Volumetric Display Research

The goal of this project was to research and develop a volumetric display system that allows a three-dimensional CAD file to be displayed in real space. The system used a Xilinx Zynq SoC to process a CAD model into a series of two-dimensional images to be projected onto a spinning helicoid surface using DLP technology. The SoC contained a combination of custom logic on FPGA fabric as well as software on an embedded processor to implement the unique system functionality

Educating About Transport History: Developing Object-Learning Programs at the London Transport Museum

Incorporating engineering objects into educational outreach programs is a proven means to excite students about transport engineering. Grounded in theories of museum education and object-based learning, we offer means to help the London Transport Museum (LTM) achieve this mission: narratives on various disciplines of transport engineering, an engineering object catalog, and “toolkits” for using objects in engineering education programs. These resources and suggestions for acquiring new engineering objects are designed to enhance current and future program development

Hospitality and Cleaning on Campus

This project improved the efficiency and capabilities of two work areas in the self-sufficient San Francisco Agricultural School: morning cleaning and hotel operations. Interviews, focus groups, survey results, and scientific management principles were employed. Operational analyses identified problems in cleaning group distributions and processes, as well as hotel services and organization. Deliverables and recommendations - including cleaning checklists, group assignments, hotel scripts, and spreadsheets - were provided to increase proficiency. All methods and deliverables are simple enough to be later replicated by the school

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

Background: Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia’s pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species. Results: We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago. Conclusions: Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

Background: Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia's pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species. Results: We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago. Conclusions: Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle

The First Extrasolar Planet Discovered with a New Generation High Throughput Doppler Instrument

We report the detection of the first extrasolar planet, ET-1 (HD 102195b), using the Exoplanet Tracker (ET), a new generation Doppler instrument. The planet orbits HD 102195, a young star with solar metallicity that may be part of the local association. The planet imparts radial velocity variability to the star with a semiamplitude of $63.4\pm2.0$ m s$^{-1}$ and a period of 4.11 days. The planetary minimum mass ($m \sin i$) is $0.488\pm0.015$ $M_J$.Comment: 42 pages, 11 figures and 5 tables, Accepted for publication in Ap

Discovery of a Low-Redshift Hot Dust-Obscured Galaxy

We report the discovery of the hyperluminous, highly obscured AGN WISE J190445.04+485308.9 (W1904+4853 hereafter, $L_{bol} = 1.1 \times 10^{13} \ L_{\odot}$) at z=0.415. Its well-sampled spectral energy distribution (SED) is dominated by infrared dust emission, though broad emission lines are detected in the optical spectra. These features suggest that W1904+4853 contains an actively accreting supermassive black hole hidden in its dusty cocoon, resembling the observed properties of Hot Dust-Obscured Galaxies (Hot DOGs), a population previously only identified at z>1.0. Using the broad component of the MgII emission line, we estimate a black hole mass of$log \ (M_{BH}/M_{\odot}) = 8.4 \pm 0.3$. The corresponding Eddington ratio of$1.4 \pm 0.2$implies that the central black hole accretion is at the theoretical limit of isotropic accretion. The rest-frame UV-optical SED and [O II] emission line also indicate that the host galaxy of W1904+4853 harbors strong star formation activity at the rate of up to$\sim 45 \ M_{\odot} \ yr^{-1}$. With an estimated stellar mass of$3 \times 10^{10} \ M_{\odot}$, the host galaxy appears to be a starburst system with respect to the main sequence of the star-forming galaxies at the same redshift. Although blueshifted and asymmetric [O III] emission provides evidence of an outflow, we estimate it to be an order of magnitude smaller than the star formation rate, indicating that the current obscured AGN activity at the center has not yet produced significant feedback on the host galaxy star formation activity. W1904+4853 supports the interpretation that Hot DOGs are a rare transitional phase of AGN accretion in galaxy evolution, a phase that can persist into the present-day Universe.Comment: 19 pages, 6 figures, submitted to Ap

Making Big Data Useful for Health Care: A Summary of the Inaugural MIT Critical Data Conference

With growing concerns that big data will only augment the problem of unreliable research, the Laboratory of Computational Physiology at the Massachusetts Institute of Technology organized the Critical Data Conference in January 2014. Thought leaders from academia, government, and industry across disciplines--including clinical medicine, computer science, public health, informatics, biomedical research, health technology, statistics, and epidemiology--gathered and discussed the pitfalls and challenges of big data in health care. The key message from the conference is that the value of large amounts of data hinges on the ability of researchers to share data, methodologies, and findings in an open setting. If empirical value is to be from the analysis of retrospective data, groups must continuously work together on similar problems to create more effective peer review. This will lead to improvement in methodology and quality, with each iteration of analysis resulting in more reliability

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin