Effect of pooling samples on the efficiency of comparative studies using microarrays

Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray experiments for detecting differentially expressed genes, recent publications have addressed the problem of the efficiency of sample-pooling, and some approximate formulas were provided for the power and sample size calculations. It is desirable to have exact formulas for these calculations and have the approximate results checked against the exact ones. We show that the difference between the approximate and exact results can be large. In this study, we have characterized quantitatively the effect of pooling samples on the efficiency of microarray experiments for the detection of differential gene expression between two classes. We present exact formulas for calculating the power of microarray experimental designs involving sample pooling and technical replications. The formulas can be used to determine the total numbers of arrays and biological subjects required in an experiment to achieve the desired power at a given significance level. The conditions under which pooled design becomes preferable to non-pooled design can then be derived given the unit cost associated with a microarray and that with a biological subject. This paper thus serves to provide guidance on sample pooling and cost effectiveness. The formulation in this paper is outlined in the context of performing microarray comparative studies, but its applicability is not limited to microarray experiments. It is also applicable to a wide range of biomedical comparative studies where sample pooling may be involved.Comment: 8 pages, 1 figure, 2 tables; to appear in Bioinformatic

A Catalog of Absorption Lines in Eight HST/STIS E230M 1.0 < z < 1.7 Quasar Spectra

We have produced a catalog of line identifications and equivalent width measurements for all absorption features in eight ultraviolet echelle quasar spectra. These spectra were selected as having the highest signal-to-noise among the HST/STIS spectra obtained with the E230M grating. We identify 56 metal-line systems toward the eight quasars, and present plots of detected transitions, aligned in velocity-space. We found that about 1/4 - 1/3 of the features in the Lya forest region, redward of the incidence of the Lyb forest, are metal lines. High ionization transitions are common. We see both O VI and C IV in 88 - 90% of the metal-line systems for which the spectra cover the expected wavelength. Si III is seen in 58%, while low ionization absorption in C II, Si II, and/or Al II is detected in 50% of the systems for which they are covered. This catalog will facilitate future studies of the Lya forest and of metal-line systems of various types.Comment: 13 pages, 2 figures, submitted to Monthly Notices of the Royal Astronomical Society, a complete version with the appendix and all figures is available at http://www.astro.psu.edu/users/misawa/pub/Paper/qalcat.pdf.g

Photoionization and Photoelectric Loading of Barium Ion Traps

Simple and effective techniques for loading barium ions into linear Paul traps are demonstrated. Two-step photoionization of neutral barium is achieved using a weak intercombination line (6s2 1S0 6s6p 3P1, 791 nm) followed by excitation above the ionization threshold using a nitrogen gas laser (337 nm). Isotopic selectivity is achieved by using a near Doppler-free geometry for excitation of the triplet 6s6p 3P1 state. Additionally, we report a particularly simple and efficient trap loading technique that employs an in-expensive UV epoxy curing lamp to generate photoelectrons.Comment: 5 pages, Accepted to PRA 3/20/2007 -fixed typo -clarified figure 3 caption -added reference [15

A CASE STUDY OF STRIDE FREQUENCY AND SWING TIME IN ELITE ABLE-BODIED SPRINT RUNNING: IMPLICATIONS FOR AMPUTEE DEBATE

Recent research into trans-tibial double-amputee sprint performance has debated the possible inherent advantages, disadvantages and limitations to sprinting with prosthetic limbs compared to healthy limbs. Biomechanical data gathered throughout a training season from an elite able-bodied sprinter provide a new perspective on this debate. Peak stride frequency was measured at 2.62 Hz, and the corresponding swing time was estimated to be 0.287 s in the able-bodied sprinter. Published swing time and stride frequency values from the double-amputee at maximum velocity, thought to be beyond biological limits, therefore may not be so, although previously published research has provided evidence that some joint kinetic values from the double-amputee have not been shown in elite able-bodied sprinting

A CASE STUDY OF STRIDE FREQUENCY AND SWING TIME IN ELITE ABLEBODIED SPRINT RUNNING: IMPLICATIONS FOR AMPUTEE DEBATE

Recent research into trans-tibial double-amputee sprint performance has debated the possible inherent advantages, disadvantages and limitations to sprinting with prosthetic limbs compared to healthy limbs. Biomechanical data gathered throughout a training season from an elite able-bodied sprinter provide a new perspective on this debate. Peak stride frequency was measured at 2.62 Hz, and the corresponding swing time was estimated to be 0.287 s in the able-bodied sprinter. Published swing time and stride frequency values from the double-amputee at maximum velocity, thought to be beyond biological limits, therefore may not be so, although previously published research has provided evidence that some joint kinetic values from the double-amputee have not been shown in elite able-bodied sprinting

Gender-Inclusive HCI Research and Design: A Conceptual Review

Previous research has investigated gender and its implications for HCI. We consider inclusive design of technology whatever the gender of its users of particular importance. This conceptual review provides an overview of the motivations that have driven research in gender and inclusive HCI design. We review the empirical evidence for the impact of gender in thinking and behavior which underlies HCI research and design. We then present how HCI design might inadvertently embed and perpetuate gender stereotypes. We then present current HCI design approaches to tackle gender stereotypes and to produce gender-inclusive designs. We conclude by discussing possible future directions in this area

Dense sphere packings from optimized correlation functions

Elementary smooth functions (beyond contact) are employed to construct pair correlation functions that mimic jammed disordered sphere packings. Using the g2-invariant optimization method of Torquato and Stillinger [J. Phys. Chem. B 106, 8354, 2002], parameters in these functions are optimized under necessary realizability conditions to maximize the packing fraction phi and average number of contacts per sphere Z. A pair correlation function that incorporates the salient features of a disordered packing and that is smooth beyond contact is shown to permit a phi of 0.6850: this value represents a 45% reduction in the difference between the maximum for congruent hard spheres in three dimensions, pi/sqrt{18} ~ 0.7405, and 0.64, the approximate fraction associated with maximally random jammed (MRJ) packings in three dimensions. We show that, surprisingly, the continued addition of elementary functions consisting of smooth sinusoids decaying as r^{-4} permits packing fractions approaching pi/sqrt{18}. A translational order metric is used to discriminate between degrees of order in the packings presented. We find that to achieve higher packing fractions, the degree of order must increase, which is consistent with the results of a previous study [Torquato et al., Phys. Rev. Lett. 84, 2064, 2000].Comment: 26 pages, 9 figures, 1 table; added references, fixed typos, simplified argument and discussion in Section IV

Demonstration of Entanglement of Electrostatically Coupled Singlet-Triplet Qubits

Quantum computers have the potential to solve certain interesting problems significantly faster than classical computers. To exploit the power of a quantum computation it is necessary to perform inter-qubit operations and generate entangled states. Spin qubits are a promising candidate for implementing a quantum processor due to their potential for scalability and miniaturization. However, their weak interactions with the environment, which leads to their long coherence times, makes inter-qubit operations challenging. We perform a controlled two-qubit operation between singlet-triplet qubits using a dynamically decoupled sequence that maintains the two-qubit coupling while decoupling each qubit from its fluctuating environment. Using state tomography we measure the full density matrix of the system and determine the concurrence and the fidelity of the generated state, providing proof of entanglement