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.

     

Sandwiched liquid metal membrane (SLiMM) for hydrogen purification

Palladium‐based membranes are currently the most advanced membranes for hydrogen separation and are on the verge of practical application. However, the search for alternative membranes continues in an effort to lower their cost and susceptibility to poisons. Here for the first time we report a novel sandwiched liquid metal membrane (SLiMM) for hydrogen separation. Permeation experiments indicate that the Ga/SiC SLiMM has a permeability of at 500°C, which is 35 time higher than that for Pd under similar conditions. This promises a potential for application of SliMM in hydrogen purification. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1483–1488, 2017     

Electrodeposition of insulating poly(phenylene oxide) films with variable thickness

Ability to control key characteristics of electrodeposited polymers plays a vital role for their applications. In this work the results on tailoring the thickness of electronically insulating poly(phenylene oxide) (PPO) type polymer films have been showed. Pinhole‐free PPO films with variable thickness in the range of 10–50 nm were grown by controlling the potential applied during the electrochemical polymerization on the surface of titanium nitride (TiN) substrates. The insulating properties of the PPO film were confirmed by testing its permeability to redox species by cyclic voltammetry. Thermal stability of the PPO films with different thicknesses was investigated by in‐situ spectroscopic ellipsometry up to 400 °C in various environments. This insight is important for the optimization of the PPO anneal conditions in order to remove the residual solvent and potentially improve the polymer chains stacking. Our results provide the basis for electrodeposition of PPO films with variable thickness for diverse applications. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134, 44533.     

Environmental factors influencing annual sucker (Catostomus sp.) migration into a Great Lakes tributary

Fish migration in rivers is a growing area of concern as mounting anthropogenic influences, particularly fragmentation from dams and barriers, constitute major threats to global river species diversity. Barriers can impede the movement of fishes between areas critical to the completion of their lifecycle, affecting both population and ecosystem viability. In response, fish passage solutions have been identified as a critical need to maintain fisheries viability in the Laurentian Great Lakes, and around the world. Pivotal to the success of these fish passage solutions is a more complete understanding of the movement phenology and environmental cues that instigate migration. We used a dual-frequency identification sonar (DIDSON) to evaluate environmental triggers of river entry during spring and summer for three size classes of migratory fishes in the Boardman River, a Lake Michigan tributary. Our results indicate that medium size fish (>30 cm and < 50 cm), primarily composed of white sucker Catostomus commersonii and longnose sucker Catostomus catostomus were 21% more likely to enter the river at sunset and 25% less likely at midnight in comparison to midday. Entry rates of medium fish increased 6% for every 1 °C increase in river temperature, 4% for every 1 m³/s increase in river discharge from the day prior, and were reduced by 1% for every 10 cm increase in lake level. Understanding these processes in the tributaries of the Great Lakes is important to inform the fish passage solutions currently being developed for the Boardman River, and to inform management regulations for Great Lakes migratory fishes.     

The effects of mass transport and chemical reaction on pollutant removal in a three-phase slurry adsorber-reactor

The analysis of the effects of mass transport and chemical reaction on pollutant removal from a gas-phase in a three-phase slurry adsorber-reactor is presented. A mathematical model, consisting of four coupled differential equations, was developed to describe the process and solved numerically. The modeling assumptions included: perfect mixing in the three-phase slurry, Henry's law, a linear adsorption isotherm and a second order, irreversible chemical reaction. The model was found to adequately represent limited existing experimental data and to qualitatively predict the effects of the various transport coefficients on the pollutant removal efficiency of the process. The model was also used for design analysis. Although the model-process achieved significant pollutant removal for representative operating conditions, the percent removal was ultimately limited by mass transport from the gas bubbles to the liquid slurry.     

The Return of Ozone and the Hydroxyl Radical to Wastewater Disinfection

The City of Phoenix, Arizona is investigating various disinfection technologies for its 91st Avenue wastewater treatment facility: (1) ultraviolet light (UV), (2) ozone, (3) UV/hydrogen peroxide, (4) ozone/hydrogen peroxide, (5) and UV/ozone. In addition to providing disinfection, the City would like to consider the removal of endocrine disrupting chemicals (EDCs) and personal and pharmaceutical care products (PPCPs) in the treatment technology evaluation. To identify the most economical disinfection system, the evaluation included bench-scale testing of the technologies considered and a year-long water quality monitoring study. This paper presents the results of the bench-scale analyses and estimated capital and O&M costs.     

On a numerical relaxation method for a chemical reaction-diffusion problem with an instantaneous and irreversible reaction

In this paper we deal with a numerical method for a free boundary value problem in 1D, describing a chemical diffusion problem accompanied by an irreversible and instantaneous reaction which gives rise to a moving internal boundary. Basically, the method consists of four steps: (1) a Landau transformation mapping each of the 2 time varying intervals on a fixed domain, which results in a strongly nonlinear boundary value problem; (2) a central difference method with respect to the space variable, that takes properly into account the various transition conditions; (3) the construction of an ODE containing a relaxation parameter ε to represent the movement of the internal boundary; (4) a time integration of the resulting stiff system of ODEs by suitable computer packages. The numerical method is evaluated by comparison with an analytical solution for a special but nontrivial case, and by a mass-balance argument. The presented method can be extended to the case of several irreversible and instantaneous reactions.     

Analysis of molecular interactions in poly(methacrylic acid-g-ethylene glycol) hydrogels

Molecular and structural changes of the P(MAA-g-EG) hydrogels were investigated in their hydrated state using attenuated total reflectance Fourier transform infrared spectroscopy. FTIR studies identified the formation of hydrogen-bonded complexes at low pH and polyelectrolyte complexes at high pH. Hydrogen bonding and electrostatic repulsion were not affected by the grafted PEG molecular weight in the hydrogels. Additionally, investigation of the macroscopic swelling properties showed that the presence of the grafted PEG chain in the P(MAA-g-EG) hydrogels contributed to the formation of hydrogen bonds.     

Turnover of cholesterol and dipalmitoyl phosphatidylcholine in surfactant of adult rat lung

In order to compare the turnover of two major surfactant components, [1α,2α(n)-³H]cholesterol and [methyl ¹⁴ C choline] dipalmitoyl phosphatidylcholine (DPPC) were introduced as lamellar bodiesvia the trachea into lightly anesthetized rats which were then allowed to recover. The radiotracers were assumed to have entered the alveolar surfactant pool and to have subsequently recycled in part into the lamellar bodies of alveolar type II cells. For DPPC, the specific activityvs. time curves of tubular myelin rich (alv-1) and tubular myelin poor (alv-2) alveolar lavage fractions were similar, and there was a plausible precursor-product relationship between lamellar bodies and either (or both) of these compartments. In contrast, however, the specific activities of alv-1 and alv-2 for cholesterol were quite different, allowing us to reject the hypothesis of a precursor-product relationship between classical lamellar bodies and alv-2. The estimated turover time for DPPC in alv-1 was 240 or 206 min, depending on which subfraction of lamellar bodies one takes to be the precursor. For cholesterol it was 583 or 624 min. These longer turnover times for cholesterol should lead to a greater than twofold increase in the relative concentration of cholesterol in the putative product compartment. Such an increase was not found. We interpret this as reflecting either noncompartmental behavior of the alveolar surfactant pool, or multiple pools of lamellar bodies with different turnover times. We conclude that two major components of pulmonary surfactant, cholesterol and DPPC, are handled differently, and that for at least one of these substances, the widely accepted scenario of a compartmental precursor-product relationship between lamellar bodies and alveolar surfactant must be rejected.     

Quantitative analysis of oil removal from cotton fabrics through thein situ formation of microemulsions by solid-state nuclear magnetic resonance

Solubilization and subsequent removal of soybean oil from cotton fabrics through thein situ formation of microemulsions were evaluated by solid-state nuclear magnetic resonance (NMR) spectrometry. Regions of water-in-oil and oil-in-water microemulsions were identified for systems that contained polyoxyethylene (60) sorbitol hexaoleate, soybean oil, and an aqueous phase composed of water/ethanol or isopropanol (80:20 wt%) at 25°C. The amount of oil removed from the cotton fabrics was determined by solid-state NMR after constructing a calibration curve relating the intensity of camphor/oil NMR signals (I_c/I_o) to their molar ratio (M_c/M_o). A precision Crockmeter (Mul-Tech Industries, New York, NY) was used to reproducibly remove soybean oil stain from cotton fabric, which was subsequently analyzed by NMR. Typically, more than 90% of the oil stain was removed after 200 revolutions of the Crockmeter finger with 2 wt% surfactant at 25°C. Increasing the amount of surfactant to 6 wt% improved soybean oil removal from the fabric to 99 wt%.