On the Effect of Quantum Interaction Distance on Quantum Addition Circuits

We investigate the theoretical limits of the effect of the quantum interaction distance on the speed of exact quantum addition circuits. For this study, we exploit graph embedding for quantum circuit analysis. We study a logical mapping of qubits and gates of any $\Omega(\log n)$-depth quantum adder circuit for two $n$-qubit registers onto a practical architecture, which limits interaction distance to the nearest neighbors only and supports only one- and two-qubit logical gates. Unfortunately, on the chosen $k$-dimensional practical architecture, we prove that the depth lower bound of any exact quantum addition circuits is no longer $\Omega(\log {n})$, but $\Omega(\sqrt[k]{n})$. This result, the first application of graph embedding to quantum circuits and devices, provides a new tool for compiler development, emphasizes the impact of quantum computer architecture on performance, and acts as a cautionary note when evaluating the time performance of quantum algorithms.Comment: accepted for ACM Journal on Emerging Technologies in Computing System

Design, engineering and utility of biotic games

Games are a significant and defining part of human culture, and their utility beyond pure entertainment has been demonstrated with so-called ‘serious games’. Biotechnology – despite its recent advancements – has had no impact on gaming yet. Here we propose the concept of ‘biotic games’, i.e., games that operate on biological processes. Utilizing a variety of biological processes we designed and tested a collection of games: ‘Enlightenment’, ‘Ciliaball’, ‘PAC-mecium’, ‘Microbash’, ‘Biotic Pinball’, ‘POND PONG’, ‘PolymerRace’, and ‘The Prisoner's Smellemma’. We found that biotic games exhibit unique features compared to existing game modalities, such as utilizing biological noise, providing a real-life experience rather than virtual reality, and integrating the chemical senses into play. Analogous to video games, biotic games could have significant conceptual and cost-reducing effects on biotechnology and eventually healthcare; enable volunteers to participate in crowd-sourcing to support medical research; and educate society at large to support personal medical decisions and the public discourse on bio-related issues

Anisotropy of Growth of the Close-Packed Surfaces of Silver

The growth morphology of clean silver exhibits a profound anisotropy: The growing surface of Ag(111) is typically very rough while that of Ag(100) is smooth and flat. This serious and important difference is unexpected, not understood, and hitherto not observed for any other metal. Using density functional theory calculations of self-diffusion on flat and stepped Ag(100) we find, for example, that at flat regions a hopping mechanism is favored, while across step edges diffusion proceeds by an exchange process. The calculated microscopic parameters explain the experimentally reported growth properties.Comment: RevTeX, 4 pages, 3 figures in uufiles form, to appear in Phys. Rev. Let

Bcl6 promotes follicular helper T-cell differentiation and PD-1 expression in a Blimp1-independent manner in mice

The transcription factors Bcl6 and Blimp1 have opposing roles in the development of the follicular helper T (TFH) cells: Bcl6 promotes and Blimp1 inhibits TFH-cell differentiation. Similarly, Bcl6 activates, while Blimp1 represses, expression of the TFH-cell marker PD-1. However, Bcl6 and Blimp1 repress each other's expression, complicating the interpretation of the regulatory network. Here we sought to clarify the extent to which Bcl6 and Blimp1 independently control TFH-cell differentiation by generating mice with T-cell specific deletion of both Bcl6 and Blimp1 (double conditional KO [dcKO] mice). Our data indicate that Blimp1 does not control TFH-cell differentiation independently of Bcl6. However, a population of T follicular regulatory (TFR) cells developed independently of Bcl6 in dcKO mice. We have also analyzed regulation of IL-10 and PD-1, two genes controlled by both Bcl6 and Blimp1, and observed that Bcl6 regulates both genes independently of Blimp1. We found that Bcl6 positively regulates PD-1 expression by inhibiting the ability of T-bet/Tbx21 to repress Pdcd1 transcription. Our data provide a novel mechanism for positive control of gene expression by Bcl6, and illuminate how Bcl6 and Blimp1 control TFH-cell differentiation

Roles of T follicular helper cells and T follicular regulatory cells in Autoantibody Production in IL-2-deficient mice

Autoantibodies can result from excessive T follicular helper (Tfh) cell activity, whereas T follicular regulatory (Tfr) cells negatively regulate autoantibody production. IL-2 knockout (KO) mice on the BALB/c background have elevated Tfh responses, produce autoantibodies, and develop lethal autoimmunity. We analyzed Tfh and Tfr cells in IL-2 KO mice on the C57BL/6 (B6) genetic background. In B6 IL-2 KO mice, the spontaneous formation of Tfh cells and germinal center B cells was greatly enhanced, along with production of anti-DNA autoantibodies. IL-2 has been reported to repress Tfr cell differentiation; however, Tfr cells were not increased over wild-type levels in the B6 IL-2 KO mice. To assess Tfh and Tfr cell regulation of autoantibody production in IL-2 KO mice, we generated IL-2 KO mice with a T cell-specific deletion of the master Tfh cell transcription factor Bcl6. In IL-2 KO Bcl6 conditional KO (2KO-Bcl6TC) mice, Tfh cells, Tfr cells, and germinal center B cells were ablated. In contrast to expectations, autoantibody IgG titers in 2KO-Bcl6TC mice were significantly elevated over autoantibody IgG titers in IL-2 KO mice. Specific deletion of Tfr cells with Foxp3-cre Bcl6-flox alleles in IL-2 KO mice led to early lethality, before high levels of autoantibodies could develop. We found IL-2+/+ Tfr cell-deficient mice produce significant levels of autoantibodies. Our overall findings provide evidence that Tfh cells are dispensable for high-level production of autoantibodies and also reveal a complex interplay between Tfh and Tfr cells in autoantibody production and autoimmune disease

A high-throughput \u3ci\u3ede novo\u3c/i\u3e sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode webcite

Ab initio study of step formation and self-diffusion on Ag(100)

Using the plane wave pseudopotential method we performed density functional theory calculations on the stability of steps and self-diffusion processes on Ag(100). Our calculated step formation energies show that the {111}-faceted step is more stable than the {110}-faceted step. In accordance with experimental observations we find that the equilibrium island shape should be octagonal very close to a square with predominately {111}-faceted steps. For the (100) surface of fcc metals atomic migration proceeds by a hopping or an exchange process. For Ag(100) we find that adatoms diffuse across flat surfaces preferentially by hopping. Adatoms approaching the close-packed {111}-faceted step edges descend from the upper terrace to the lower level by an atomic exchange with an energy barrier almost identical to the diffusion barrier on flat surface regions. Thus, within our numerical accuracy (approx +- 0.05 eV) there is no additional step-edge barrier to descent. This provides a natural explanation for the experimental observations of the smooth two-dimensional growth in homoepitaxy of Ag(100). Inspection of experimental results of other fcc crystal surfaces indicates that our result holds quite generally.Comment: 10 pages, 9 figures. Submitted to Phys. Rev B (October 31, 1996

Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) play critical roles in a wide spectrum of biological processes and have been shown to be important effectors in the intricate host-pathogen interaction networks. Avian influenza virus (AIV) not only causes significant economic losses in poultry production, but also is of great concern to human health. The objective of this study was to identify miRNAs associated with AIV infections in chickens.</p> <p>Results</p> <p>Total RNAs were isolated from lung and trachea of low pathogenic H5N3 infected and non-infected SPF chickens at 4 days post-infection. A total of 278,398 and 340,726 reads were obtained from lung and trachea, respectively. And 377 miRNAs were detected in lungs and 149 in tracheae from a total of 474 distinct chicken miRNAs available at the miRBase, respectively. Seventy-three and thirty-six miRNAs were differentially expressed between infected and non-infected chickens in lungs and tracheae, respectively. There were more miRNAs highly expressed in non-infected tissues than in infected tissues. Interestingly, some of these differentially expressed miRNAs, including miR-146, have been previously reported to be associated with immune-related signal pathways in mammals.</p> <p>Conclusion</p> <p>To our knowledge, this is the first study on miRNA gene expression in AIV infected chickens using a deep sequencing approach. During AIV infection, many host miRNAs were differentially regulated, supporting the hypothesis that certain miRNAs might be essential in the host-pathogen interactions. Elucidation of the mechanism of these miRNAs on the regulation of host-AIV interaction will lead to the development of new control strategies to prevent or treat AIV infections in poultry.</p

105110^{51} Ergs: The Evolution of Shell Supernova Remnants

This paper reports on a workshop hosted by the University of Minnesota, March 23-26, 1997. It addressed fundamental dynamical issues associated with the evolution of shell supernova remnants and the relationships between supernova remnants and their environments. The workshop considered, in addition to classical shell SNRs, dynamical issues involving X-ray filled composite remnants and pulsar driven shells, such as that in the Crab Nebula. Approximately 75 participants with wide ranging interests attended the workshop. An even larger community helped through extensive on-line debates prior to the meeting. Each of the several sessions, organized mostly around chronological labels, also addressed some underlying, general physical themes: How are SNR dynamics and structures modified by the character of the CSM and the ISM and vice versa? How are magnetic fields generated in SNRs and how do magnetic fields influence SNRs? Where and how are cosmic-rays (electrons and ions) produced in SNRs and how does their presence influence or reveal SNR dynamics? How does SNR blast energy partition into various components over time and what controls conversion between components? In lieu of a proceedings volume, we present here a synopsis of the workshop in the form of brief summaries of the workshop sessions. The sharpest impressions from the workshop were the crucial and under-appreciated roles that environments have on SNR appearance and dynamics and the critical need for broad-based studies to understand these beautiful, but enigmatic objects. \\Comment: 54 pages text, no figures, Latex (aasms4.sty). submitted to the PAS