Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA

The structure of a catalytically active subdomain of the NanA sialidase from S. pneumoniae is reported to a resolution of 2.5 Å. The complex with the inhibitor Neu5Ac2en identifies the key catalytic residues and provides a platform for structure-based development of specific inhibitors

Online dosimetric evaluation of larynx SBRT: A pilot study to assess the necessity of adaptive replanning

PURPOSE: We have initiated a multi-institutional phase I trial of 5-fraction stereotactic body radiotherapy (SBRT) for Stage III-IVa laryngeal cancer. We conducted this pilot dosimetric study to confirm potential utility of online adaptive replanning to preserve treatment quality. METHODS: We evaluated ten cases: five patients enrolled onto the current trial and five patients enrolled onto a separate phase I SBRT trial for early-stage glottic larynx cancer. Baseline SBRT treatment plans were generated per protocol. Daily cone-beam CT (CBCT) or diagnostic CT images were acquired prior to each treatment fraction. Simulation CT images and target volumes were deformably registered to daily volumetric images, the original SBRT plan was copied to the deformed images and contours, delivered dose distributions were re-calculated on the deformed CT images. All of these were performed on a commercial treatment planning system. In-house software was developed to propagate the delivered dose distribution back to reference CT images using the deformation information exported from the treatment planning system. Dosimetric differences were evaluated via dose-volume histograms. RESULTS: We could evaluate dose within 10 minutes in all cases. Prescribed coverage to gross tumor volume (GTV) and clinical target volume (CTV) was uniformly preserved; however, intended prescription dose coverage of planning treatment volume (PTV) was lost in 53% of daily treatments (mean: 93.9%, range: 83.9-97.9%). Maximum bystander point dose limits to arytenoids, parotids, and spinal cord remained respected in all cases, although variances in carotid artery doses were observed in a minority of cases. CONCLUSIONS: Although GTV and CTV SBRT dose coverage is preserved with in-room three-dimensional image guidance, PTV coverage can vary significantly from intended plans and dose to critical structures may exceed tolerances. Online adaptive treatment re-planning is potentially necessary and clinically applicable to fully preserve treatment quality. Confirmatory trial accrual and analysis remains ongoing

Statistical implications of pooling RNA samples for microarray experiments

BACKGROUND: Microarray technology has become a very important tool for studying gene expression profiles under various conditions. Biologists often pool RNA samples extracted from different subjects onto a single microarray chip to help defray the cost of microarray experiments as well as to correct for the technical difficulty in getting sufficient RNA from a single subject. However, the statistical, technical and financial implications of pooling have not been explicitly investigated. RESULTS: Modeling the resulting gene expression from sample pooling as a mixture of individual responses, we derived expressions for the experimental error and provided both upper and lower bounds for its value in terms of the variability among individuals and the number of RNA samples pooled. Using virtual pooling of data from real experiments and computer simulations, we investigated the statistical properties of RNA sample pooling. Our study reveals that pooling biological samples appropriately is statistically valid and efficient for microarray experiments. Furthermore, optimal pooling design(s) can be found to meet statistical requirements while minimizing total cost. CONCLUSIONS: Appropriate RNA pooling can provide equivalent power and improve efficiency and cost-effectiveness for microarray experiments with a modest increase in total number of subjects. Pooling schemes in terms of replicates of subjects and arrays can be compared before experiments are conducted

Freezing of the quantum Hall liquid at ν=\nu = 1/7 and 1/9

We compare the free energy computed from the ground state energy and low-lying excitations of the 2-D Wigner solid and the fractional quantum Hall liquid, at magnetic filling factors $\nu = 1/7$ and 1/9. We find that the Wigner solid melts into the fractional quantum Hall liquid at roughly the same temperature as that of some recent luminescence experiments, while it remains a solid at the lower temperatures characteristic of the transport experiments. We propose this melting as a consistent interpretation of both sets of experiments.Comment: uses RevTeX 2.0 or 3.

Laughlin liquid - Wigner solid transition at high density in wide quantum wells

Assuming that the phase transition between the Wigner solid and the Laughlin liquid is first-order, we compare ground-state energies to find features of the phase diagram at fixed $\nu$. Rather than use the Coulomb interaction, we calculate the effective interaction in a square quantum well, and fit the results to a model interaction with length parameter $\lambda$ roughly proportional to the width of the well. We find a transition to the Wigner solid phase at high density in very wide wells, driven by the softening of the interaction at short distances, as well as the more well-known transition to the Wigner solid at low density, driven by Landau-level mixing.Comment: RevTeX 3.0, 3 Postscript figures appended in uuencoded forma

Engineering Superfluidity in Electron-Hole Double Layers

We show that band-structure effects are likely to prevent superfluidity in semiconductor electron-hole double-layer systems. We suggest the possibility that superfluidity could be realized by the application of uniaxial pressure perpendicular to the electron and hole layers.Comment: 4 pages, includes 3 figure

A GPU-based finite-size pencil beam algorithm with 3D-density correction for radiotherapy dose calculation

Targeting at the development of an accurate and efficient dose calculation engine for online adaptive radiotherapy, we have implemented a finite size pencil beam (FSPB) algorithm with a 3D-density correction method on GPU. This new GPU-based dose engine is built on our previously published ultrafast FSPB computational framework [Gu et al. Phys. Med. Biol. 54 6287-97, 2009]. Dosimetric evaluations against Monte Carlo dose calculations are conducted on 10 IMRT treatment plans (5 head-and-neck cases and 5 lung cases). For all cases, there is improvement with the 3D-density correction over the conventional FSPB algorithm and for most cases the improvement is significant. Regarding the efficiency, because of the appropriate arrangement of memory access and the usage of GPU intrinsic functions, the dose calculation for an IMRT plan can be accomplished well within 1 second (except for one case) with this new GPU-based FSPB algorithm. Compared to the previous GPU-based FSPB algorithm without 3D-density correction, this new algorithm, though slightly sacrificing the computational efficiency (~5-15% lower), has significantly improved the dose calculation accuracy, making it more suitable for online IMRT replanning