Optimized partial-coverage functional analysis pipeline (OPFAP): a semi-automated pipeline for skull stripping and co-registration of partial-coverage,ultra-high-field functional images

Objective

Ultra-high-field functional MRI (UHF-fMRI) allows for higher spatiotemporal resolution imaging. However, higher-resolution imaging entails coverage limitations. Processing partial-coverage images using standard pipelines leads to sub-optimal results. We aimed to develop a simple, semi-automated pipeline for processing partial-coverage UHF-fMRI data using widely used image processing algorithms.

Materials and methods

We developed automated pipelines for optimized skull stripping and co-registration of partial-coverage UHF functional images, using built-in functions of the Centre for Functional Magnetic Resonance Imaging of the Brain's (FMRIB’s) Software library (FSL) and advanced normalization tools. We incorporated the pipelines into the FSL’s functional analysis pipeline and provide a semi-automated optimized partial-coverage functional analysis pipeline (OPFAP).

Results

Compared to the standard pipeline, the OPFAP yielded images with 15 and 30% greater volume of non-zero voxels after skull stripping the functional and anatomical images, respectively (all p =?0.0004), which reflected the conservation of cortical voxels lost when the standard pipeline was used. The OPFAP yielded the greatest Dice and Jaccard coefficients (87 and 80%, respectively; all p <?0.0001) between the co-registered participant gyri maps and the template gyri maps, demonstrating the goodness of the co-registration results. Furthermore, the greatest volume of group-level activation in the most number of functionally relevant regions was observed when the OPFAP was used. Importantly, group-level activations were not observed when using the standard pipeline.

Conclusion

These results suggest that the OPFAP should be used for processing partial-coverage UHF-fMRI data for detecting high-resolution macroscopic blood oxygenation level-dependent activations.

     

Enhanced oil recovery chemical needs

A large fraction of known petroleum resources will not be recoverable by conventional methods. Enhanced oil recovery (EOR) is costly, but a significant amount of production is possible at current world oil prices, and additional production is possible at prices equivalent to synthetic alternates. Many opportunities exist for uses of chemicals in EOR. In particular, polymers and surfactants that are effective and stable at high temperatures and high salinities are needed for surfactant flooding to achieve its potential. Potential markets can be large in the 1990s and beyond. Many factors other than improved chemicals will impact on the future development of EOR. Risks to the chemical industry in new product development would appear to be reasonable, as long as oil producers continue a major effort to develop EOR processes.     

Selection of Processing Temperature to Minimize Product Temperature Variability in Food Heating Processes

Random variability in product thermal properties combined with non-uniformity in the process environment can cause a distribution in product temperature at the end of a heating stage. This unwanted dispersion can affect the integrity and profitability of the operation. The dispersion can be quantified with the statistics of range, minimum or variance. This paper demonstrates how the magnitude of this dispersion is sensitive to the level of processing temperature that is employed. It explains and gives a criterion by which the process environment can be judged as being either uniform or non-uniform. Furthermore the paper demonstrates that using a certain processing time will minimize the variance in product temperature. Using a case study, involving the heat treatment of foods, the strategies that can be employed to control product temperature dispersion, through selection of the process temperature, are outlined.     

Statistical Algorithms for Designing Geophysical Surveys to Detect UXO Target Areas

The U.S. Department of Defense is in the process of assessing and remediating closed, transferred, and transferring military training ranges across the United States. Many of these sites have areas that are known to contain unexploded ordnance (UXO). Other sites or portions of sites are not expected to contain UXO, but some verification of this expectation using geophysical surveys is needed. Many sites are so large that it is often impractical and/or cost prohibitive to perform surveys over 100% of the site. In such cases, it is particularly important to be explicit about the performance required of the surveys. This article presents the statistical algorithms developed to support the design of geophysical surveys along transects (swaths) to find target areas (TAs) of anomalous geophysical readings that may indicate the presence of UXO. The algorithms described here determine (1) the spacing between transects that should be used for the surveys to achieve a specified probability of traversing the TA, (2) the probability of both traversing and detecting a TA of anomalous geophysical readings when the spatial density of anomalies within the TA is either uniform (unchanging over space) or has a bivariate normal distribution, and (3) the probability that a TA exists when it was not found by surveying along transects. These algorithms have been implemented in the Visual Sample Plan (VSP) software to develop cost-effective transect survey designs that meet performance objectives.     

The dynamic response characteristics of traumatic brain injury

Traumatic brain injury (TBI) continues to be a leading cause of morbidity and mortality throughout the world. Research has been undertaken in order to better understand the characteristics of the injury event and measure the risk of injury to develop more effective environmental, technological, and clinical management strategies. This research used methods that have limited applications to predicting human responses. This limits the current understanding of the mechanisms of TBI in humans. As a result, the purpose of this research was to examine the characteristics of impact and dynamic response that leads to a high risk of sustaining a TBI in a human population. Twenty TBI events collected from hospital reports and eyewitness accounts were reconstructed in the laboratory using a combination of computational mechanics models and Hybrid III anthropometric dummy systems. All cases were falls, with an average impact velocity of approximately 4.0 m/s onto hard impact surfaces. The results of the methodology were consistent with current TBI research, describing TBI to occur in the range of 335–445 g linear accelerations and 23.7–51.2 krad/s² angular accelerations. More significantly, this research demonstrated that lower responses in the antero-posterior direction can cause TBI, with lateral impact responses requiring larger magnitudes for the same types of brain lesions. This suggests an increased likelihood of sustaining TBI for impacts to the front or back of the head, a result that has implications affecting current understanding of the mechanisms of TBI and associated threshold parameters.     

Assessment of the ability of seaweed extracts to protect against hydrogen peroxide and tert-butyl hydroperoxide induced cellular damage in Caco-2 cells

The ability of brown seaweed extracts, Ascophyllum nodosum, Laminaria hyperborea, Pelvetia canaliculata, Fucus vesiculosus and Fucus serratus to protect against tert-butyl hydroperoxide (tert-BOOH) induced stress in Caco-2 cells was investigated. Oxidative stress was determined by measuring alteration in the enzymatic activity of catalase (CAT) and superoxide dismutases (SOD) and cellular levels of glutathione (GSH). L. hyperborea, P. canaliculata and F. serratus significantly protected against tert-BOOH induced SOD reduction but did not protect against the reduction in CAT activity or the increased cellular levels of GSH. The ability of F. serratus and F. vesiculosus to protect against H₂O₂ and tert-BOOH induced DNA damage was also assessed. The DNA protective effects of the two seaweed extracts was compared to those of three metal chelators; deferoxamine mesylate (DFO), 1,10-phenanthroline (o-phen) and 1,2-Bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid tetrakis (BAPTA-AM). F. serratus and F. vesiculosus significantly protected (P < 0.05) against H₂O₂ (50 μM) induced DNA damage but not tert-BOOH induced damage.     

What is the energy balance of grass biomethane in Ireland and other temperate northern European climates?

Biofuels have had bad press in recent years. There are primarily two distinct issues. The biofuel crops with the best yields (such as sugarcane or oil palm) grow in tropical countries where habitat destruction has occurred in association with the biofuel system. First generation indigenous energy crops commonly used for transport fuel in Europe (such as rapeseed and wheat) have low yields and/or the energy balance of the associated biofuel system is poor. This paper shows that grass is a crop with significant yields and grass biomethane (a gaseous renewable transport biofuel) has a very good energy balance and does not involve habitat destruction, land use change, new farming practices or annual tilling. The gross and net energy production per hectare are almost identical to palm oil biodiesel; the net energy of the grass system is at least 50% better than the next best indigenous European biofuel system investigated. Ten percent of Irish grasslands could fuel over 55% of the Irish private car fleet.     

Chemical bath deposition of cadmium sulphide on silicon nitride: Influence of surface treatment on film growth

Nanoparticulate cadmium sulphide was grown by a chemical bath method on PECVD silicon nitride with various surface treatments. It was found that the packing density of the film increased in the order: untreated surface < mercaptopropyl-derivatised surface < ultra-thin (discontinuous) gold- or platinum-treated surface. This behaviour was rationalised by assuming that surface concentrations of Cd²⁺ or S²⁻ could be increased over the bulk values by producing a surface with ‘soft base’ or ‘soft acid’ chemistry, respectively.Nanoparticle diameters were larger with ultra-thin platinum treatment than with gold. These observations may allow ordered arrays of cadmium sulphide nanoparticles to be prepared by a masking - gold seeding - bath deposition procedure.     

Family stress and parental responses to children’s negative emotions: Tests of the spillover, crossover, and compensatory hypotheses.

The relations between 4 sources of family stress (marital dissatisfaction, home chaos, parental depressive symptoms, and job role dissatisfaction) and the emotion socialization practice of mothers’ and fathers’ responses to children’s negative emotions were examined. Participants included 101 couples with 7-year-old children. Dyadic analyses were conducted using the Actor–Partner Interdependence Model and relations were tested in terms of the spillover, crossover, and compensatory hypotheses. Results suggest that measures of family stress relate to supportive and nonsupportive parental responses, though many of these relations differ by parent gender. The results are discussed in terms of the 3 theoretical hypotheses, all of which are supported to some degree depending on the family stressor examined. (PsycINFO Database Record (c) 2010 APA, all rights reserved)