Nuclear Magnetic Resonance and Magneto-Optics

Contains reports on three research projects

Nuclear Magnetic Resonance and Hyperfine Structure

Contains reports on three research projects

The nonlinear time-dependent response of isotactic polypropylene

Tensile creep tests, tensile relaxation tests and a tensile test with a constant rate of strain are performed on injection-molded isotactic polypropylene at room temperature in the vicinity of the yield point. A constitutive model is derived for the time-dependent behavior of semi-crystalline polymers. A polymer is treated as an equivalent network of chains bridged by permanent junctions. The network is modelled as an ensemble of passive meso-regions (with affine nodes) and active meso-domains (where junctions slip with respect to their positions in the bulk medium with various rates). The distribution of activation energies for sliding in active meso-regions is described by a random energy model. Adjustable parameters in the stress--strain relations are found by fitting experimental data. It is demonstrated that the concentration of active meso-domains monotonically grows with strain, whereas the average potential energy for sliding of junctions and the standard deviation of activation energies suffer substantial drops at the yield point. With reference to the concept of dual population of crystalline lamellae, these changes in material parameters are attributed to transition from breakage of subsidiary (thin) lamellae in the sub-yield region to fragmentation of primary (thick) lamellae in the post-yield region of deformation.Comment: 29 pages, 12 figure

A single amino acid switch converts the sleeping beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming

The Sleeping Beauty (SB) transposon is an advanced tool for genetic engineering and a useful model to investigate cut-and-paste DNA transposition in vertebrate cells. Here, we identify novel SB transposase mutants that display efficient and canonical excision but practically unmeasurable genomic re-integration. Based on phylogenetic analyses, we establish compensating amino acid replacements that fully rescue the integration defect of these mutants, suggesting epistasis between these amino acid residues. We further show that the transposons excised by the exc(+)/int(-) transposase mutants form extrachromosomal circles that cannot undergo a further round of transposition, thereby representing dead-end products of the excision reaction. Finally, we demonstrate the utility of the exc(+)/int(-) transposase in cassette removal for the generation of reprogramming factor-free induced pluripotent stem cells. Lack of genomic integration and formation of transposon circles following excision is reminiscent of signal sequence removal during V(D)J recombination, and implies that cut-and-paste DNA transposition can be converted to a unidirectional process by a single amino acid change

Structured Sparsity: Discrete and Convex approaches

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure

Intersection form, laminations and currents on free groups

Let $F_N$ be a free group of rank $N\ge 2$, let $\mu$ be a geodesic current on $F_N$ and let $T$ be an $\mathbb R$-tree with a very small isometric action of $F_N$. We prove that the geometric intersection number $$ is equal to zero if and only if the support of $\mu$ is contained in the dual algebraic lamination $L^2(T)$ of $T$. Applying this result, we obtain a generalization of a theorem of Francaviglia regarding length spectrum compactness for currents with full support. As another application, we define the notion of a \emph{filling} element in $F_N$ and prove that filling elements are "nearly generic" in $F_N$. We also apply our results to the notion of \emph{bounded translation equivalence} in free groups.Comment: revised version, to appear in GAF

Mapping Exoplanets

The varied surfaces and atmospheres of planets make them interesting places to live, explore, and study from afar. Unfortunately, the great distance to exoplanets makes it impossible to resolve their disk with current or near-term technology. It is still possible, however, to deduce spatial inhomogeneities in exoplanets provided that different regions are visible at different times---this can be due to rotation, orbital motion, and occultations by a star, planet, or moon. Astronomers have so far constructed maps of thermal emission and albedo for short period giant planets. These maps constrain atmospheric dynamics and cloud patterns in exotic atmospheres. In the future, exo-cartography could yield surface maps of terrestrial planets, hinting at the geophysical and geochemical processes that shape them.Comment: Updated chapter for Handbook of Exoplanets, eds. Deeg & Belmonte. 17 pages, including 6 figures and 4 pages of reference

Ultrafast 3d spin-echo acquisition improves gadolinium-enhanced mri signal contrast enhancement

Long scan times of 3D volumetric MR acquisitions usually necessitate ultrafast in vivo gradient-echo acquisitions, which are intrinsically susceptible to magnetic field inhomogeneities. This is especially problematic for contrast-enhanced (CE)-MRI applications, where non-negligible T 2 & z.ast; effect of contrast agent deteriorates the positive signal contrast and limits the available range of MR acquisition parameters and injection doses. To overcome these shortcomings without degrading temporal resolution, ultrafast spin-echo acquisitions were implemented. Specifically, a multiplicative acceleration factor from multiple spin echoes (??32) and compressed sensing (CS) sampling (??8) allowed highly-accelerated 3D Multiple-Modulation- Multiple-Echo (MMME) acquisition. At the same time, the CE-MRI of kidney with Gd-DOTA showed significantly improved signal enhancement for CS-MMME acquisitions (??7) over that of corresponding FLASH acquisitions (??2). Increased positive contrast enhancement and highly accelerated acquisition of extended volume with reduced RF irradiations will be beneficial for oncological and nephrological applications, in which the accurate in vivo 3D quantification of contrast agent concentration is necessary with high temporal resolution.open0

Deriving and critiquing an empirically-based framework for pharmaceutical ethics.

Background: The pharmaceutical industry has been responsible for major medical advances, but the industry has also been heavily criticized. Such criticisms, and associated regulatory responses, are no doubt often warranted, but do not provide a framework for those who wish to reason systematically about the moral dimensions of drug development. We set out to develop such a framework using Beauchamp and Childress’s “four principles” as organizing categories. Methods: We conducted a qualitative interview study of people working in the “medical affairs” departments of pharmaceutical companies to determine: (1) whether our data could meaningfully be organized under the headings of “autonomy,” “beneficence,” “nonmaleficence,” and “justice”; (2) how principles might be expressed in this particular commercial setting; and (3) if these principles are expressed, whether and how competing principles are balanced. We then critiqued these findings using existing normative theory. Results: Our interviews demonstrated that three of Beauchamp and Childress’ four principles were salient to our participants: beneficence, non-maleficence, and justice. Within each of these principles, participants had two broad ethical orientations: an altruistic public focus (“other-ness”) and a commitment to their companies (“firm-ness”). Our participants also demonstrated efforts to balance these principles and highlighted the importance of phronesis (or practical wisdom) in balancing and enacting principles. Notably, however, our participants did not spontaneously emphasize the importance of autonomy. Conclusions: It is possible to use qualitative empirical research, together with normative analysis, to derive a framework for pharmaceutical ethics. We suggest that our framework would be useful for those who wish to reason ethically within, or in collaboration with, the pharmaceutical industry. Keywords: Empirical ethics, principle-based ethics, pharmaceutical industry, pharmaceutical ethics, qualitative researchNHMRC Career Development Fellowship APP106356