nucleosome positioning that render cells susceptible to lineage transition.National Cancer Institute ; F31-CA183405 - National Institutes of Health ; 1122374 - National Science Foundation ; Ludwig Center for Molecular Oncology at Massachusetts Institute of Technology ; Koch Institute ; Dana-Farber/Harvard Cancer Center ; P30-CA14051 - Koch Institute ; NCI ; NIH ; National Science Foundatio

Studies on porcine circovirus type 2 vaccination of 5-day-old piglets

Porcine circovirus type 2 (PCV2) vaccines have become widely used since they became available in 2006. It is not uncommon for producers to use PCV2 vaccines in pigs younger than what is approved by manufacturers. The objective of this study was to determine the efficacy of a chimeric and a subunit PCV2 vaccine administered at 5 or 21 days of age. Forty-eight PCV2-naïve piglets were randomly divided into six groups of eight pigs each. Vaccination was done at day 5 or day 21, followed by triple challenge with PCV2, porcine parvovirus (PPV), and porcine reproductive and respiratory syndrome virus (PRRSV) at day 49. Vaccinated pigs seroconverted to PCV2 approximately 14 days postvaccination and had a detectable neutralizing antibody response by 21 days postvaccination regardless of age at vaccination. At day 49, the pigs vaccinated with the chimeric vaccine had significantly higher levels of neutralizing antibodies than the pigs vaccinated with the subunit vaccine. After challenge, vaccinated pigs had significantly decreased levels of PCV2 viremia and a decreased prevalence and severity of microscopic lesions compared to the positive-control group, which had severe lymphoid lesions associated with abundant PCV2 antigen, compatible with PCV-associated disease. The results of this study indicate that, under the conditions of this study, vaccination of PCV2-naïve pigs at day 5 or day 21 resulted in development of a detectable humoral immune response and provided reduction or complete protection against PCV2 viremia and PCV2-associated lesions after triple challenge with PCV2, PPV, and PRRSV

Short Telomeres Initiate Telomere Recombination in Primary and Tumor Cells

Human tumors that lack telomerase maintain telomeres by alternative lengthening mechanisms. Tumors can also form in telomerase-deficient mice; however, the genetic mechanism responsible for tumor growth without telomerase is unknown. In yeast, several different recombination pathways maintain telomeres in the absence of telomerase—some result in telomere maintenance with minimal effects on telomere length. To examine non-telomerase mechanisms for telomere maintenance in mammalian cells, we used primary cells and lymphomas from telomerase-deficient mice (mTR−/− and Eμmyc+mTR−/−) and CAST/EiJ mouse embryonic fibroblast cells. These cells were analyzed using pq-ratio analysis, telomere length distribution outliers, CO-FISH, Q-FISH, and multicolor FISH to detect subtelomeric recombination. Telomere length was maintained during long-term growth in vivo and in vitro. Long telomeres, characteristic of human ALT cells, were not observed in either late passage or mTR−/− tumor cells; instead, we observed only minimal changes in telomere length. Telomere length variation and subtelomeric recombination were frequent in cells with short telomeres, indicating that length maintenance is due to telomeric recombination. We also detected telomere length changes in primary mTR−/− cells that had short telomeres. Using mouse mTR+/− and human hTERT+/− primary cells with short telomeres, we found frequent length changes indicative of recombination. We conclude that telomere maintenance by non-telomerase mechanisms, including recombination, occurs in primary cells and is initiated by short telomeres, even in the presence of telomerase. Most intriguing, our data indicate that some non-telomerase telomere maintenance mechanisms occur without a significant increase in telomere length