Faculty Scholarship
Showing 251 - 260 of 733 Items
An empirical study of memory sharing in virtual machines
Date: 2019-01-01
Creator: Sean Barker, Timothy Wood, Prashant Shenoy, Ramesh Sitaraman
Access: Open access
- Content-based page sharing is a technique often used in virtualized environments to reduce server memory requirements. Many systems have been proposed to capture the benefits of page sharing. However, there have been few analyses of page sharing in general, both considering its real-world utility and typical sources of sharing potential. We provide insight into this issue through an exploration and analysis of memory traces captured from real user machines and controlled virtual machines. First, we observe that absolute sharing levels (excluding zero pages) generally remain under 15%, contrasting with prior work that has often reported savings of 30% or more. Second, we find that sharing within individual machines often accounts for nearly all (>90%) of the sharing potential within a set of machines, with inter-machine sharing contributing only a small amount. Moreover, even small differences between machines significantly reduce what little inter-machine sharing might otherwise be possible. Third, we find that OS features like address space layout randomization can further diminish sharing potential. These findings both temper expectations of real-world sharing gains and suggest that sharing efforts may be equally effective if employed within the operating system of a single machine, rather than exclusively targeting groups of virtual machines.
A two-hybrid assay to study protein interactions within the secretory pathway
Date: 2010-12-01
Creator: Danielle H. Dube, Bin Li, Ethan J. Greenblatt, Sadeieh Nimer, Amanda K., Raymond, Jennifer J. Kohler
Access: Open access
- Interactions of transcriptional activators are difficult to study using transcription-based two-hybrid assays due to potent activation resulting in false positives. Here we report the development of the Golgi two-hybrid (G2H), a method that interrogates protein interactions within the Golgi, where transcriptional activators can be assayed with negligible background. The G2H relies on cell surface glycosylation to report extracellularly on protein-protein interactions occurring within the secretory pathway. In the G2H, protein pairs are fused to modular domains of the reporter glycosyltransferase, Och1p, and proper cell wall formation due to Och1p activity is observed only when a pair of proteins interacts. Cells containing interacting protein pairs are identified by selectable phenotypes associated with Och1p activity and proper cell wall formation: cells that have interacting proteins grow under selective conditions and display weak wheat germ agglutinin (WGA) binding by flow cytometry, whereas cells that lack interacting proteins display stunted growth and strong WGA binding. Using this assay, we detected the interaction between transcription factor MyoD and its binding partner Id2. Interfering mutations along the MyoD:Id2 interaction interface ablated signal in the G2H assay. Furthermore, we used the G2H to detect interactions of the activation domain of Gal4p with a variety of binding partners. Finally, selective conditions were used to enrich for cells encoding interacting partners. The G2H detects protein-protein interactions that cannot be identified via traditional two-hybrid methods and should be broadly useful for probing previously inaccessible subsets of the interactome, including transcriptional activators and proteins that traffic through the secretory pathway. © 2010 Dube et al.
Learning by lending
Date: 2019-01-01
Creator: Matthew Botsch, Victoria Vanasco
Access: Open access
- This paper studies bank learning through repeated interactions with borrowers from a new perspective. To understand learning by lending, we adapt a methodology from labor economics to analyze how loan contract terms evolve as banks acquire new information about borrowers. We construct “proxy” variables for this information using data from borrowers’ out-of-sample, future credit performance. Due to the timing of their construction, banks could not have used these variables directly to price loans. We nonetheless find that these proxies increasingly predict loan prices as relationships progress, even after controlling for possible omitted variable bias. Our methodology provides strong evidence that: (a) bank learning affects loan prices, and (b) relationship benefits are heterogeneous. In particular, higher quality borrowers face differentially lower spreads as their relationship with lenders develop – and banks learn about their quality – while lower quality borrowers see loan prices increase and their loan amounts fall. We further find suggestive evidence that banks incorporate CEO-specific information into loan prices.
Wandering words: Tracing changes in words used by teacher tweeters over time
Date: 2017-01-01
Creator: Stephen Houser, Doris Santoro, Clare Bates Congdon, Jessica Hochman
Access: Open access
- Public school teachers in the United States are often constrained in terms of their ability to express their moral views on issues that affect their schools, classrooms, students, and teaching practices, but are able to express their ideas, concerns, and frustrations as private citizens using social media. Previously we developed the Tweet Capture and Clustering System (TCCS) in order to explore how teachers use Twitter, looking at word usage among a group of teacher tweeters, and attempting to find clusters of teachers who have similar patterns of word usage in their tweets. In the work reported here, we look at teacher tweeters across the 12 months of 2016, seeking to understand how the clusters and the words used in these clusters vary from month to month. In this initial look at the dynamics of the system, we see some evidence of word usage changing across the 12-month period. This initial work suggests that extending TCCS to have temporal topic tracing as a core capability will be a meaningful addition to of the system. Copyright held by the author(s).
On kindleberger and hegemony: From berlin to MIT and back
Date: 2014-01-01
Creator: Stephen Meardon
Access: Open access
- The most conspicuous idea of Charles P. Kindleberger’s later career is the value of a single country acting as stabilizer of an international economy prone to instability. It runs through his widely read books, The World in Depression, 1929-1939 (1973), Manias, Panics, and Crashes (1978), A Financial History of Western Europe (1984), and kindred works. This essay traces Kindleberger’s attachment to the idea of “hegemonic stability” back to his tenure as chief of the State Department’s Division of German and Austrian Economic Affairs from 1945 to 1947 and adviser to the European Recovery Program from 1947 to 1948. In both capacities Kindleberger observed and participated indirectly in the 1948 monetary reform in Western Germany. In the 1990s, during his octogenary decade, he revisited the German monetary reform with a fellow participant, economist, and longtime friend, F. Taylor Ostrander. Their collaborative essay became Kindleberger’s effort to reclaim hegemonic stability theory from the scholars who developed it following his works of the 1970s and 1980s.
“Magali García Ramis: La historia que uno se inventa”. A Body of One’s Own: Conversations with Caribbean Women Writers
Date: 2007-01-01
Creator: Nadia V. Celis Salgado, Magali García Ramis
Access: Open access
A structural role for arginine in proteins: Multiple hydrogen bonds to backbone carbonyl oxygens
Date: 1994-01-01
Creator: C. L. Borders, John A. Broadwater, Paula A. Bekeny, Johanna E. Salmon, Ann S., Lee, Aimee M. Eldridge, Virginia B. Pett
Access: Open access
- We propose that arginine side chains often play a previously unappreciated general structural role in the maintenance of tertiary structure in proteins, wherein the positively charged guanidinium group forms multiple hydrogen bonds to backbone carbonyl oxygens. Using as a criterion for a “structural” arginine one that forms 4 or more hydrogen bonds to 3 or more backbone carbonyl oxygens, we have used molecular graphics to locate arginines of interest in 4 proteins: Arg 180 in Thermus thermophilus manganese superoxide dismutase, Arg 254 in human carbonic anhydrase II, Arg 31 in Streptomyces rubiginosus xylose isomerase, and Arg 313 in Rhodospirillum rubrum ribulose‐1,5‐bisphosphate carboxylase/oxygenase. Arg 180 helps to mold the active site channel of superoxide dismutase, whereas in each of the other enzymes the structural arginine is buried in the “mantle” (i.e., inside, but near the surface) of the protein interior well removed from the active site, where it makes 5 hydrogen bonds to 4 backbone carbonyl oxygens. Using a more relaxed criterion of 3 or more hydrogen bonds to 2 or more backbone carbonyl oxygens, arginines that play a potentially important structural role were found in yeast enolase, Bacillus stearothermophilus glyceraldehyde‐3‐phosphate dehydrogenase, bacteriophage T4 and human lysozymes, Enteromorpha prolifera plastocyanin, HIV‐1 protease, Trypanosoma brucei brucei and yeast triosephosphate isomerases, and Escherichia coli trp aporepressor (but not trp repressor or the trp repressor/operator complex). In addition to helping form the active site funnel in superoxide dismutase, the structural arginines found in this study play such diverse roles as stapling together 3 strands of backbone from different regions of the primary sequence, and tying α‐helix to α‐helix, βturn to β‐turn, and subunit to subunit. Copyright © 1994 The Protein Society
Differential neuropeptide modulation of premotor and motor neurons in the lobster cardiac ganglion
Date: 2020-10-01
Creator: Emily R. Oleisky, Meredith E. Stanhope, J. Joe Hull, Andrew E. Christie, Patsy S., Dickinson
Access: Open access
- The American lobster, Homarus americanus, cardiac neuromuscular system is controlled by the cardiac ganglion (CG), a central pattern generator consisting of four premotor and five motor neurons. Here, we show that the premotor and motor neurons can establish independent bursting patterns when decoupled by a physical ligature. We also show that mRNA encoding myosuppressin, a cardioactive neuropeptide, is produced within the CG. We thus asked whether myosuppressin modulates the decoupled premotor and motor neurons, and if so, how this modulation might underlie the role(s) that these neurons play in myosuppressin's effects on ganglionic output. Although myosuppressin exerted dose-dependent effects on burst frequency and duration in both premotor and motor neurons in the intact CG, its effects on the ligatured ganglion were more complex, with different effects and thresholds on the two types of neurons. These data suggest that the motor neurons are more important in determining the changes in frequency of the CG elicited by low concentrations of myosuppressin, whereas the premotor neurons have a greater impact on changes elicited in burst duration. A single putative myosuppressin receptor (MSR-I) was previously described from the Homarus nervous system. We identified four additional putative MSRs (MSR-II-V) and investigated their individual distributions in the CG premotor and motor neurons using RT-PCR. Transcripts for only three receptors (MSR-II-IV) were amplified from the CG. Potential differential distributions of the receptors were observed between the premotor and motor neurons; these differences may contribute to the distinct physiological responses of the two neuron types to myosuppressin. NEW & NOTEWORTHY Premotor and motor neurons of the Homarus americanus cardiac ganglion (CG) are normally electrically and chemically coupled, and generate rhythmic bursting that drives cardiac contractions; we show that they can establish independent bursting patterns when physically decoupled by a ligature. The neuropeptide myosuppressin modulates different aspects of the bursting pattern in these neuron types to determine the overall modulation of the intact CG. Differential distribution of myosuppressin receptors may underlie the observed responses to myosuppressin.
Ocean primary production derived from satellite data: An evaluation with atmospheric oxygen measurements
Date: 1999-06-01
Creator: Yves Balkanski, Patrick Monfray, Mark Battle, Martin Heimann
Access: Open access
- Recently, very precise measurements have detected the seasonal variability in the atmospheric O2/N2 ratio at several sites in the northern and southern hemispheres. In this paper, we derive marine primary productivity (PP) from satellite ocean color data. To infer air-sea oxygen fluxes, a simple one-dimensional diagnostic model of ocean biology has been developed that depends on only two parameters: a time delay between organic production and oxidation (set to 2 weeks) and an export scale length (50 m). This model gives a global net community production of 4.3 mol C m-2 yr-1 in the euphotic zone and 3.2 mol C m-2 yr-1 in the mixed layer. This last value corresponds to a global f ratio (net community production (NCP)/PP) at the base of the mixed layer of 0.37. The air-sea fluxes derived from this model are then used at the base of a three-dimensional atmospheric model to compare the atmospheric seasonal cycle of O2/N2 at five sites: Cape Grim (40.6S, 144.6E), Baring Head (41.3S, 174.8E), Mauna Loa (19.5N,154.8W), La Jolla (32.9N, 117.3W), and Barrow (71.3N, 156.6W). The agreement between model and observations is very encouraging. We infer from the agreement that the seasonal variations in O2/N2 are largely controlled by the photosynthesis rate but also by the remineralization linked to the deepening and shoaling of the mixed layer. Lateral ventilation to high latitudes may also be an important factor controlling the amplitude of the seasonal cycle.
Disruption of topoisomerase II perturbs pairing in Drosophila cell culture
Date: 2007-09-01
Creator: Benjamin R. Williams, Jack R. Bateman, Natasha D. Novikov, C. Ting Wu
Access: Open access
- Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. Here, we explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), we assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. We have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc167 cells into G1, S, and G2 subpopulations, we show that even progression through these stages of the cell cycle does not significantly change pairing levels. Finally, our data indicate that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing. Copyright © 2007 by the Genetics Society of America.