Grid infrastructures for secure access to and use of bioinformatics data: experiences from the BRIDGES project

The BRIDGES project was funded by the UK Department of Trade and Industry (DTI) to address the needs of cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) cardiovascular functional genomics (CFG) project. Security was at the heart of the BRIDGES project and an advanced data and compute grid infrastructure incorporating latest grid authorisation technologies was developed and delivered to the scientists. We outline these grid infrastructures and describe the perceived security requirements at the project start including data classifications and how these evolved throughout the lifetime of the project. The uptake and adoption of the project results are also presented along with the challenges that must be overcome to support the secure exchange of life science data sets. We also present how we will use the BRIDGES experiences in future projects at the National e-Science Centre

Mid- and Long-Term Effects of Wildfire and Debris Flows on Stream Ecosystem Metabolism

Wildfire is an important and prevalent agent of disturbance in vegetated landscapes across much of the Earth’s surface, including forested watersheds in the arid western USA. Between 1992 and 2003, \u3e40% of the watersheds in the upper reaches of the Boise River watershed in central Idaho burned. The purpose of our study was to investigate the legacy effects of wildfire on stream ecosystems by analyzing the relationship between wildfire and resulting debris flows and their joint effects on stream ecosystem metabolism in 31 streams. The watersheds of ∼½ of these streams burned within the last 11 y, and some of these burned watersheds also experienced large-scale debris flows 1 y postfire. Streams with burned watersheds recovered quickly, and estimates of photosynthetically active radiation, gross primary production, and ecosystem respiration were indistinguishable from those in streams draining unburned watersheds. However, streams that experienced debris flows after their watersheds burned were remarkably different. They exhibited higher production and incident light and lower ecosystem respiration. Debris flows resulted in nearly complete removal of streamside vegetation, slowed recovery of the riparian canopy, and altered stream ecosystem metabolism. Our results suggest a synergistic interaction between wildfire and associated geomorphological processes whereby debris flows delay succession of stream ecosystems, possibly resulting in altered recovery trajectories, communities, and foodweb interactions

An Irrigation Canal as a Lotic Mesocosm: Examining the Relationship Between Macroinvertebrate Benthos and Drift

We explored the notion that small canals could be good experimental proxies of streams by documenting physiochemical parameters and macroinvertebrate community development in an aridland irrigation canal. Further, we tested the production-compensation hypothesis between benthic invertebrates and invertebrates in the water column (drift). If the hypothesis held, invertebrates in the drift would be low until the benthic carrying capacity was reached; then organisms in the drift would increase as individuals avoided overcrowded conditions in the substrate. In a small, naturalized freshwater canal, we sampled macroinvertebrates in the substrate and those in the drift once every 2 weeks over 170 days (May–October). We placed macroinvertebrates into functional feeding groups (FFG) and examined these groups along with total density and taxa richness. We found no density-dependent relationship either in FFG or total density between the benthos and invertebrates in the drift. Our negative results might indicate that the stream benthos did not reach carrying capacity (partially affected by adult emergence in the autumn), the invertebrate dynamics in the canal did not adequately represent those occurring in a natural stream, or the duration of our study was too short. However, the invertebrate community in the canal did follow community buildup patterns for small streams reported in the literature, and it also resembled the community in a nearby natural stream. We suggest that naturalized canals could be used as “mesocosms,” mimicking small natural streams, in which highly manipulative experiments could be conducted. In addition, the effects of temporary and permanent canals across the arid western landscape have been understudied and represent a new area of ecological research

Contracts for Cross-Organizational Workflow Management

Nowadays, many organizations form dynamic partnerships to deal effectively with market requirements. As companies use automated workflow systems to control their processes, a way of linking workflow processes in different organizations is useful in turning the co-operating companies into a seamless operating virtual enterprise. The CrossFlow Esprit project aims at developing information technology for advanced process support in dynamic virtual organizations with contract based service trading. Contracts are necessary for flexible service outsourcing. This report presents contracts as a way of finding suitable partners, connect WFMSs of different kinds, control outsourced workflow, and share an abstraction of the workflow specification between the partners. The contract defines the data, process, and conditions relevant to the co-operation and the outsourced workflow on an abstract level. This information can be fed through an interface to the WFMSs on both sides of the outsourcing in order to automate fully the co-operation between the partners

BEC-BCS crossover in an optical lattice

We present the microscopic theory for the BEC-BCS crossover of an atomic Fermi gas in an optical lattice, showing that the Feshbach resonance underlying the crossover in principle induces strong multiband effects. Nevertheless, the BEC-BCS crossover itself can be described by a single-band model since it occurs at magnetic fields that are relatively far away from the Feshbach resonance. A criterion is proposed for the latter, which is obeyed by most known Feshbach resonances in ultracold atomic gases.Comment: 4 pages, 3 figure

In memoriam of Alexander Golovin (1939–2013)

No abstract available

Trajectory extraction for analysis of unsafe driving behaviour

The environment of the vehicle can significantly influence the driving situation. Which conditions lead to unsafe driving behaviour is not always clear, also not to a human driver, as the causes might be unconscious, and thus cannot be revealed by expert interviews. Therefore, it is important to investigate how such situations can be reliably detected, and then search for their triggers. It is conceivable that such insecure situations (e.g. near-accidents, U-turns, avoiding obstacles) are reflected, for example, as anomalies in the movement trajectories of road users. Collecting real world traffic data in driving studies is very time consuming and expensive. However, a lot of roads or public areas are already monitored with video cameras. In addition, nowadays more and more of such video data is made publicly available over the internet so that the amount of free video data is increasing. This research will exploit the use of such kind of opportunistic VGI. In the paper the first step of an automatic analysis are presented, namely: to introduce a real time processing pipeline to extract road user trajectories from surveillance video data

Present Effects of Past Wildfires on Leaf Litter Breakdown in Stream Ecosystems

We investigated the present effects from a 10-year-old wildfire on leaf litter breakdown rates in 3 headwater streams in central Idaho. These systems experienced a massive debris flow one year after the fire. Based on soil instability and burn patterns, we identified 3 stream conditions: unburned, burned only, and burned/scoured. We placed leaf bags containing willow leaves (Salix sp.) in each stream type and removed bags at various time intervals until all bags were collected 100 days after their introduction. Leaf material was dried and weighed, and decay rate coefficients were calculated. Macroinvertebrates colonizing the bags were enumerated and identified, and selected taxa were placed into trophic groups. We found that the unburned stream had the fastest leaf litter breakdown rate, the lowest level of incident light reaching the stream, and the largest amount of benthic organic matter. The burned/scoured stream was nearly opposite in all respects. Numbers of 2 detritivore invertebrate taxa, Serratella tibialis and Zapada oregonensis, were highest in the unburned stream but lowest in the burned/scoured stream. A third taxon, Baetis sp., showed the opposite relationship. Presence of predatory invertebrates did not affect detritivore abundance or leaf decay rate in the bags. Our research suggests that recovery response variables of some stream systems may not have returned to prefire levels even a decade after the initial wildfire. In this study, the recovery of our streams appears to be connected to the return of the riparian zone, though fire-induced debris flows may slow or alter final recovery of the stream system

Minimally Invasive Stent Screw-Assisted Internal Fixation Technique Corrects Kyphosis in Osteoporotic Vertebral Fractures with Severe Collapse: A Pilot "Vertebra Plana" Series.

BACKGROUND AND PURPOSE Fractures with "vertebra plana" morphology are characterized by severe vertebral body collapse and segmental kyphosis; there is no established treatment standard for these fractures. Vertebroplasty and balloon kyphoplasty might represent an undertreatment, but surgical stabilization is challenging in an often elderly osteoporotic population. This study assessed the feasibility, clinical outcome, and radiologic outcome of the stent screw-assisted internal fixation technique using a percutaneous implant of vertebral body stents and cement-augmented pedicle screws in patients with non-neoplastic vertebra plana fractures. MATERIALS AND METHODS Thirty-seven consecutive patients with vertebra plana fractures were treated with the stent screw-assisted internal fixation technique. Vertebral body height, local and vertebral kyphotic angles, outcome scales (numeric rating scale and the Patient's Global Impression of Change), and complications were assessed. Imaging and clinical follow-up were obtained at 1 and 6 months postprocedure. RESULTS Median vertebral body height restoration was 7 mm (+74%), 9 mm (+150%), and 3 mm (+17%) at the anterior wall, middle body, and posterior wall, respectively. Median local and vertebral kyphotic angles correction was 8° and 10° and was maintained through the 6-month follow-up. The median numeric rating scale score improved from 8/10 preprocedure to 3/10 at 1 and 6 months (P < .001). No procedural complications occurred. CONCLUSIONS The stent screw-assisted internal fixation technique was effective in obtaining height restoration, kyphosis correction, and pain relief in patients with severe vertebral collapse