Top Quark Physics at the Tevatron

We review the field of top-quark physics with an emphasis on experimental techniques. The role of the top quark in the Standard Model of particle physics is summarized and the basic phenomenology of top-quark production and decay is introduced. We discuss how contributions from physics beyond the Standard Model could affect top-quark properties or event samples. The many measurements made at the Fermilab Tevatron, which test the Standard Model predictions or probe for direct evidence of new physics using the top-quark event samples, are reviewed here.Comment: 50 pages, 17 figures, 2 tables; version accepted by Review of Modern Physic

Mitral Annulus Segmentation From Three-Dimensional Ultrasound

An accurate and reproducible segmentation of the mitral valve annulus from 3D ultrasound is useful to clinicians and researchers in applications such as pathology diagnosis and mitral valve modeling. Current segmentation methods, however, are based on 2D information, resulting in inaccuracies and a lack of spatial coherence. We present a segmentation algorithm which, given a single user-specified point near the center of the valve, uses maxflow and active contour methods to delineate the annulus geometry in 3D. Preliminary comparisons to manual segmentations and a sensitivity study show the algorithm is both accurate and robust.Engineering and Applied Science

Achieving an Optimal Childhood Vaccine Policy

Policies to remove parents' ability to opt-out from school immunization requirements on the basis of religious or personal beliefs (ie, nonmedical exemptions) may be a useful strategy to increase immunization rates and prevent outbreaks of vaccine-preventable disease. However, there is uncertainty about the effectiveness of this strategy and the range of possible outcomes. We advocate for a more deliberative process through which a broad range of outcomes is scrutinized and the balance of values underlying the policy decision to eliminate nonmedical exemptions is clearly articulated. We identify 3 outcomes that require particular consideration before policies to eliminate nonmedical exemptions are implemented widely and outline a process for making the values underlying such policies more explicit

Computing exponentially faster: Implementing a nondeterministic universal Turing machine using DNA

The theory of computer science is based around Universal Turing Machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of UTMs. The nondeterministic polynomial (NP) time complexity class of problems is the most significant in computer science, and an efficient (i.e. polynomial P) way to solve such problems would be of profound economic and social importance. By definition nondeterministic UTMs (NUTMs) solve NP complete problems in P time. However, NUTMs have previously been believed to be physically impossible to construct. Thue string rewriting systems are computationally equivalent to UTMs, and are naturally nondeterministic. Here we describe the physical design for a NUTM that implements a universal Thue system. The design exploits the ability of DNA to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that this design works using both computational modelling and in vitro molecular biology experimentation. The current design has limitations, such as restricted error-correction. However, it opens up the prospect of engineering NUTM based computers able to outperform all standard computers on important practical problems

Long-term and recent changes in sea level in the Falkland Islands

Mean sea level measurements made at Port Louis in the Falkland Islands in 1981-2, 1984 and 2009, together with values from the nearby permanent tide gauge at Port Stanley, have been compared to measurements made at Port Louis in 1842 by James Clark Ross. The long-term rate of change of sea level is estimated to have been +0.75 ± 0.35 mm/year between 1842 and the early 1980s, after correction for air pressure effects and for vertical land movement due to Glacial Isostatic Adjustment (GIA). The 2009 Port Louis data set is of particular importance due to the availability of simultaneous information from Port Stanley. The data set has been employed in two ways, by providing a short recent estimate of mean sea level itself, and by enabling the effective combination of measurements at the two sites. The rate of sea level rise observed since 1992, when the modern Stanley gauge was installed, has been larger at 2.51 ± 0.58 mm/year, after correction for air pressure and GIA. This rate compares to a value of 2.79 ± 0.42 mm/year obtained from satellite altimetry in the region over the same period. Such a relatively recent acceleration in the rate of sea level rise is consistent with findings from other locations in the southern hemisphere and globall

Structural basis of Ac-SDKP hydrolysis by Angiotensin-I converting enzyme

Angiotensin-I converting enzyme (ACE) is a zinc dipeptidylcarboxypeptidase with two active domains and plays a key role in the regulation of blood pressure and electrolyte homeostasis, making it the principal target in the treatment of cardiovascular disease. More recently, the tetrapetide N-acetyl-Ser–Asp–Lys–Pro (Ac-SDKP) has emerged as a potent antifibrotic agent and negative regulator of haematopoietic stem cell differentiation which is processed exclusively by ACE. Here we provide a detailed biochemical and structural basis for the domain preference of Ac-SDKP. The high resolution crystal structures of N-domain ACE in complex with the dipeptide products of Ac-SDKP cleavage were obtained and offered a template to model the mechanism of substrate recognition of the enzyme. A comprehensive kinetic study of Ac-SDKP and domain co-operation was performed and indicated domain interactions affecting processing of the tetrapeptide substrate. Our results further illustrate the molecular basis for N-domain selectivity and should help design novel ACE inhibitors and Ac-SDKP analogues that could be used in the treatment of fibrosis disorders