Kaess, Michael; Johannsson, Hordur; Roberts, Richard; Ila, Viorela; Leonard, John Joseph; Dellaert, Frank
We present iSAM2, a fully incremental, graph-based version of incremental smoothing and mapping (iSAM). iSAM2 is based on a novel graphical model-based interpretation of incremental sparse matrix factorization methods, afforded by the recently introduced Bayes tree data structure. The original iSAM algorithm incrementally maintains the square root information matrix by applying matrix factorization updates. We analyze the matrix updates as simple editing operations on the Bayes tree and the conditional densities represented by its cliques. Based on that insight, we present a new method to incrementally change the variable ordering which has a large effect on efficiency. The efficiency and...
Thompson, Anne W.; Huang, Katherine H.; Saito, Mak A.; Chisholm, Sallie (Penny)
Prochlorococcus contributes significantly to ocean primary productivity. The link
between primary productivity and iron in specific ocean regions is well established
and iron-limitation of Prochlorococcus cell division rates in these regions has been
demonstrated. However, the extent of ecotypic variation in iron metabolism among
Prochlorococcus and the molecular basis for differences is not understood. Here, we
examine the growth and transcriptional response of Prochlorococcus strains, MED4
and MIT9313, to changing iron concentrations. During steady-state, MIT9313
sustains growth at an order-of-magnitude lower iron concentration than MED4. To
explore this difference, we measured the whole-genome transcriptional response of
each strain to abrupt iron starvation and rescue. Only four of the 1159...
Chervachidze, Serguei; Costello, James; Wheaton, William C.
In this paper we revisit many studies that have attempted to explain the determinants of real estate capitalization rates. We introduce two new innovations. First we are able to identify two macroeconomic factors that greatly impact cap rates besides risk free treasury rates. These are the general corporate risk premium operating in the economy, and the amount of debt (liquidity) available. The addition of these factors greatly adds to the ability of previous models to explain the secular fall of cap rates in the last decade and the recent rise. In addition, we use innovative tests for “structural” shifts in...
Seslen, Tracey; Wheaton, William C.
This study analyzes the impact of contemporaneous loan stress on the termination of loans in the commercial mortgage-backed securities pool from 1992 to 2004 using a novel measure, based on changes in net operating incomes and property values at the metropolitan statistical area-property-type-year level. Employing a semi-parametric competing risks model for a variety of specifications, we find that the probability of default is extremely low even at very high levels of stress, although the coefficient estimates of greatest interest are very statistically significant. These results suggest substantial lender forbearance and are consistent with previous research that models default as a...
Radtke, Gregg A.; Hadjiconstantinou, Nicolas; Wagner, Wolfgang
We present an efficient particle simulation method for the Boltzmann transport equation based on the low-variance deviational simulation Monte Carlo approach to the variable-hard-sphere gas. The proposed method exhibits drastically reduced statistical uncertainty for low-signal problems compared to standard particle methods such as the direct simulation Monte Carlo method. We show that by enforcing mass conservation, accurate simulations can be performed in the transition regime requiring as few as ten particles per cell, enabling efficient simulation of multidimensional problems at arbitrarily small deviation from equilibrium.
Porter, Stephen Calder; Forbes, Peter; Manzi, Shannon; Kalish, Leslie A.
Objective The authors examined the validity of documentation produced during paediatric emergency care to determine if a patient-driven health information technology called ParentLink produced higher-quality data than documentation completed by nurses and physicians.
Design The authors analysed the quality of information across elements of allergies to medications and the history of present illness (HPI) collected during a quasi-experimental intervention study where control periods with usual care alternated with intervention periods when ParentLink was operational. Documentation by emergency department (ED) providers was abstracted and compared with information generated through ParentLink. The criterion standard for the history of allergies to medications was a...
Fox, James G.; Kuipers, Ernst J.
The association between chronic active gastritis and pre-neoplastic conditions as well as invasive cancer of the stomach was established several decades ago. The risk of progression depended on the severity and distribution of gastritis, with cancer, in particular, occurring in subjects with pan-gastritis. Subsequently, Helicobacter pylori was recognised as the primary cause of chronic active gastritis, and it was demonstrated that the pattern of gastritis corresponded with the colonisation pattern of H pylori. We and others then showed both in animals and in humans that this pattern of colonisation and associated gastritis primarily depended on the level of acid output....
Gareau, Melanie G.; Wine, Eytan; Rodrigues, David M.; Cho, Joon Ho; Whary, Mark T.; Philpott, Dana J.; MacQueen, Glenda; Sherman, Philip M.
Background: The brain–gut axis is a key regulator of normal intestinal physiology; for example, psychological stress is linked to altered gut barrier function, development of food allergies and changes in behaviour. Whether intestinal events, such as enteric bacterial infections and bacterial colonisation, exert a reciprocal effect on stress-associated behaviour is not well established.
Objective: To determine the effects of either acute enteric infection or absence of gut microbiota on behaviour, including anxiety and non-spatial memory formation.
Methods: Behaviour was assessed following infection with the non-invasive enteric pathogen, Citrobacter rodentium in both C57BL/6 mice and germ-free Swiss-Webster mice, in the presence or absence...
Quercia, Daniele; Di Lorenzo, Giusy; Calabrese, Francesco; Ratti, Carlo
Television and newspapers sit at the top of many agency marketing plans, while outdoor advertising stays at the
bottom. The reason for this is that it’s difficult to account for who views a billboard, so there is no way of consistently determining the effectiveness of outdoor advertising. As a result, agencies do not consider the medium and allocate their money elsewhere. To change this situation, one needs to create new credible audience measurements for the outdoor marketing industry. Here we propose a new way of performing audience measurements that combines mobile phone location estimations with information freely available on the Internet....
Resch, Bernd; Lipson, Sam; Bers, Josh; Ratti, Carlo; Mittlboeck, Manfred; Welsh, Matt; Britter, Rex E.; Blaschke, Thomas
Pervasive environmental monitoring implies a wide range of technical, but
also socio-political challenges, and this applies especially to the sensitive context of
the city. In this paper, we elucidate issues for bringing out pervasive urban sensor
networks and associated concerns relating to fine-grained information provision. We
present the Common Scents project, which is based on the Live Geography
approach, and show how it can overcome these challenges. As opposed to hitherto
sensing networks, which are mostly built up in monolithic and closed systems, the
Common Scents approach aims to establish an open, standards based and modular
infrastructure. This ensures interoperability, portability and flexibility, which are crucial
prerequisites for pervasive...
Wu, Jonathan; Mari-Buye, Nuria; Fernandez Muinos, Teresa; Borros, Salvador; Favia, Pietro; Semino, Carlos Eduardo
Background: Isolated hepatocytes removed from their microenvironment soon lose their hepatospecific functions when cultured. Normally hepatocytes are commonly maintained under limited culture medium supply as well as scaffold thickness. Thus, the cells are forced into metabolic stress that degenerate liver specific functions. This study aims to improve hepatospecific activity by creating a platform based on classical collagen sandwich cultures. Results: The modified sandwich cultures replace collagen with self-assembling peptide, RAD16-I, combined with functional peptide motifs such as the integrin-binding sequence RGD and the laminin receptor binding sequence YIG to create a cell-instructive scaffold. In this work, we show that a...
Norville, Julie E.; Derda, Ratmir; Gupta, Saurabh; Drinkwater, Kelly A.; Belcher, Angela M.; Leschziner, Andres E.; Knight, Thomas F., Jr.
Background: BioBrick standard biological parts are designed to make biological systems easier to engineer (e.g. assemble, manipulate, and modify). There are over 5,000 parts available in the Registry of Standard Biological Parts that can be easily assembled into genetic circuits using a standard assembly technique. The standardization of the assembly technique has allowed for wide distribution to a large number of users -- the parts are reusable and interchangeable during the assembly process. The standard assembly process, however, has some limitations. In particular it does not allow for modification of already assembled biological circuits, addition of protein tags to pre-existing...
Mohl, Mathias; Salari, Raheleh; Will, Sebastian; Backofen, Rolf; Sahinalp, S. Cenk
Abstract Background Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programming formulations of the problem. Results In this paper, we introduce sparsification to significantly speedup the dynamic programming approaches for pseudoknotted RNA structure prediction, which also lower the space requirements. Although sparsification has been applied to a number of RNA-related structure prediction problems in the past few years, we provide the first application of sparsification to pseudoknotted RNA structure prediction specifically and to handling gapped fragments more generally -...
Hassan, Musa A.; Good, Barbara; Hanrahan, James P.; Campion, Deirdre; Sayers, Gearoid; Mulcahy, Grace; Sweeney, Torres
Suffolk sheep carrying the DRB1*1101 (previously referred to as-DRB1*0203 or G2) allele have been reported to show increased resistance to natural Teladorsagia circumcincta infection compared to non-carriers. The objective of this study was to compare the biochemical and physiological responses of DRB1*1101 carrier and non-carrier twin lambs to an experimental infection with 3 x 10 [superscript 4] L3 Teladorsagia circumcincta. The variables studied included worm burden, faecal egg count, abomasal mast cells, IgA, IgE, IgG1 plus IgG2 and haematological parameters at 0, 3, 7, 21 and 35 days post infection (dpi), and duodenal smooth muscle contractility at 0 and 35...
Rismani-Yazdi, Hamid; Haznedaroglu, Berat Z; Bibby, Kyle; Peccia, Jordan; Rismani-Yazdi, Hamid; Haznedaroglu, Berat Z.; Bibby, Kyle; Peccia, Jordan
Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production. Results Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45%...
Gerardi, Craig; Buongiorno, Jacopo; Hu, Lin-wen; McKrell, Thomas J.
Abstract Infrared thermometry was used to obtain first-of-a-kind, time- and space-resolved data for pool boiling phenomena in water-based nanofluids with diamond and silica nanoparticles at low concentration (<0.1 vol.%). In addition to macroscopic parameters like the average heat transfer coefficient and critical heat flux [CHF] value, more fundamental parameters such as the bubble departure diameter and frequency, growth and wait times, and nucleation site density [NSD] were directly measured for a thin, resistively heated, indium-tin-oxide surface deposited onto a sapphire substrate. Consistent with other nanofluid studies, the nanoparticles caused deterioration in the nucleate boiling heat transfer (by as much as...
Kurs, Andre B.; Kesler, Morris; Johnson, Steven G.
We propose a design for a conductive wire composed of several mutually insulated coaxial conducting shells. With the help of numerical optimization, it is possible to obtain electrical resistances significantly lower than those of a heavy-gauge copper wire or litz wire in the 2–20 MHz range. Moreover, much of the reduction in resistance can be achieved for just a few shells; in contrast, litz wire would need to contain ∼ 10[superscript 4] strands to perform comparably in this frequency range.
Stohl, A.; Seibert, P.; Arduini, J.; Eckhardt, S.; Fraser, P. J.; Greally, B. R.; Lunder, Chris R.; Maione, Michela; Muhle, Jens; O'Doherty, Simon; Prinn, Ronald G.; Reimann, S.; Saito, T.; Schmidbauer, N.; Simmonds, P. G.; Vollmer, M. K.; Weiss, R. F.; Yokouchi, Y.
A new analytical inversion method has been developed to determine the regional and global emissions of long-lived atmospheric trace gases. It exploits in situ measurement data from three global networks and builds on backward simulations with a Lagrangian particle dispersion model. The emission information is extracted from the observed concentration increases over a baseline that is itself objectively determined by the inversion algorithm. The method was applied to two hydrofluorocarbons (HFC-134a, HFC-152a) and a hydrochlorofluorocarbon (HCFC-22) for the period January 2005 until March 2007. Detailed sensitivity studies with synthetic as well as with real measurement data were done to quantify...
Diez Silva, Monica; Dao, Ming; Han, Jongyoon; Lim, Chwee Teck; Suresh, Subra
The biconcave shape and corresponding deformability of the human red blood cell
(RBC) is an essential feature of its biological function. This feature of RBCs can be
critically affected by genetic or acquired pathological conditions. In this review, we
highlight new dynamic in vitro assays that explore various hereditary blood disorders
and parasitic infectious diseases that cause disruption of RBC morphology and
mechanics. In particular, recent advances in high-throughput microfluidic devices make
it possible to sort/identify healthy and pathological human RBCs with different
In a series of recent papers David Velleman has argued that it is morally wrong to bring a child
into existence with the intention that the child will not have contact with one or both biological
parents. (Velleman, 2005, 2008) Put another way, “other things being equal, children should be
raised by their biological parents.” (Velleman, 2005 362fn 3) The primary targets of his
argument are those who use anonymous donor egg or sperm to conceive a child. On his view,
there is a significant value in being parented by and having ongoing contact with one’s biological
relatives. “What is most troubling about gamete donation is...