Estimates of electronic coupling for excess electron transfer in DNA

Electronic coupling Vda is one of the key parameters that determine the rate of charge transfer through DNA. While there have been several computational studies of Vda for hole transfer, estimates of electronic couplings for excess electron transfer (ET) in DNA remain unavailable. In the paper, an efficient strategy is established for calculating the ET matrix elements between base pairs in a π stack. Two approaches are considered. First, we employ the diabatic-state (DS) method in which donor and acceptor are represented with radical anions of the canonical base pairs adenine-thymine (AT) and guanine-cytosine (GC). In this approach, similar values of Vda are obtained with the standard 6-31 G* and extended 6-31++ G* basis sets. Second, the electronic couplings are derived from lowest unoccupied molecular orbitals (LUMOs) of neutral systems by using the generalized Mulliken-Hush or fragment charge methods. Because the radical-anion states of AT and GC are well reproduced by LUMOs of the neutral base pairs calculated without diffuse functions, the estimated values of Vda are in good agreement with the couplings obtained for radical-anion states using the DS method. However, when the calculation of a neutral stack is carried out with diffuse functions, LUMOs of the system exhibit the dipole-bound character and cannot be used for estimating electronic couplings. Our calculations suggest that the ET matrix elements Vda for models containing intrastrand thymine and cytosine bases are essentially larger than the couplings in complexes with interstrand pyrimidine bases. The matrix elements for excess electron transfer are found to be considerably smaller than the corresponding values for hole transfer and to be very responsive to structural changes in a DNA stack

Efficient topology estimation for large scale optical mapping

Large scale image mosaicing methods are in great demand among scientists who study different aspects of the seabed, and have been fostered by impressive advances in the capabilities of underwater robots in gathering optical data from the seafloor. Cost and weight constraints mean that lowcost Remotely operated vehicles (ROVs) usually have a very limited number of sensors. When a low-cost robot carries out a seafloor survey using a down-looking camera, it usually follows a predetermined trajectory that provides several non time-consecutive overlapping image pairs. Finding these pairs (a process known as topology estimation) is indispensable to obtaining globally consistent mosaics and accurate trajectory estimates, which are necessary for a global view of the surveyed area, especially when optical sensors are the only data source. This thesis presents a set of consistent methods aimed at creating large area image mosaics from optical data obtained during surveys with low-cost underwater vehicles. First, a global alignment method developed within a Feature-based image mosaicing (FIM) framework, where nonlinear minimisation is substituted by two linear steps, is discussed. Then, a simple four-point mosaic rectifying method is proposed to reduce distortions that might occur due to lens distortions, error accumulation and the difficulties of optical imaging in an underwater medium. The topology estimation problem is addressed by means of an augmented state and extended Kalman filter combined framework, aimed at minimising the total number of matching attempts and simultaneously obtaining the best possible trajectory. Potential image pairs are predicted by taking into account the uncertainty in the trajectory. The contribution of matching an image pair is investigated using information theory principles. Lastly, a different solution to the topology estimation problem is proposed in a bundle adjustment framework. Innovative aspects include the use of fast image similarity criterion combined with a Minimum spanning tree (MST) solution, to obtain a tentative topology. This topology is improved by attempting image matching with the pairs for which there is the most overlap evidence. Unlike previous approaches for large-area mosaicing, our framework is able to deal naturally with cases where time-consecutive images cannot be matched successfully, such as completely unordered sets. Finally, the efficiency of the proposed methods is discussed and a comparison made with other state-of-the-art approaches, using a series of challenging datasets in underwater scenarios

Nature of Airline Demand

The Airline Industry • Big and Wide and Tall • Characteristics • Changes in Demand • Key Issues

Verification of computed tomographic estimates of cochlear implant array position: A micro-CT and histological analysis

We examine the efficacy two volume spatial registration of pre and postoperative clinical computed tomography (CT) imaging to verify post-operative electrode array placement in cochlear implant (CI) patients. To measure the degree of accuracy with which the composite image predicts in-vivo placement of the array, we replicate the CI surgical process in cadaver heads. Pre-operative, post-operative, micro CT imaging and histology are utilized for verification.

Estimates of Avian Mortality Attributed to Vehicle Collisions in Canada

Although mortality of birds from collisions with vehicles is estimated to be in the millions in the USA, Europe, and the UK, to date, no estimates exist for Canada. To address this, we calculated an estimate of annual avian mortality attributed to vehicular collisions during the breeding and fledging season, in Canadian ecozones, by applying North American literature values for avian mortality to Canadian road networks. Because owls are particularly susceptible to collisions with vehicles, we also estimated the number of roadkilled Barn owls (Tyto alba) in its last remaining range within Canada. (This species is on the IUCN red list and is also listed federally as threatened; Committee on the Status of Endangered Wildlife in Canada 2010, International Union for the Conservation of Nature 2012). Through seven Canadian studies in existence, 80 species and 2,834 specimens have been found dead on roads representing species from 14 orders of birds. On Canadian 1 and 2-lane paved roads outside of major urban centers, the unadjusted number of bird mortalities/yr during an estimated 4-mo (122-d) breeding and fledging season for most birds in Canada was 4,650,137 on roads traversing through deciduous, coniferous, cropland, wetlands and nonagricultural landscapes with less than 10% treed area. On average, this represents 1,167 birds killed/100 km in Canada. Adjusted for scavenging, this estimate was 13,810,906 (3,462 dead birds/100 km). For barn owls, the unadjusted number of birds killed annually on 4-lane roads during the breeding and fledging season, within the species geographic range in southern British Columbia, was estimated as 244 owls and, when adjusted for scavenging and observer bias (3.6 factor), the total was 851 owls.

Avian mortalities due to transmission line collisions: a review of current estimates and field methods with an emphasis on applications to the Canadian electric network

Birds are vulnerable to collisions with human-made fixed structures. Despite ongoing development and increases in infrastructure, we have few estimates of the magnitude of collision mortality. We reviewed the existing literature on avian mortality associated with transmission lines and derived an initial estimate for Canada. Estimating mortality from collisions with power lines is challenging due to the lack of studies, especially from sites within Canada, and due to uncertainty about the magnitude of detection biases. Detection of bird collisions with transmission lines varies due to habitat type, species size, and scavenging rates. In addition, birds can be crippled by the impact and subsequently die, although crippling rates are poorly known and rarely incorporated into estimates. We used existing data to derive a range of estimates of avian mortality associated with collisions with transmission lines in Canada by incorporating detection, scavenging, and crippling biases. There are 231,966 km of transmission lines across Canada, mostly in the boreal forest. Mortality estimates ranged from 1 million to 229.5 million birds per year, depending on the bias corrections applied. We consider our most realistic estimate, taking into account variation in risk across Canada, to range from 2.5 million to 25.6 million birds killed per year. Data from multiple studies across Canada and the northern U.S. indicate that the most vulnerable bird groups are (1) waterfowl, (2) grebes, (3) shorebirds, and (4) cranes, which is consistent with other studies. Populations of several groups that are vulnerable to collisions are increasing across Canada (e.g., waterfowl, raptors), which suggests that collision mortality, at current levels, is not limiting population growth. However, there may be impacts on other declining species, such as shorebirds and some species at risk, including Alberta’s Trumpeter Swans (Cygnus buccinator) and western Canada’s endangered Whooping Cranes (Grus americana). Collisions may be more common during migration, which underscores the need to understand impacts across the annual cycle. We emphasize that these estimates are preliminary, especially considering the absence of Canadian studies.

Off-road sampling reveals a different grassland bird community than roadside sampling: implications for survey design and estimates to guide conservation

Grassland bird species continue to decline steeply across North America. Road-based surveys such as the North American Breeding Bird Survey (BBS) are often used to estimate trends and population sizes and to build species distribution models for grassland birds, although roadside survey counts may introduce bias in estimates because of differences in habitats along roadsides and in off-road surveys. We tested for differences in land cover composition and in the avian community on 21 roadside-based survey routes and in an equal number of adjacent off-road walking routes in the grasslands of southern Alberta, Canada. Off-road routes (n = 225 point counts) had more native grassland and short shrubs and less fallow land and road area than the roadside routes (n = 225 point counts). Consequently, 17 of the 39 bird species differed between the two route types in frequency of occurrence and relative abundance, measured using an indicator species analysis. Six species, including five obligate grassland species, were more prevalent at off-road sites; they included four species listed under the Canadian federal Species At Risk Act or listed by the Committee on the Status of Endangered Wildlife in Canada: Sprague’s Pipit (Anthus spragueii), Baird’s Sparrow (Ammodramus bairdii), the Chestnut-collared Longspur (Calcarius ornatus), and McCown’s Longspur (Rhynchophanes mccownii). The six species were as much as four times more abundant on off-road sites. Species more prevalent along roadside routes included common species and those typical of farmland and other human-modified habitats, e.g., the European Starling (Sturnus vulgaris), the Black-billed Magpie (Pica hudsonia), and the House Sparrow (Passer domesticus). Differences in avian community composition between roadside and off-road surveys suggest that the use of BBS data when generating population estimates or distribution models may overestimate certain common species and underestimate others of conservation concern. Our results highlight the need to develop appropriate corrections for bias in estimates derived from roadside sampling, and the need to design surveys that sample bird communities across a more representative cross-section of the landscape, both near and far from roads. 

Evaluation of reanalysis rainfall estimates over Ethiopia

There is a pressing need for good rainfall data for the African continent both for humanitarian and climatological purposes. Given the sparseness of ground-based observations, one source of rainfall information is Numerical Weather Prediction (NWP) model outputs. The aim of this article is to investigate the quality of two NWP products using Ethiopia as a test case. The two products evaluated are the ERA-40 and NCEP reanalysis rainfall products. Spatial, seasonal and interannual variability of rainfall have been evaluated for Kiremt (JJAS) and Belg (FMAM) seasons at a spatial scale that reflects the local variability of the rainfall climate using a method which makes optimum use of sparse gauge validation data. We found that the spatial pattern of the rainfall climatology is captured well by both models especially for the main rainy season Kiremt. However, both models tend to overestimate the mean rainfall in the northwest, west and central regions but underestimate in the south and east. The overestimation is greater for NCEP in Belg season and greater for ERA-40 in Kiremt Season. ERA-40 captures the annual cycle over most of the country better than NCEP, but strongly exaggerates the Kiremt peak in the northwest and west. The overestimation in Kiremt appears to have been reduced since the assimilation of satellite data increased around 1990. For both models the interannual variability is less well captured than the spatial and seasonal variability. Copyright © 2008 Royal Meteorological Society