Simulations of the effect of diffusion on asymmetric spin echo based quantitative BOLD: An investigation of the origin of deoxygenated blood volume overestimation

Quantitative BOLD (qBOLD) is a technique for mapping oxygen extraction fraction (OEF) and deoxygenated blood volume (DBV) in the human brain. Recent measurements using an asymmetric spin echo (ASE) based qBOLD approach produced estimates of DBV which were systematically higher than measurements from other techniques. In this study, we investigate two hypotheses for the origin of this DBV overestimation using simulations and consider the implications for experimental measurements. Investigations were performed by combining Monte Carlo simulations of extravascular signal with an analytical model of the intravascular signal.Hypothesis 1: DBV overestimation is due to the presence of intravascular signal which is not accounted for in the analysis model. Intravascular signal was found to have a weak effect on qBOLD parameter estimates.Hypothesis 2: DBV overestimation is due to the effects of diffusion which are not accounted for in the analysis model. The effect of diffusion on the extravascular signal was found to result in a vessel radius dependent variation in qBOLD parameter estimates. In particular, DBV overestimation peaks for vessels with radii from 20 to 30 μm and is OEF dependent. This results in the systematic underestimation of OEF.Implications: The impact on experimental qBOLD measurements was investigated by simulating a more physiologically realistic distribution of vessel sizes with a small number of discrete radii. Overestimation of DBV consistent with previous experiments was observed, which was also found to be OEF dependent. This results in the progressive underestimation of the measured OEF. Furthermore, the relationship between the measured OEF and the true OEF was found to be dependent on echo time and spin echo displacement time. The results of this study demonstrate the limitations of current ASE based qBOLD measurements and provide a foundation for the optimisation of future acquisition approaches

Solutions to Defect-Related Problems in Implanted Silicon by Controlled Injection of Vacancies by High-Energy Ion Irradiation

Amorphization and a dual implant technique have been used to manipulate residual defects that persist following implantation and post-implant thermal treatments. Residual defects can often be attributed to ion-induced defect excesses. A defect is considered to be excess when it occurs in a localized region at a concentration greater than its complement. Sources of excess defects include spatially separated Frenkel pairs, excess interstitials resulting from the implanted atoms, and sputtering. Pre-amorphizing prior to dopant implantation has been proposed to eliminate dopant broadening due to ion channeling as well as dopant diffusion during subsequent annealing. However, transient-enhanced diffusion (TED) of implanted boron has been observed in pre-amorphized Si. The defects driving this enhanced boron diffusion are thought to be the extended interstitial-type defects that form below the amorphous-crystalline interface during implantation. A dual implantation process was applied in an attempt to reduce or eliminate this interfacial defect band. High-energy, ion implantation is known to inject a vacancy excess in this region. Vacancies were implanted at a concentration coincident with the excess interstitials below the a-c interface to promote recombination between the two defect species. Preliminary results indicate that a critical fluence, i.e., a sufficient vacancy concentration, will eliminate the interstitial defects. The effect of the reduction or elimination of these interfacial defects upon TED of boron will be discussed. Rutherford backscattering/channeling and cross section transmission electron microscopy analyses were used to characterize the defect structure within the implanted layer. Secondary ion mass spectroscopy was used to profile the dopant distributions

Feshbach resonances in a quasi-2D atomic gas

Strongly confining an ultracold atomic gas in one direction to create a quasi-2D system alters the scattering properties of this gas. We investigate the effects of confinement on Feshbach scattering resonances and show that strong confinement results in a shift in the position of the Feshbach resonance as a function of the magnetic field. This shift, as well as the change of the width of the resonance, are computed. We find that the resonance is strongly damped in the thermal gas, but in the condensate the resonance remains sharp due to many-body effects. We introduce a 2D model system, suited for the study of resonant superfluidity, and having the same scattering properties as the tightly confined real system near a Feshbach resonance. Exact relations are derived between measurable quantities and the model parameters.Comment: 8 pages, 2 figure

Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5–10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72825/1/j.1462-2920.2007.01250.x.pd

Genetic Variation in Heat Tolerance of the Coral Platygyra Daedalea Indicates Potential for Adaptation to Ocean Warming

Ocean warming represents the greatest threat to the persistence of reef ecosystems. Most coral populations are projected to experience temperatures above their current bleaching thresholds annually by 2050. Adaptation to higher temperatures is necessary if corals are to persist in a warming future. While many aspects of heat stress have been well studied, few data are available for predicting the capacity for adaptive cross-generational responses in corals. Consistent sets of heat tolerant genomic markers that reliably predict thermal tolerance have yet to be identified. To address this knowledge gap, we quantified the heritability and genetic variation associated with heat tolerance in Platygyra daedalea from the Great Barrier Reef. We tracked the survival of ten quantitative genetic crosses of larvae produced form six parental colonies in a heat tolerance selection experiment. We also identified allelic shifts in heat-selected (35°C) survivors compared with paired, non-selected controls (27°C). The narrow-sense heritability of survival under heat stress was 0.66 and a total of 1,069 single nucleotide polymorphisms (SNPs) were associated with different survival probabilities. While 148 SNPs were shared between several experimental crosses, no common SNPs were identified for all crosses, which suggests that specific combinations of many markers are responsible for heat tolerance. However, we found two regions that overlap with previously identified loci associated with heat tolerance in Persian Gulf populations of P. daedalea, which reinforces the importance of these markers for heat tolerance. These results illustrate the importance of high heritability and the complexity of the genomic architecture underpinning host heat tolerance. These findings suggest that this P. daedalea population has the genetic prerequisites for adaptation to increasing temperatures. This study also provides knowledge for the development of high throughput genomic tools which may screen for variation within and across populations to enhance adaptation through assisted gene flow and assisted migration

Control of an atom laser using feedback

A generalised method of using feedback to control Bose-Einstein condensates is introduced. The condensates are modelled by the Gross-Pitaevskii equation, so only semiclassical fluctations can be suppressed, and back-action from the measurement is ignored. We show that for any available control, a feedback scheme can be found to reduce the energy while the appropriate moment is still dynamic. We demonstrate these schemes by considering a condensate trapped in a harmonic potential that can be modulated in strength and position. The formalism of our feedback scheme also allows the inclusion of certain types of non-linear controls. If the non-linear interaction between the atoms can be controlled via a Feshbach resonance, we show that the feedback process can operate with a much higher efficiency.Comment: 6 pages, 7 figure

Quantum limits on phase-shift detection using multimode interferometers

Fundamental phase-shift detection properties of optical multimode interferometers are analyzed. Limits on perfectly distinguishable phase shifts are derived for general quantum states of a given average energy. In contrast to earlier work, the limits are found to be independent of the number of interfering modes. However, the reported bounds are consistent with the Heisenberg limit. A short discussion on the concept of well-defined relative phase is also included.Comment: 6 pages, 3 figures, REVTeX, uses epsf.st

Critical number of atoms for attractive Bose-Einstein condensates with cylindrically symmetrical traps

We calculated, within the Gross-Pitaevskii formalism, the critical number of atoms for Bose-Einstein condensates with two-body attractive interactions in cylindrical traps with different frequency ratios. In particular, by using the trap geometries considered by the JILA group [Phys. Rev. Lett. 86, 4211 (2001)], we show that the theoretical maximum critical numbers are given approximately by $N_c = 0.55 ({l_0}/{|a|})$. Our results also show that, by exchanging the frequencies $\omega_z$ and $\omega_\rho$, the geometry with $\omega_\rho < \omega_z$ favors the condensation of larger number of particles. We also simulate the time evolution of the condensate when changing the ground state from $a=0$ to $a<0$ using a 200ms ramp. A conjecture on higher order nonlinear effects is also added in our analysis with an experimental proposal to determine its signal and strength.Comment: (4 pages, 2 figures) To appear in Physical Review

Properties of a Dilute Bose Gas near a Feshbach Resonance

In this paper, properties of a homogeneous Bose gas with a Feshbach resonance are studied in the dilute region at zero temperature. The stationary state contains condensations of atoms and molecules. The ratio of the molecule density to the atom density is $\pi na^3$. There are two types of excitations, molecular excitations and atomic excitations. Atomic excitations are gapless, consistent with the traditional theory of a dilute Bose gas. The molecular excitation energy is finite in the long wavelength limit as observed in recent experiments on $^{85}$Rb. In addition, the decay process of the condensate is studied. The coefficient of the three-body recombination rate is about 140 times larger than that of a Bose gas without a Feshbach resonance, in reasonably good agreement with the experiment on $^{23}$Na.Comment: 11 pages, 1 figure, comparison between the calculated three-body recombination rate and the experimental data for Na system has been adde