Reproducibility of MRI-based white matter tract estimation using multi-fiber probabilistic tractography: effect of user-defined parameters and regions

Objective

There is a pressing need to assess user-dependent reproducibility of multi-fibre probabilistic tractography in order to encourage clinical implementation of these advanced and relevant approaches. The goal of this study was to evaluate both intrinsic and inter-user reproducibility of corticospinal tract estimation.

Materials and methods

Six clinical datasets including motor functional and diffusion MRI were used. Three users performed an independent tractography analysis following identical instructions. Dice indices were calculated to quantify the reproducibility of seed region, fMRI-based end region, and streamline maps.

Results

The inter-user reproducibility ranged 41–93%, 29–94%, and 50–92%, for seed regions, end regions, and streamline maps, respectively. Differences in streamline maps correlated with differences in seed and end regions. Good inter-user agreement in seed and end regions, yielded inter-user reproducibility close to the intrinsic reproducibility (92–97%) and in most cases higher than 80%.

Discussion

Uncertainties related to user-dependent decisions and the probabilistic nature of the analysis should be considered when interpreting probabilistic tractography data. The standardization of the methods used to define seed and end regions is a necessary step to improve the accuracy and robustness of multi-fiber probabilistic tractography in a clinical setting. Clinical users should choose a feasible compromise between reproducibility and analysis duration.

     

Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs

Rift Valley fever virus (RVFV) is a mosquito-transmitted virus from the Bunyaviridae family that causes high rates of mortality and morbidity in humans and ruminant animals. Previous studies indicated that DEAD-box helicase 17 (DDX17) restricts RVFV replication by recognizing two primary non-coding RNAs in the S-segment of the genome: the intergenic region (IGR) and 5′ non-coding region (NCR). However, we lack molecular insights into the direct binding of DDX17 with RVFV non-coding RNAs and information on the unwinding of both non-coding RNAs by DDX17. Therefore, we performed an extensive biophysical analysis of the DDX17 helicase domain (DDX17_135–555) and RVFV non-coding RNAs, IGR and 5’ NCR. The homogeneity studies using analytical ultracentrifugation indicated that DDX17_135–555, IGR, and 5’ NCR are pure. Next, we performed small-angle X-ray scattering (SAXS) experiments, which suggested that DDX17 and both RNAs are homogenous as well. SAXS analysis also demonstrated that DDX17 is globular to an extent, whereas the RNAs adopt an extended conformation in solution. Subsequently, microscale thermophoresis (MST) experiments were performed to investigate the direct binding of DDX17 to the non-coding RNAs. The MST experiments demonstrated that DDX17 binds with the IGR and 5’ NCR with a dissociation constant of 5.77 ± 0.15 µM and 9.85 ± 0.11 µM, respectively. As DDX17_135–555 is an RNA helicase, we next determined if it could unwind IGR and NCR. We developed a helicase assay using MST and fluorescently-labeled oligos, which suggested DDX17_135–555 can unwind both RNAs. Overall, our study provides direct evidence of DDX17_135–555 interacting with and unwinding RVFV non-coding regions.     

Chloroform Hydrodechlorination on Palladium Surfaces: A Comparative DFT Study on Pd(111), Pd(100), and Pd(211)

Topics in Catalysis - Palladium has been shown to be an effective catalyst for chloroform hydrodechlorination, which serves as a promising treatment method for industrial chloroform waste. To...     

Radon and moisture impacts from interventions integrated with housing energy retrofits

Energy retrofits can reduce air exchange, raising the concern of whether indoor radon and moisture levels could increase. This pre/post-intervention study explored whether simple radon interventions implemented in conjunction with energy retrofits can prevent increases in radon and moisture levels. Treatment homes (n = 98) were matched with control (no energy retrofits or radon intervention) homes (n = 12). Control homes were matched by geographic location and foundation type. t-tests were used to determine whether post-energy retrofit radon and moisture level changes in treatment homes significantly differed from those in control homes. The radon interventions succeeded in preventing statistically significant increases in first floor radon using arithmetic (p = 0.749) and geometric means (p = 0.120). In basements, arithmetic (p = 0.060) and geometric (p = 0.092) mean radon levels statistically significantly increased, consistent with previous studies which found that basement radon levels may increase even if first floor levels remain unchanged. Changes in infiltration were related to changes in radon (p = 0.057 in basements; p = 0.066 on first floors). Only 58% of the change in infiltration was due to air sealing, with the rest due to weather changes. There was no statistically significant association between air sealing itself and radon levels on the first floor (p = 0.664). Moisture levels also did not significantly increase.     

Time-Resolved Structural Kinetics of an Organic Mixed Ionic–Electronic Conductor

The structure and packing of organic mixed ionic–electronic conductors have an especially significant effect on transport properties. In operating devices, this structure is not fixed but is responsive to changes in electrochemical potential, ion intercalation, and solvent swelling. Toward this end, the steady-state and transient structure of the model organic mixed conductor, poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), is characterized using multimodal time-resolved operando techniques. Steady-state operando X-ray scattering reveals a doping-induced lamellar expansion of 1.6 Å followed by 0.4 Å relaxation at high doping levels. Time-resolved operando X-ray scattering reveals asymmetric rates of lamellar structural change during doping and dedoping that do not directly depend on potential or charging transients. Time-resolved spectroscopy establishes a link between structural transients and the complex kinetics of electronic charge carrier subpopulations, in particular the polaron–bipolaron equilibrium. These findings provide insight into the factors limiting the response time of organic mixed-conductor-based devices, and present the first real-time observation of the structural changes during doping and dedoping of a conjugated polymer system via X-ray scattering.     

A visible-light and infrared video database for performance evaluation of video/image fusion methods

Multidimensional Systems and Signal Processing - In general, the fusion of visible-light and infrared images produces a composite representation where both data are pictured in a single image. The...     

Indoor boundary layer chemistry modeling

Ozone (O₃) chemistry is thought to dominate the oxidation of indoor surfaces. We consider the hypothesis that reactions taking place within indoor boundary layers result in greater than anticipated hydroxyl radical (OH) deposition rates. We develop models that account for boundary layer mass‐transfer phenomena, O₃‐terpene chemistry and OH formation, removal, and deposition; we solve these analytically and by applying numerical methods. For an O₃‐limonene system, we find that OH flux to a surface with an O₃ reaction probability of 10^?8 is 4.3 × 10^?5 molec/(cm² s) which is about 10 times greater than predicted by a traditional boundary layer theory. At very low air exchange rates the OH surface flux can be as much as 10% of that for O₃. This effect becomes less pronounced for more O₃‐reactive surfaces. Turbulence intensity does not strongly influence the OH concentration gradient except for surfaces with an O₃ reaction probability >10^?4. Although the O₃ flux dominates OH flux under most conditions, OH flux can be responsible for as much as 10% of total oxidant uptake to otherwise low‐reactivity surfaces. Further, OH chemistry differs from that for ozone; therefore, its deposition is important in understanding the chemical evolution of some indoor surfaces and surface films.     

Essential oil nanoemulsions: antibacterial activity in contaminated fruit juices

Many human acid tolerant bacterial and fungal pathogens can be transmitted through the consumption of the contaminated fruit juices. We aim to formulate essential oil nanoemulsions (basil, black seed, turmeric, clove & cinnamon), determine their ability to clear contamination by food borne bacterial pathogens from fruit juices. The antibacterial activity of the optimised formulations was tested in the fruit juices against bacterial pathogens causing gastrointestinal tract infections. The minimum bactericidal concentration (MBC) of clove emulsions ranged from 15.6 to 25 μL mL⁻¹. Cinnamon oil emulsion had an MBC ranging between 15 and 31 μL mL⁻¹. At MBC, cinnamon oil emulsions caused a 6log₁₀ decrease in viable counts by 8 h and maintained the sterility of fruit juices for 7 days at ambient temperature. Thus, clove and cinnamon microemulsions can be used as juice additives to control food borne bacterial pathogens and maintain the bacterial sterility of fruit juices.     

Impact of defects on the decomposition of chemical warfare agent simulants in Zr-based metal organic frameworks

Metal organic frameworks (MOFs) containing zirconium secondary building units (SBUs) in UiO-67 and related MOFs, are highly active for neutralizing both the chemical warfare agents and simulants, such as dimethyl methylphosphonate (DMMP). However, two recent publications gave conflicting reports of DMMP reaction with UiO-67 under ultra high vacuum (UHV) conditions, with one reporting chemisorption and reaction (Wang et al., J Phys Chem C, 2017, 121, 11261–11272) and the other reporting only physisorption and reversible desorption (Ruffley et al., J Phys Chem C, 2019, 123, 19748–19758) from very similar temperature programmed desorption experiments. We show that the discrepancy between these experiments may be explained by different levels of missing linker defects in the UiO-67 samples. We present density functional theory calculations showing that SBU sites having two-adjacent missing linkers exhibit reaction barriers that are about 30 kJ/mol lower than SBU sites having a single missing linker. We also show that topology of the undercoordinated sites plays an important role in the reaction barrier under UHV conditions.     

The influence of iodide on glass transition temperature of high-pressure nuclear waste glasses

The glass transition temperature (T_g) is a key parameter to investigate for application in nuclear waste immobilization in borosilicate glasses. T_g for several glasses containing iodine (I) has been measured in order to determine the I effect on T_g. Two series of glass composition (ISG and NH) containing up to 2.5 mol% I and synthesized under high pressure (0.5 to 1.5 GPa) have been investigated using differential scanning calorimetry (DSC). The I local environment in glasses has been determined using X-ray photoelectron spectroscopy and revealed that I is dissolved under its iodide form (I⁻). Results show that T_g is decreased with the I addition in the glass in agreement with previous results. We also observed that this T_g decrease is a strong function of glass composition. For NH, 2.5 mol% I induces a decrease of 24°C in T_g, whereas for ISG, 1.2 mol% decreases the T_g by 64°C. We interpret this difference as the result of the I dissolution mechanism and its effect on the polymerization of the boron network. The I dissolution in ISG is accompanied by a depolymerization of the boron network, whereas it is the opposite in NH. Although ISG corresponds to a standardized glass, for the particular case of I immobilization it appears less adequate than NH considering that the decrease in T_g for NH is small in comparison to ISG.