Quantitative Analysis of Arterial Spin Labeling FMRI Data Using a General Linear Model

Arterial spin labeling techniques can yield quantitative measures of perfusion by fitting a kinetic model to difference images (tagged-control). Because of the noisy nature of the difference images investigators typically average a large number of tagged versus control difference measurements over long periods of time. This averaging requires that the perfusion signal be at a steady state and not at the transitions between active and baseline states in order to quantitatively estimate activation induced perfusion. This can be an impediment for functional magnetic resonance imaging task experiments. In this work, we introduce a general linear model (GLM) that specifies Blood Oxygenation Level Dependent (BOLD) effects and arterial spin labeling modulation effects and translate them into meaningful, quantitative measures of perfusion by using standard tracer kinetic models. We show that there is a strong association between the perfusion values using our GLM method and the traditional subtraction method, but that our GLM method is more robust to noise

Complex-valued analysis of arterial spin labeling–based functional magnetic resonance imaging signals

Cerebral blood flow-dependent phase differences between tagged and control arterial spin labeling images are reported. A biophysical model is presented to explain the vascular origin of this difference. Arterial spin labeling data indicated that the phase difference is largest when the arterial component of the signals is preserved but is greatly reduced as the arterial contribution is suppressed by postinversion delays or flow-crushing gradients. Arterial vasculature imaging by saturation data of activation and hypercapnia conditions showed increases in phase accompanying blood flow increases. An arterial spin labeling functional magnetic resonance imaging study yielded significant activation by magnitude-only, phase-only, and complex analyses when preserving the whole arterial spin labeling signal. After suppression of the arterial signal by postinversion delays, magnitude-only and complex models yielded similar activation levels, but the phase-only model detected nearly no activation. When flow crushers were used for arterial suppression, magnitude-only activation was slightly lower and fluctuations in phase were dramatically higher than when postinversion delays were used. Although the complex analysis performed did not improve detection, a simulation study indicated that the complex-valued activation model exhibits combined magnitude and phase detection power and thus maximizes sensitivity under ideal conditions. This suggests that, as arterial spin labeling imaging and image correction methods develop, the complex-valued detection model may become helpful in signal detection. Magn Reson Med, 2009. © 2009 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64527/1/22106_ftp.pd

Real-time observations of single bacteriophage λ DNA ejections in vitro

The physical, chemical, and structural features of bacteriophage genome release have been the subject of much recent attention. Many theoretical and experimental studies have centered on the internal forces driving the ejection process. Recently, Mangenot et al. [Mangenot S, Hochrein M, Rädler J, Letellier L (2005) Curr Biol 15:430–435.] reported fluorescence microscopy of phage T5 ejections, which proceeded stepwise between DNA nicks, reaching a translocation speed of 75 kbp/s or higher. It is still unknown how high the speed actually is. This paper reports real-time measurements of ejection from phage {lambda}, revealing how the speed depends on key physical parameters such as genome length and ionic state of the buffer. Except for a pause before DNA is finally released, the entire 48.5-kbp genome is translocated in {approx}1.5 s without interruption, reaching a speed of 60 kbp/s. The process gives insights particularly into the effects of two parameters: a shorter genome length results in lower speed but a shorter total time, and the presence of divalent magnesium ions (replacing sodium) reduces the pressure, increasing ejection time to 8–11 s. Pressure caused by DNA–DNA interactions within the head affects the initiation of ejection, but the close packing is also the dominant source of friction: more tightly packed phages initiate ejection earlier, but with a lower initial speed. The details of ejection revealed in this study are probably generic features of DNA translocation in bacteriophages and have implications for the dynamics of DNA in other biological systems

Visual Function Questionnaire as an outcome measure for homonymous hemianopia: subscales and supplementary questions, analysis from the VISION trial

Background: We conduct supplementary analyses of the NEI VFQ-25 data to evaluate where changes occurred within subscales of the NEI VFQ-25 leading to change in the composite scores between the three treatment arms, and evaluate the NEI VFQ-25 with and without the Neuro 10 supplement. Methods: A prospective, multicentre, parallel, single-blind, three-arm RCT of fourteen UK acute stroke units was conducted. Stroke survivors with homonymous hemianopia were recruited. Interventions included: Fresnel prisms for minimum 2 h, 5 days/week over 6-weeks (Arm a), Visual search training for minimum 30 min, 5 days/week over 6-weeks (Arm b) and standard care-information only (Arm c). Primary and secondary outcomes (including NEI VFQ-25 data) were measured at baseline, 6, 12 and 26 weeks after randomisation. Results: Eighty seven patients were recruited (69% male; mean age (SD) equal to 69 (12) years). At 26 weeks, outcomes for 24, 24 and 22 patients, respectively, were compared to baseline. NEI VFQ-25 (with and without Neuro 10) responses improved from baseline to 26 weeks with visual search training compared to Fresnel prisms and standard care. In subscale analysis, the most impacted across all treatment arms was ‘driving’ whilst the least impacted were ‘colour vision’ and ‘ocular pain’. Conclusions: Composite scores differed systematically for the NEI VFQ-25 (Neuro 10) versus NEI VFQ-25 at all time points. For subscale scores, descriptive statistics suggest clinically relevant improvement in distance activities and vision-specific dependency subscales for NEI VFQ-25 scores in the visual search treatment arm. Trial Registration: Current Controlled Trials ISRCTN05956042

Impacts of Wetland Restoration Efforts on an Amphibian Assemblage in a Multi-invader Community

The success of restoration in attaining wildlife conservation goals can be strongly dependent on both site-scale and landscape-scale habitat characteristics, particularly for species with complex life cycles. Wetland management activities typically target plant communities, and bottom-up responses in higher trophic levels may be dependent on spatially explicit habitat use. We surveyed plant and amphibian assemblages at 26 sites enrolled in the Wetlands Reserve Program (WRP) in the Willamette Valley, Oregon to determine the relative influence of plant management, non-native species, and surrounding landscape on amphibian counts across multiple life history stages. Explanatory variables negatively associated with native anuran counts included percent invasive plant cover, non-native fish presence, invasive bullfrog counts, and area of urban land cover. In addition, native anurans were positively associated with WRP site age, suggesting that the benefits of restored wetlands may increase over time. This study emphasized the importance of adaptive approaches to maintaining diverse communities in restored habitats by considering impacts of synergistic stressors in a multi-invader context. Although invasive plant management provided indirect benefits to native amphibians, the most effective way to enhance native amphibian populations may be through eliminating the strong top-down forces exerted by non-native vertebrates.Keywords: WRP, Invasive species, Landscape, Restoration, Wetlands, Amphibian

The Inflaton and Time in the Matter-Gravity System

The emergence of time in the matter-gravity system is addressed within the context of the inflationary paradigm. A quantum minisuperspace-homogeneous minimally coupled inflaton system is studied with suitable initial conditions leading to inflation and the system is approximately solved in the limit for large scale factor. Subsequently normal matter (either non homogeneous inflaton modes or lighter matter) is introduced as a perturbation and it is seen that its presence requires the coarse averaging of a gravitational wave function (which oscillates at trans-Planckian frequencies) having suitable initial conditions. Such a wave function, which is common for all types of normal matter, is associated with a ``time density'' in the sense that its modulus is related to the amount of time spent in a given interval (or the rate of flow of time). One is then finally led to an effective evolution equation (Schroedinger Schwinger-Tomonaga) for ``normal'' matter. An analogy with the emergence of a temperature in statistical mechanics is also pointed out.Comment: 14 pages, late

Self-consistent anisotropic oscillator with cranked angular and vortex velocities

The Kelvin circulation is the kinematical Hermitian observable that measures the true character of nuclear rotation. For the anisotropic oscillator, mean field solutions with fixed angular momentum and Kelvin circulation are derived in analytic form. The cranking Lagrange multipliers corresponding to the two constraints are the angular and vortex velocities. Self-consistent solutions are reported with a constraint to constant volume.Comment: 12 pages, LaTex/RevTex, Phys. Rev. C4

A systematic study of spin-dependent recombination in GaAs1−x_{1-x}Nx_x as a function of nitrogen content

A systematic study of spin-dependent recombination (SDR) under steady-state optical pumping conditions in dilute nitride semiconductors as a function of nitrogen content is reported. The alloy content is determined by a fit of the photoluminescence (PL) intensity using a Roosbroeck-Shockley relation and verified by a study of the GaN-like LO$_2$ phonon peak in a Raman spectroscopy map. PL spectra taken from alloys of the form GaAs$_{1-x}$N$_x$ where $0.022 < x < 0.036$ exhibit PL intensity increases when switching from a linearly- to a circularly-polarized pump up to a factor of 5 for $x = 0.022$. This work used a 1.39 eV laser with a radius of 0.6 $\mu$m. The observed SDR ratio monotonically decreases with increasing $x$, reaching 1.5 for $x = 0.036$. Moreover, the excitation power required to obtain maximum SDR systematically increases with increasing $x$, varying from 0.6 mW for $x = 0.022$ to 15 mW for $x = 0.036$. These observations are consistent with an increase in the density of electronically active defects with increasing nitrogen content, both those responsible for the SDR as well as other, standard Shockley-Read-Hall (SRH) centers.Comment: 11 pages, 5 figures; work presented at the International Conference on the Physics of Semiconductors, Sydney, 202

A tad too high: Sensitivity to UV-B radiation may limit invasion potential of American bullfrogs (Lithobates catesbeianus) in the Pacific Northwest invasion range

Biological invasion potential can be strongly influenced by abiotic factors such as temperature, water availability, and solar radiation. Invasive species that possess phenotypically plastic traits can mediate impacts from these stressors, but may be unable to recognize and respond to dangerous levels in a novel environment. Understanding potential constraints on appropriate trait responses induced by abiotic stressors can aid in the management and control of important invaders. Our study explored tolerance and plastic trait response to UV-B radiation in an invasive anuran, the American bullfrog (Lithobates catesbeianus Shaw, 1802). We experimentally quantified larval mortality rates and color change responses across two larval size classes. In a second experiment, we investigated the potential for a correlated color change and behavioral (refuge use) response in the small size class. We predicted that individuals would respond to stressful and potentially harmful UV-B exposure rates with darkening of body coloration, and when refuge was available, a correlated defense strategy utilizing both color change and refuge. We found an increase in larval mortality across both size classes at UV-B exposure rates typical to both low and high elevation aquatic breeding sites (10-12 μW/cm² and 20-24 μW/cm² , respectively). Only bullfrog larvae in the small size class exhibited a darkening in body color when exposed to high UV-B treatments. Although this smaller size class did exhibit color plasticity, individuals did not correlate changes in body coloration with changes in refuge use. These results suggest ontogenetic differences (estimated by size class) in plastic color response to UV-B stress as well as constraints on behavioral use of refuge. These findings are important in understanding differences in bullfrog occupancy of breeding habitats across an elevational gradient, particularly in Oregon’s Cascade Mountain Range, where bullfrog distributions are currently limited at elevations above 1000 m.Keywords: Amphibian, Ultraviolet radiation, Color, Plasticity, American bullfrog, Invasion, BehaviorThis is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Regional Euro-Asian Biological Invasions Centre