Bioluminescence tomography with Gaussian prior

Parameterizing the bioluminescent source globally in Gaussians provides several advantages over voxel representation in bioluminescence tomography. It is mathematically unique to recover Gaussians [Med. Phys. 31(8), 2289 (2004)] and practically sufficient to approximate various shapes by Gaussians in diffusive medium. The computational burden is significantly reduced since much fewer unknowns are required. Besides, there are physiological evidences that the source can be modeled by Gaussians. The simulations show that the proposed model and algorithm significantly improves accuracy and stability in the presence of Gaussian or non- Gaussian sources, noisy data or the optical background mismatch. It is also validated through in vivo experimental data

Reversible spin-optical interface in luminescent organic radicals

Molecules present a versatile platform for quantum information science, and are candidates for sensing and computation applications. Robust spin-optical interfaces are key to harnessing the quantum resources of materials. To date, carbon-based candidates have been non-luminescent, which prevents optical read-out. Here we report the first organic molecules displaying both efficient luminescence and near-unity generation yield of high-spin multiplicity excited states. This is achieved by designing an energy resonance between emissive doublet and triplet levels, here on covalently coupled tris(2,4,6-trichlorophenyl) methyl-carbazole radicals (TTM-1Cz) and anthracene. We observe the doublet photoexcitation delocalise onto the linked acene within a few picoseconds and subsequently evolve to a pure high spin state (quartet for monoradicals, quintet for biradical) of mixed radical-triplet character near 1.8 eV. These high-spin states are coherently addressable with microwaves even at 295 K, with optical read-out enabled by intersystem crossing to emissive states. Furthermore, for the biradical, on return to the ground state the previously uncorrelated radical spins either side of the anthracene show strong spin correlation. Our approach simultaneously supports a high efficiency of initialisation, spin manipulations and light-based read-out at room temperature. The integration of luminescence and high-spin states creates an organic materials platform for emerging quantum technologies

Magnetic interactions in iron superconductors: A review

High temperature superconductivity in iron pnictides and chalcogenides emerges when a magnetic phase is suppressed. The multi-orbital character and the strength of correlations underlie this complex phenomenology, involving magnetic softness and anisotropies, with Hund's coupling playing an important role. We review here the different theoretical approaches used to describe the magnetic interactions in these systems. We show that taking into account the orbital degree of freedom allows us to unify in a single phase diagram the main mechanisms proposed to explain the (\pi,0) order in iron pnictides: the nesting-driven, the exchange between localized spins, and the Hund induced magnetic state with orbital differentiation. Comparison of theoretical estimates and experimental results helps locate the Fe superconductors in the phase diagram. In addition, orbital physics is crucial to address the magnetic softness, the doping dependent properties, and the anisotropies.Comment: Invited review article for a focus issue of Comptes Rendus Physique: 26 pages, 10 figures. Revised version, as accepted. Small changes throughout the text plus new subsection (Sec. IIIE

Stochastic Gravity: Theory and Applications

Whereas semiclassical gravity is based on the semiclassical Einstein equation with sources given by the expectation value of the stress-energy tensor of quantum fields, stochastic semiclassical gravity is based on the Einstein-Langevin equation, which has in addition sources due to the noise kernel. In the first part, we describe the fundamentals of this new theory via two approaches: the axiomatic and the functional. In the second part, we describe three applications of stochastic gravity theory. First, we consider metric perturbations in a Minkowski spacetime, compute the two-point correlation functions of these perturbations and prove that Minkowski spacetime is a stable solution of semiclassical gravity. Second, we discuss structure formation from the stochastic gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in the gravitational background of a black hole and describe the metric fluctuations near the event horizon of an evaporating black holeComment: 100 pages, no figures; an update of the 2003 review in Living Reviews in Relativity gr-qc/0307032 ; it includes new sections on the Validity of Semiclassical Gravity, the Stability of Minkowski Spacetime, and the Metric Fluctuations of an Evaporating Black Hol

Regulatory feedback response mechanisms to phosphate starvation in rice

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses

α-Synuclein in human cerebrospinal fluid is principally derived from neurons of the central nervous system

The source of Parkinson disease-linked α-synuclein (aSyn) in human cerebrospinal fluid (CSF) remains unknown. We decided to measure the concentration of aSyn and its gradient in human CSF specimens and compared it with serum to explore its origin. We correlated aSyn concentrations in CSF versus serum (QaSyn) to the albumin quotient (Qalbumin) to evaluate its relation to blood–CSF barrier function. We also compared aSyn with several other CSF constituents of either central or peripheral sources (or both) including albumin, neuron-specific enolase, β-trace protein and total protein content. Finally, we examined whether aSyn is present within the structures of the choroid plexus (CP). We observed that QaSyn did not rise or fall with Qalbumin values, a relative measure of blood–CSF barrier integrity. In our CSF gradient analyses, aSyn levels decreased slightly from rostral to caudal fractions, in parallel to the recorded changes for neuron-specific enolase; the opposite trend was recorded for total protein, albumin and β-trace protein. The latter showed higher concentrations in caudal CSF fractions due to the diffusion-mediated transfer of proteins from blood and leptomeninges into CSF in the lower regions of the spine. In postmortem sections of human brain, we detected highly variable aSyn reactivity within the epithelial cell layer of CP in patients diagnosed with a range of neurological diseases; however, in sections of mice that express only human SNCA alleles (and in those without any Snca gene expression), we detected no aSyn signal in the epithelial cells of the CP. We conclude from these complementary results that despite its higher levels in peripheral blood products, neurons of the brain and spinal cord represent the principal source of aSyn in human CSF

Value of MRI and diffusion-weighted MRI for the diagnosis of locally recurrent rectal cancer

OBJECTIVES: To evaluate the accuracy of standard MRI, diffusion-weighted MRI (DWI) and fusion images for the diagnosis of locally recurrent rectal cancer in patients with a clinical suspicion of recurrence. METHODS: Forty-two patients with a clinical suspicion of recurrence underwent 1.5-T MRI consisting of standard T2-weighted FSE (3 planes) and an axial DWI (b0,500,1000). Two readers (R1,R2) independently scored the likelihood of recurrence; [1] on standard MRI, [2] on standard MRI+DWI, and [3] on T2-weighted+DWI fusion images. RESULTS: 19/42 patients had a local recurrence. R1 achieved an area under the ROC-curve (AUC) of 0.99, sensitivity 100% and specificity 83% on standard MRI versus 0.98, 100% and 91% after addition of DWI (p = 0.78). For R2 these figures were 0.87, 84% and 74% on standard MRI and 0.91, 89% and 83% with DWI (p = 0.09). Fusion images did not significantly improve the performance. Interobserver agreement was kappa0.69 for standard MRI, kappa0.82 for standard MRI+DWI and kappa0.84 for the fusion images. CONCLUSIONS: MRI is accurate for the diagnosis of locally recurrent rectal cancer in patients with a clinical suspicion of recurrence. Addition of DWI does not significantly improve its performance. However, with DWI specificity and interobserver agreement increase. Fusion images do not improve accuracy

Combining Independent, Weighted P-Values: Achieving Computational Stability by a Systematic Expansion with Controllable Accuracy

Given the expanding availability of scientific data and tools to analyze them, combining different assessments of the same piece of information has become increasingly important for social, biological, and even physical sciences. This task demands, to begin with, a method-independent standard, such as the -value, that can be used to assess the reliability of a piece of information. Good's formula and Fisher's method combine independent -values with respectively unequal and equal weights. Both approaches may be regarded as limiting instances of a general case of combining -values from groups; -values within each group are weighted equally, while weight varies by group. When some of the weights become nearly degenerate, as cautioned by Good, numeric instability occurs in computation of the combined -values. We deal explicitly with this difficulty by deriving a controlled expansion, in powers of differences in inverse weights, that provides both accurate statistics and stable numerics. We illustrate the utility of this systematic approach with a few examples. In addition, we also provide here an alternative derivation for the probability distribution function of the general case and show how the analytic formula obtained reduces to both Good's and Fisher's methods as special cases. A C++ program, which computes the combined -values with equal numerical stability regardless of whether weights are (nearly) degenerate or not, is available for download at our group website http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/CoinedPValues.html

Edge states in a two-dimensional honeycomb lattice of massive magnetic skyrmions

We study the collective dynamics of a two-dimensional honeycomb lattice of magnetic skyrmions. By performing large-scale micromagnetic simulations, we find multiple chiral and non-chiral edge modes of skyrmion oscillations in the lattice. The non-chiral edge states are due to the Tamm-Shockley mechanism, while the chiral ones are topologically protected against structure defects and hold different handednesses depending on the mode frequency. To interpret the emerging multiband nature of the chiral edge states, we generalize the massless Thiele's equation by including a second-order inertial term of skyrmion mass as well as a third-order non-Newtonian gyroscopic term, which allows us to model the band structure of skrymion oscillations. Theoretical results compare well with numerical simulations. Our findings uncover the importance of high order effects in strongly coupled skyrmions and are helpful for designing novel topological devices.Comment: 6 pages,4 figures,accepted by Physical Review B as a Rapid Communicatio