State Space Methods in Stata

We illustrate how to estimate parameters of linear state-space models using the Stata program sspace. We provide examples of how to use sspace to estimate the parameters of unobserved-component models, vector autoregressive moving-average models, and dynamic-factor models. We also show how to compute one-step, filtered, and smoothed estimates of the series and the states; dynamic forecasts and their confidence intervals; and residuals.

State Space Methods in Stata

We illustrate how to estimate parameters of linear state-space models using the Stata program sspace. We provide examples of how to use sspace to estimate the parameters of unobserved-component models, vector autoregressive moving-average models, and dynamic-factor models. We also show how to compute one-step, filtered, and smoothed estimates of the series and the states; dynamic forecasts and their confidence intervals; and residuals

The University of Michigan Biological Station 1909 - 1983

75th Anniversary VolumeThe University of Michigan Biological Station occupies a position of distinction among biological institutions. It is of singular importance among biologists, for it was here that a large number of biologists received their first experience with field biology. A decade ago, when I first assembled a listing of the mailing addresses of former students and staff, I found scarcely an institution of higher learning in America without at least one faculty member who had studied at Douglas Lake. For large numbers of former students, the Biological Station experience was the most important formative event of their college careers. Former students occupy positions of great distinction throughout the world in government, industry and academia. Their contributions to our knowledge of the biosphere are enormous and their influence on other scholars as amplified through their teaching has been immense. Beyond that, large numbers of individuals who had the good fortune to take classes at the Biological Station have had their lives enriched through a sharpened ability to understand and appreciate the incredible beauty of the natural world. An excellent history of the Biological Station was written by LaRue (1944). Further elaboration of the history is contained, as reminiscences by former administrators, professors, and students, in the Semicentennial Celebration Proceedings of the University of Michigan Biological Station, June 16-19, 1959. Here, I shall highlight some of the early history, a goodly amount recorded for the first time, and then describe developments of the most recent 25 years. The importance of the Biological Station is as great or greater today than it ever was as the human species continues to exploit and degrade the global ecosystem. The necessity for a thorough understanding of natural and disturbed ecosystems is increasingly urgent. Not withstanding the great advances being made in molecular biology and in genetic engineering, the necessity to understand thoroughly the biological composition, form, and function of the world in which we live, remains of paramount importance. Failure to balance this understanding against the advances of technology can only lead to human catastrophe. The Biological Station today continues its central role with educating each class of young disciples of biology and of promoting the scholarship of knowledge concerning all aspects of the living world. The University of Michigan must never withdraw from this obligation.http://deepblue.lib.umich.edu/bitstream/2027.42/94412/1/75th_Anniversary.PD

A Pilot and Feasibility Study to Evaluate Small and Large Bite Fascial Closure Techniques

Introduction. Few randomized controlled studies have been conducted comparing a small to large fascial bite technique, yet recommendations have been made to standardize small bite closures.  However, large scale randomized controlled trials require considerable effort and may benefit from a pilot study. Methods. This multi-center randomized controlled pilot study of adult patients undergoing median laparotomy incision investigated the feasibility of studying the outcomes between small and large surgical closure techniques. Results. Fifty of 100 planned patients consented, 32 patients completed surgery and 19 patients completed the one-year ultrasound.  Enrollment was 2.7 versus 8 patients per month pre/post addition of study coordinator.  Clinical results are summarized for feasibility demonstration purposes, but not analyzed for hypothesis testing.  The total cost of the pilot study was $19,152.50 and took 22 months from first surgery to final one-year ultrasound.  Conclusions. This feasibility assessment demonstrates the complexity of planning a large scale randomized trial evaluating small and large bite surgical closure technique.  To expand this pilot study to a full scaled sample size study would require dedicated personnel and large grant funding.

Towards Mirror Symmetry as Duality for Two-Dimensional Abelian Gauge Theories

Superconformal sigma models with Calabi--Yau target spaces described as complete intersection subvarieties in toric varieties can be obtained as the low-energy limit of certain abelian gauge theories in two dimensions. We formulate mirror symmetry for this class of Calabi--Yau spaces as a duality in the abelian gauge theory, giving the explicit mapping relating the two Lagrangians. The duality relates inequivalent theories which lead to isomorphic theories in the low-energy limit. This formulation suggests that mirror symmetry could be derived using abelian duality. The application of duality in this context is complicated by the presence of nontrivial dynamics and the absence of a global symmetry. We propose a way to overcome these obstacles, leading to a more symmetric Lagrangian. The argument, however, fails to produce a derivation of the conjecture.Comment: 14 pages, latex, no figure

Bacterial nitrate assimilation: gene distribution and regulation

In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism

Comprehensive Simultaneous Shipboard and Airborne Characterization of Exhaust from a Modern Container Ship at Sea

We report the first joint shipboard and airborne study focused on the chemical composition and water-uptake behavior of particulate ship emissions. The study focuses on emissions from the main propulsion engine of a Post-Panamax class container ship cruising off the central coast of California and burning heavy fuel oil. Shipboard sampling included micro-orifice uniform deposit impactors (MOUDI) with subsequent off-line analysis, whereas airborne measurements involved a number of real-time analyzers to characterize the plume aerosol, aged from a few seconds to over an hour. The mass ratio of particulate organic carbon to sulfate at the base of the ship stack was 0.23 ± 0.03, and increased to 0.30 ± 0.01 in the airborne exhaust plume, with the additional organic mass in the airborne plume being concentrated largely in particles below 100 nm in diameter. The organic to sulfate mass ratio in the exhaust aerosol remained constant during the first hour of plume dilution into the marine boundary layer. The mass spectrum of the organic fraction of the exhaust aerosol strongly resembles that of emissions from other diesel sources and appears to be predominantly hydrocarbon-like organic (HOA) material. Background aerosol which, based on air mass back trajectories, probably consisted of aged ship emissions and marine aerosol, contained a lower organic mass fraction than the fresh plume and had a much more oxidized organic component. A volume-weighted mixing rule is able to accurately predict hygroscopic growth factors in the background aerosol but measured and calculated growth factors do not agree for aerosols in the ship exhaust plume. Calculated CCN concentrations, at supersaturations ranging from 0.1 to 0.33%, agree well with measurements in the ship-exhaust plume. Using size-resolved chemical composition instead of bulk submicrometer composition has little effect on the predicted CCN concentrations because the cutoff diameter for CCN activation is larger than the diameter where the mass fraction of organic aerosol begins to increase significantly. The particle number emission factor estimated from this study is 1.3 × 10^(16) (kg fuel)^(−1), with less than 1/10 of the particles having diameters above 100 nm; 24% of particles (>10 nm in diameter) activate into cloud droplets at 0.3% supersaturation

Weight change and sulfonylurea therapy are related to 3 year change in microvascular function in people with type 2 diabetes

Aims/hypothesis: Although cardiovascular disease is the biggest cause of death in people with diabetes, microvascular complications have a significant impact on quality of life and financial burden of the disease. Little is known about the progression of microvascular dysfunction in the early stages of type 2 diabetes before the occurrence of clinically apparent complications. We aimed to explore the determinants of endothelial-dependent and -independent microvascular function progression over a 3 year period, in people with and without both diabetes and few clinical microvascular complications. Methods: Demographics were collected in 154 participants with type 2 diabetes and in a further 99 participants without type 2 diabetes. Skin microvascular endothelium-dependent response to iontophoresis of acetylcholine and endothelium-independent responses to sodium nitroprusside were measured using laser Doppler fluximetry. All assessments were repeated 3 years later. Results: People with type 2 diabetes had impaired endothelial-dependent microvascular response compared with those without (AUC 93.9 [95% CI 88.1, 99.4] vs 111.9 [102.3, 121.4] arbitrary units [AU] × min, p < 0.001, for those with vs without diabetes, respectively). Similarly, endothelial-independent responses were attenuated in those with diabetes (63.2 [59.2, 67.2] vs 75.1 [67.8, 82.4] AU × min, respectively, p = 0.002). Mean microvascular function declined over 3 years in both groups to a similar degree (pinteraction 0.74 for response to acetylcholine and 0.69 for response to sodium nitroprusside). In those with diabetes, use of sulfonylurea was associated with greater decline (p = 0.022 after adjustment for co-prescriptions, change in HbA1c and weight), whereas improving glycaemic control was associated with less decline of endothelial-dependent microvascular function (p = 0.03). Otherwise, the determinants of microvascular decline were similar in those with and without diabetes. The principal determinant of change in microvascular function in the whole population was weight change over 3 years, such that those that lost ≥5% weight had very little decline in either endothelial-dependent or -independent function compared with those that were weight stable, whereas those who gained weight had a greater decline in function (change in endothelial-dependent function was 1.2 [95% CI -13.2, 15.7] AU × min in those who lost weight; -15.8 [-10.5, -21.0] AU × min in those with stable weight; and -37.8 [-19.4, -56.2] AU × min in those with weight gain; ptrend < 0.001). This association of weight change with change in endothelial function was driven by people with diabetes; in people without diabetes, the relationship was nonsignificant. Conclusions/interpretation: Over 3 years, physiological change in weight was the greatest predictor of change in microvascular function.This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.This work was supported by the Innovative Medicines Initiative (the SUMMIT consortium, IMI-2008/115006).published version, accepted version (12 month embargo

A novel method for radiotherapy patient identification using surface imaging

Performing a procedure on the wrong patient or site is one of the greatest errors that can occur in medicine. The addition of automation has been shown to reduce errors in many processes. In this work we explore the use of an automated patient identification process using optical surface imaging for radiotherapy treatments. Surface imaging uses visible light to align the patient to a reference surface in the treatment room. It is possible to evaluate the similarity between a daily set-up surface image and the reference image using distance to agreement between the points on the two surfaces. The higher the percentage overlapping points within a defined distance, the more similar the surfaces. This similarity metric was used to intercompare 16 left-sided breast patients. The reference surface for each patient was compared to 10 daily treatment surfaces for the same patient, and 10 surfaces from each of the other 15 patients (for a total of 160 comparisons per patient), looking at the percent of points overlapping. For each patient, the minimum same-patient similarity score was higher than the maximum different-patient score. For the group as a whole a threshold was able to classify correct and incorrect patients with high levels of accuracy. A 10-fold cross-validation using linear discriminant analysis gave cross-validation loss of 0.0074. An automated process using surface imaging is a feasible option to provide nonharmful daily patient identification verification using currently available technology

Characterizing the Adaptive Optics Off-Axis Point-Spread Function - I: A Semi-Empirical Method for Use in Natural-Guide-Star Observations

Even though the technology of adaptive optics (AO) is rapidly maturing, calibration of the resulting images remains a major challenge. The AO point-spread function (PSF) changes quickly both in time and position on the sky. In a typical observation the star used for guiding will be separated from the scientific target by 10" to 30". This is sufficient separation to render images of the guide star by themselves nearly useless in characterizing the PSF at the off-axis target position. A semi-empirical technique is described that improves the determination of the AO off-axis PSF. The method uses calibration images of dense star fields to determine the change in PSF with field position. It then uses this information to correct contemporaneous images of the guide star to produce a PSF that is more accurate for both the target position and the time of a scientific observation. We report on tests of the method using natural-guide-star AO systems on the Canada-France-Hawaii Telescope and Lick Observatory Shane Telescope, augmented by simple atmospheric computer simulations. At 25" off-axis, predicting the PSF full width at half maximum using only information about the guide star results in an error of 60%. Using an image of a dense star field lowers this error to 33%, and our method, which also folds in information about the on-axis PSF, further decreases the error to 19%.Comment: 29 pages, 9 figures, accepted for publication in the PAS