Optimizing Filter-Probe Diffusion Weighting in the Rat Spinal Cord for Human Translation

Diffusion tensor imaging (DTI) is a promising biomarker of spinal cord injury (SCI). In the acute aftermath, DTI in SCI animal models consistently demonstrates high sensitivity and prognostic performance, yet translation of DTI to acute human SCI has been limited. In addition to technical challenges, interpretation of the resulting metrics is ambiguous, with contributions in the acute setting from both axonal injury and edema. Novel diffusion MRI acquisition strategies such as double diffusion encoding (DDE) have recently enabled detection of features not available with DTI or similar methods. In this work, we perform a systematic optimization of DDE using simulations and an in vivo rat model of SCI and subsequently implement the protocol to the healthy human spinal cord. First, two complementary DDE approaches were evaluated using an orientationally invariant or a filter-probe diffusion encoding approach. While the two methods were similar in their ability to detect acute SCI, the filter-probe DDE approach had greater predictive power for functional outcomes. Next, the filter-probe DDE was compared to an analogous single diffusion encoding (SDE) approach, with the results indicating that in the spinal cord, SDE provides similar contrast with improved signal to noise. In the SCI rat model, the filter-probe SDE scheme was coupled with a reduced field of view (rFOV) excitation, and the results demonstrate high quality maps of the spinal cord without contamination from edema and cerebrospinal fluid, thereby providing high sensitivity to injury severity. The optimized protocol was demonstrated in the healthy human spinal cord using the commercially-available diffusion MRI sequence with modifications only to the diffusion encoding directions. Maps of axial diffusivity devoid of CSF partial volume effects were obtained in a clinically feasible imaging time with a straightforward analysis and variability comparable to axial diffusivity derived from DTI. Overall, the results and optimizations describe a protocol that mitigates several difficulties with DTI of the spinal cord. Detection of acute axonal damage in the injured or diseased spinal cord will benefit the optimized filter-probe diffusion MRI protocol outlined here

Energy dissipation and ion heating at the heliospheric termination shock

The Los Alamos hybrid simulation code is used to examine heating and the partition of dissipation energy at the perpendicular heliospheric termination shock in the presence of pickup ions. The simulations are one-dimensional in space but three-dimensional in field and velocity components, and are carried out for a range of values of pickup ion relative density. Results from the simulations show that because the solar wind ions are relatively cold upstream, the temperature of these ions is raised by a relatively larger factor than the temperature of the pickup ions. An analytic model for energy partition is developed on the basis of the Rankine-Hugoniot relations and a polytropic energy equation. The polytropic index gamma used in the Rankine-Hugoniot relations is varied to improve agreement between the model and the simulations concerning the fraction of downstream heating in the pickup ions as well as the compression ratio at the shock. When the pickup ion density is less than 20%, the polytropic index is about 5/3, whereas for pickup ion densities greater than 20%, the polytropic index tends toward 2.2, suggesting a fundamental change in the character of the shock, as seen in the simulations, when the pickup ion density is large. The model and the simulations both indicate for the upstream parameters chosen for Voyager 2 conditions that the pickup ion density is about 25% and the pickup ions gain the larger share ( approximately 90%) of the downstream thermal pressure, consistent with Voyager 2 observations near the shock

Importance of charge capture in interphase regions during readout of charge-coupled devices

The current understanding of charge transfer dynamics in charge-coupled devices (CCDs) is that charge is moved so quickly from one phase to the next in a clocking sequence and with a density so low that trapping of charge in the interphase regions is negligible. However, simulation capabilities developed at the Centre for Electronic Imaging, which includes direct input of electron density simulations, have made it possible to investigate this assumption further. As part of the radiation testing campaign of the Euclid CCD273 devices, data have been obtained using the trap pumping method, a method that can be used to identify and characterize single defects within CCDs. Combining these data with simulations, we find that trapping during the transfer of charge among phases is indeed necessary to explain the results of the data analysis. This result could influence not only trap pumping theory and how trap pumping should be performed but also how a radiation-damaged CCD is readout in the most optimal way

Exceptional Sequences on Rational C*-Surfaces

Inspired by Bondal's conjecture, we study the behavior of exceptional sequences of line bundles on rational C*-surfaces under homogeneous degenerations. In particular, we provide a sufficient criterion for such a sequence to remain exceptional under a given degeneration. We apply our results to show that, for toric surfaces of Picard rank 3 or 4, all full exceptional sequences of line bundles may be constructed via augmentation. We also discuss how our techniques may be used to construct noncommutative deformations of derived categories.Comment: 30 pages, 11 figures. Some parts of this preprint originally appeared in arXiv:0906.4292v2 but have been revised and expanded upon. Minor changes, to appear in Manuscripta Mathematic

Modeling the mobility of living organisms in heterogeneous landscapes: Does memory improve foraging success?

Thanks to recent technological advances, it is now possible to track with an unprecedented precision and for long periods of time the movement patterns of many living organisms in their habitat. The increasing amount of data available on single trajectories offers the possibility of understanding how animals move and of testing basic movement models. Random walks have long represented the main description for micro-organisms and have also been useful to understand the foraging behaviour of large animals. Nevertheless, most vertebrates, in particular humans and other primates, rely on sophisticated cognitive tools such as spatial maps, episodic memory and travel cost discounting. These properties call for other modeling approaches of mobility patterns. We propose a foraging framework where a learning mobile agent uses a combination of memory-based and random steps. We investigate how advantageous it is to use memory for exploiting resources in heterogeneous and changing environments. An adequate balance of determinism and random exploration is found to maximize the foraging efficiency and to generate trajectories with an intricate spatio-temporal order. Based on this approach, we propose some tools for analysing the non-random nature of mobility patterns in general.Comment: 14 pages, 4 figures, improved discussio

Drought and Small-Bodied Herbivores Modify Nutrient Cycling in The Semi-Arid Shortgrass Steppe

Climate change will increase the frequency of droughts over the next century, with severe consequences for ecosystem function in semi-arid grasslands. The shortgrass steppe (SGS) experiences some of the largest interannual variation in precipitation among terrestrial biomes and exhibits extremely high sensitivity to drought. Yet despite decades of research describing the consequences of drought for ecosystem function in the SGS, we currently have little information regarding the impact of drought on bioavailability of important nutrients other than nitrogen, the contribution of herbivores to bioavailable concentrations of these nutrients, and whether drought alters herbivore-derived nutrient cycling. To quantify the impacts of long-term drought and small-bodied herbivores on nutrient cycling and aboveground net primary production (ANPP), we factorially manipulated rainfall and herbivore presence in the SGS of northern Colorado. Specifically, we measured the impacts of drought and herbivores on bioavailability of ten important nutrients: aluminum, calcium, iron, potassium, magnesium, manganese, nitrate, phosphorus, sulfur, and zinc. We then correlated these nutrients with grass production to determine whether reduced plant growth under drought conditions causes a belowground buildup of nutrients. Drought reduced ANPP as expected, and also altered concentrations of many nutrients apart from N, which clustered in their drought response. In contrast, small-bodied herbivores did not affect ANPP or soil N. However, they did contribute to the bioavailable soil concentrations of two important nutrients: PO4-P and S. Importantly, drought generally did not modify the contribution of herbivores to nutrient cycling, suggesting that herbivores might be a critical component of biogeochemical cycling regardless of precipitation in semi-arid grasslands

Parton distributions with threshold resummation

We construct a set of parton distribution functions (PDFs) in which fixed-order NLO and NNLO calculations are supplemented with soft-gluon (threshold) resummation up to NLL and NNLL accuracy respectively, suitable for use in conjunction with any QCD calculation in which threshold resummation is included at the level of partonic cross sections. These resummed PDF sets, based on the NNPDF3.0 analysis, are extracted from deep-inelastic scattering, Drell-Yan, and top quark pair production data, for which resummed calculations can be consistently used. We find that, close to threshold, the inclusion of resummed PDFs can partially compensate the enhancement in resummed matrix elements, leading to resummed hadronic cross-sections closer to the fixed-order calculation. On the other hand, far from threshold, resummed PDFs reduce to their fixed-order counterparts. Our results demonstrate the need for a consistent use of resummed PDFs in resummed calculations.Comment: 43 pages, 17 figures, accepted for publication in JHE

Static Torsion Testing and Modeling of a Variable Thickness Hybrid Composite Bull Gear

Torsional strength of a variable thickness hybrid gear web was measured by performing static testing on the part in a large torsion test frame. The outer rim of the hybrid gear web was fixed to the bottom of the test frame and loading was applied to the web through a shaft. The test setup included the installation of digital image correlation (DIC) systems to obtain deformation and strain measurements from the surfaces of the hybrid gear web and the mechanical test equipment to ensure reliability of the test. The results indicated that the variable thickness hybrid gear web achieved approximately twice the torsional strength compared to that of previous hybrid gear designs. The DIC analysis showed significantly more straining of the loading shaft than the actual test article. Additionally, the results demonstrated the importance and affect that the metallic, lobed interlock features had on the principal strain and out-of-plane displacement fields. The analysis revealed that the fixed outer rim was in fact rotating and a rigid body motion compensation (RBMC) function was computed to determine the actual rotation of the hub and composite web relative to the outer rim. Modeling simulations were performed for the variable thickness hybrid gear web and correlated well with the RBMC rotational deformation seen in the DIC analysis. In addition to benchmarking the load capacity of the hybrid gear web, measuring its strength is useful information to define the parameters needed for dynamic, endurance, and other testing of the part

Coherent Neutrino Interactions in a Dense Medium

Motivated by the effect of matter on neutrino oscillations (the MSW effect) we study in more detail the propagation of neutrinos in a dense medium. The dispersion relation for massive neutrinos in a medium is known to have a minimum at nonzero momentum p \sim (G_F\rho)/\sqrt{2}. We study in detail the origin and consequences of this dispersion relation for both Dirac and Majorana neutrinos both in a toy model with only neutral currents and a single neutrino flavour and in a realistic "Standard Model" with two neutrino flavours. We find that for a range of neutrino momenta near the minimum of the dispersion relation, Dirac neutrinos are trapped by their coherent interactions with the medium. This effect does not lead to the trapping of Majorana neutrinos.Comment: 28 pages, 6 figures, Latex; minor changes, one reference added; version to appear in Phys. Rev.