A Note on “A Catalog of Biases in Questionnaires”

The authors of A Catalog of Biases in Questionnaires in the January issue (1) provide a useful catalog of questionnaire biases, but in one of their examples, their recommended response is guilty of the same bias. This error occurs in Overlapping Interval

On the capacities of bipartite Hamiltonians and unitary gates

We consider interactions as bidirectional channels. We investigate the capacities for interaction Hamiltonians and nonlocal unitary gates to generate entanglement and transmit classical information. We give analytic expressions for the entanglement generating capacity and entanglement-assisted one-way classical communication capacity of interactions, and show that these quantities are additive, so that the asymptotic capacities equal the corresponding 1-shot capacities. We give general bounds on other capacities, discuss some examples, and conclude with some open questions.Comment: V3: extensively rewritten. V4: a mistaken reference to a conjecture by Kraus and Cirac [quant-ph/0011050] removed and a mistake in the order of authors in Ref. [53] correcte

Applications of coherent classical communication and the Schur transform to quantum information theory

Quantum mechanics has led not only to new physical theories, but also a new understanding of information and computation. Quantum information began by yielding new methods for achieving classical tasks such as factoring and key distribution but also suggests a completely new set of quantum problems, such as sending quantum information over quantum channels or efficiently performing particular basis changes on a quantum computer. This thesis contributes two new, purely quantum, tools to quantum information theory--coherent classical communication in the first half and an efficient quantum circuit for the Schur transform in the second half.Comment: 176 pages. Chapters 1 and 4 are a slightly older version of quant-ph/0512015. Chapter 2 is quant-ph/0205057 plus unpublished extensions (slightly outdated by quant-ph/0511219) and chapter 3 is quant-ph/0307091, quant-ph/0412126 and change. Chapters 5-8 are based on quant-ph/0407082, but go much furthe

Superdense coding of quantum states

We describe a method to non-obliviously communicate a 2l-qubit quantum state by physically transmitting l+o(l) qubits of communication, and by consuming l ebits of entanglement and some shared random bits. In the non-oblivious scenario, the sender has a classical description of the state to be communicated. Our method can be used to communicate states that are pure or entangled with the sender's system; l+o(l) and 3l+o(l) shared random bits are sufficient respectively.Comment: 5 pages, revtex

Allopurinol use yields potentially beneficial effects on inflammatory indices in those with recent ischemic stroke: a randomized, double-blind, placebo-controlled trial

<p><b>Background and Purpose</b>: Elevated serum uric acid level is associated with poor outcome and increased risk of recurrent events after stroke. The xanthine oxidase inhibitor allopurinol lowers uric acid but also attenuates expression of inflammatory adhesion molecules in murine models, reduces oxidative stress in the vasculature, and improves endothelial function. We sought to investigate whether allopurinol alters expression of inflammatory markers after acute ischemic stroke.</p> <p><b>Methods</b>: We performed a randomized, double-blind, placebo-controlled trial to investigate the safety, tolerability, and effect of 6 weeks’ treatment with high- (300 mg once a day) or low- (100 mg once a day) dose allopurinol on levels of uric acid and circulating inflammatory markers after ischemic stroke.</p> <p><b>Results</b>: We enrolled 50 patients with acute ischemic stroke (17, 17, and 16 in the high, low, and placebo groups, respectively). Mean (±SD) age was 70 (±13) years. Groups had similar characteristics at baseline. There were no serious adverse events. Uric acid levels were significantly reduced at both 7 days and 6 weeks in the high-dose group (by 0.14 mmol/L at 6 weeks, P=0.002). Intercellular adhesion molecule-1 concentration (ng/mL) rose by 51.2 in the placebo group, rose slightly (by 10.6) in the low-dose allopurinol group, but fell in the high-dose group (by 2.6; difference between groups P=0.012, Kruskal-Wallis test).</p> <p><b>Conclusion</b>: Allopurinol treatment is well tolerated and attenuates the rise in intercellular adhesion molecule-1 levels seen after stroke. Uric acid levels were lowered with high doses. These findings support further evaluation of allopurinol as a preventive measure after stroke.</p&gt

Compressibility of positive semidefinite factorizations and quantum models

We investigate compressibility of the dimension of positive semidefinite matrices while approximately preserving their pairwise inner products. This can either be regarded as compression of positive semidefinite factorizations of nonnegative matrices or (if the matrices are subject to additional normalization constraints) as compression of quantum models. We derive both lower and upper bounds on compressibility. Applications are broad and range from the statistical analysis of experimental data to bounding the one-way quantum communication complexity of Boolean functions.Comment: 13 page

Uselessness for an Oracle Model with Internal Randomness

We consider a generalization of the standard oracle model in which the oracle acts on the target with a permutation selected according to internal random coins. We describe several problems that are impossible to solve classically but can be solved by a quantum algorithm using a single query; we show that such infinity-vs-one separations between classical and quantum query complexities can be constructed from much weaker separations. We also give conditions to determine when oracle problems---either in the standard model, or in any of the generalizations we consider---cannot be solved with success probability better than random guessing would achieve. In the oracle model with internal randomness where the goal is to gain any nonzero advantage over guessing, we prove (roughly speaking) that $k$ quantum queries are equivalent in power to $2k$ classical queries, thus extending results of Meyer and Pommersheim.Comment: 18 pages. v2. shortened, presentation improved, same result

AnnoTrack - a tracking system for genome annotation

<p>Abstract</p> <p>Background</p> <p>As genome sequences are determined for increasing numbers of model organisms, demand has grown for better tools to facilitate unified genome annotation efforts by communities of biologists. Typically this process involves numerous experts from the field and the use of data from dispersed sources as evidence. This kind of collaborative annotation project requires specialized software solutions for efficient data tracking and processing.</p> <p>Results</p> <p>As part of the scale-up phase of the ENCODE project (Encyclopedia of DNA Elements), the aim of the GENCODE project is to produce a highly accurate evidence-based reference gene annotation for the human genome. The <it>AnnoTrack </it>software system was developed to aid this effort. It integrates data from multiple distributed sources, highlights conflicts and facilitates the quick identification, prioritisation and resolution of problems during the process of genome annotation.</p> <p>Conclusions</p> <p>AnnoTrack has been in use for the last year and has proven a very valuable tool for large-scale genome annotation. Designed to interface with standard bioinformatics components, such as DAS servers and Ensembl databases, it is easy to setup and configure for different genome projects. The source code is available at <url>http://annotrack.sanger.ac.uk</url>.</p

MHC-linked and un-linked class I genes in the wallaby

Background: MHC class I antigens are encoded by a rapidly evolving gene family comprising classical and non-classical genes that are found in all vertebrates and involved in diverse immune functions. However, there is a fundamental difference between the organization of class I genes in mammals and non-mammals. Non-mammals have a single classical gene responsible for antigen presentation, which is linked to the antigen processing genes, including TAP. This organization allows co-evolution of advantageous class Ia/ TAP haplotypes. In contrast, mammals have multiple classical genes within the MHC, which are separated from the antigen processing genes by class III genes. It has been hypothesized that separation of classical class I genes from antigen processing genes in mammals allowed them to duplicate. We investigated this hypothesis by characterizing the class I genes of the tammar wallaby, a model marsupial that has a novel MHC organization, with class I genes located within the MHC and 10 other chromosomal locations. Results: Sequence analysis of 14 BACs containing 15 class I genes revealed that nine class I genes, including one to three classical class I, are not linked to the MHC but are scattered throughout the genome. Kangaroo Endogenous Retroviruses (KERVs) were identified flanking the MHC un-linked class I. The wallaby MHC contains four non-classical class I, interspersed with antigen processing genes. Clear orthologs of non-classical class I are conserved in distant marsupial lineages. Conclusion: We demonstrate that classical class I genes are not linked to antigen processing genes in the wallaby and provide evidence that retroviral elements were involved in their movement. The presence of retroviral elements most likely facilitated the formation of recombination hotspots and subsequent diversification of class I genes. The classical class I have moved away from antigen processing genes in eutherian mammals and the wallaby independently, but both lineages appear to have benefited from this loss of linkage by increasing the number of classical genes, perhaps enabling response to a wider range of pathogens. The discovery of non-classical orthologs between distantly related marsupial species is unusual for the rapidly evolving class I genes and may indicate an important marsupial specific function