Quantum Branching Programs and Space-Bounded Nonuniform Quantum Complexity

In this paper, the space complexity of nonuniform quantum computations is investigated. The model chosen for this are quantum branching programs, which provide a graphic description of sequential quantum algorithms. In the first part of the paper, simulations between quantum branching programs and nonuniform quantum Turing machines are presented which allow to transfer lower and upper bound results between the two models. In the second part of the paper, different variants of quantum OBDDs are compared with their deterministic and randomized counterparts. In the third part, quantum branching programs are considered where the performed unitary operation may depend on the result of a previous measurement. For this model a simulation of randomized OBDDs and exponential lower bounds are presented.Comment: 45 pages, 3 Postscript figures. Proofs rearranged, typos correcte

Voltage-activated currents in somatic muscle of the nematode parasite Ascaris suum

1. Voltage-activated currents in cell bodies of the somatic muscle cells of Ascaris suum were studied using a two-microelectrode voltage-clamp technique. Cells recorded from had resting membrane potentials around -35 mV and had input conductances in the range 1-10 microS. 2. In cells bathed in artificial perienteric fluid, depolarizing steps from a holding potential of -35 mV elicited outward currents at a threshold of -15 mV. These currents had inwardly directed inflections on the rising phase, suggesting the presence of more than one current. Hyperpolarizing steps did not activate current. 3. Tetraethylammonium (TEA+, 69 mmol l-1) blocked the outward currents and allowed a voltage-dependent inactivating Ca2+ current to be observed. The peak current-voltage relationship was U-shaped with a threshold around -15 mV and peak at +5 mV. The reversal potential of the Ca2+ current was estimated by extrapolation to be +45 mV. 4. The permeability of the voltage-activated outward currents was studied by examining reversal potentials of tail currents. The reversal potentials were linearly dependent on the logarithm of the extracellular potassium concentration if extracellular [K+] was greater than 10 mmol l-1. The Na+/K+ permeability ratio of the currents was 0.04. 5. Inactivation, seen as a decline following the peak of the K+ current, was produced by maintained depolarization. The recovery from inactivation was complex and could be described by the sum of two exponentials with time constants of 0.67 s and 20.1 s. Steady-state inactivation of the K+ currents was observed at a range of holding potentials. Only a proportion (34%) of the total K+ current was inactivated by holding potentials more positive than -20 mV. 6. Extracellular application of 5 mmol l-1 4-aminopyridine (4-AP) selectively abolished an early fast component of the K+ current (the peak). The 4-AP-sensitive current decayed quickly with a time constant of around 10 ms; a Boltzmann fit to its activation curve had a half-maximal activation voltage of +14 mV and a 'slope' of 10.5 mV. The 4-AP-resistant current decayed with a time constant of around 1 s; a Boltzmann fit to its activation curve had a half-maximal activation voltage of +29 mV and a 'slope' of 12 mV. 7. Depolarization activates a Ca2+ current and two K+ currents: the K+ currents were separated into lower-threshold, fast-inactivating (Ia-like) and higher-threshold, slowly inactivating (Ik-like) currents

Entanglement and localization of wavefunctions

We review recent works that relate entanglement of random vectors to their localization properties. In particular, the linear entropy is related by a simple expression to the inverse participation ratio, while next orders of the entropy of entanglement contain information about e.g. the multifractal exponents. Numerical simulations show that these results can account for the entanglement present in wavefunctions of physical systems.Comment: 6 pages, 4 figures, to appear in the proceedings of the NATO Advanced Research Workshop 'Recent Advances in Nonlinear Dynamics and Complex System Physics', Tashkent, Uzbekistan, 200

A reversible theory of entanglement and its relation to the second law

We consider the manipulation of multipartite entangled states in the limit of many copies under quantum operations that asymptotically cannot generate entanglement. As announced in [Brandao and Plenio, Nature Physics 4, 8 (2008)], and in stark contrast to the manipulation of entanglement under local operations and classical communication, the entanglement shared by two or more parties can be reversibly interconverted in this setting. The unique entanglement measure is identified as the regularized relative entropy of entanglement, which is shown to be equal to a regularized and smoothed version of the logarithmic robustness of entanglement. Here we give a rigorous proof of this result, which is fundamentally based on a certain recent extension of quantum Stein's Lemma proved in [Brandao and Plenio, Commun. Math. 295, 791 (2010)], giving the best measurement strategy for discriminating several copies of an entangled state from an arbitrary sequence of non-entangled states, with an optimal distinguishability rate equal to the regularized relative entropy of entanglement. We moreover analyse the connection of our approach to axiomatic formulations of the second law of thermodynamics.Comment: 21 pages. revised versio

A Generalization of Quantum Stein's Lemma

We present a generalization of quantum Stein's Lemma to the situation in which the alternative hypothesis is formed by a family of states, which can moreover be non-i.i.d.. We consider sets of states which satisfy a few natural properties, the most important being the closedness under permutations of the copies. We then determine the error rate function in a very similar fashion to quantum Stein's Lemma, in terms of the quantum relative entropy. Our result has two applications to entanglement theory. First it gives an operational meaning to an entanglement measure known as regularized relative entropy of entanglement. Second, it shows that this measure is faithful, being strictly positive on every entangled state. This implies, in particular, that whenever a multipartite state can be asymptotically converted into another entangled state by local operations and classical communication, the rate of conversion must be non-zero. Therefore, the operational definition of multipartite entanglement is equivalent to its mathematical definition.Comment: 30 pages. (see posting by M. Piani arXiv:0904.2705 for a different proof of the strict positiveness of the regularized relative entropy of entanglement on every entangled state). published version

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes

Towards FAIR principles for research software

The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans and machines. Until now the FAIR principles have been mostly applied to research data. The ideas behind these principles are, however, also directly relevant to research software. Hence there is a distinct need to explore how the FAIR principles can be applied to software. In this work, we aim to summarize the current status of the debate around FAIR and software, as basis for the development of community-agreed principles for FAIR research software in the future. We discuss what makes software different from data with regard to the application of the FAIR principles, and which desired characteristics of research software go beyond FAIR. Then we present an analysis of where the existing principles can directly be applied to software, where they need to be adapted or reinterpreted, and where the definition of additional principles is required. Here interoperability has proven to be the most challenging principle, calling for particular attention in future discussions. Finally, we outline next steps on the way towards definite FAIR principles for research software

Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4

Epigenomic regulation plays a vital role in cell differentiation. The leukemic HL-60/S4 [human myeloid leukemic cell line HL-60/S4 (ATCC CRL-3306)] promyelocytic cell can be easily differentiated from its undifferentiated promyelocyte state into neutrophil- and macrophage-like cell states. In this study, we present the underlying genome and epigenome architecture of HL-60/S4 through its differentiation. We performed whole-genome bisulphite sequencing of HL-60/S4 cells and their differentiated counterparts. With the support of karyotyping, we show that HL-60/S4 maintains a stable genome throughout differentiation. Analysis of differential Cytosine-phosphate-Guanine dinucleotide methylation reveals that most methylation changes occur in the macrophage-like state. Differential methylation of promoters was associated with immune-related terms. Key immune genes, CEBPA, GFI1, MAFB and GATA1 showed differential expression and methylation. However, we observed the strongest enrichment of methylation changes in enhancers and CTCF binding sites, implying that methylation plays a major role in large-scale transcriptional reprogramming and chromatin reorganisation during differentiation. Correlation of differential expression and distal methylation with support from chromatin capture experiments allowed us to identify putative proximal and long-range enhancers for a number of immune cell differentiation genes, including CEBPA and CCNF. Integrating expression data, we present a model of HL-60/S4 differentiation in relation to the wider scope of myeloid differentiation

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human

Background: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences. Results: We sequenced normalised chicken brain and embryo RNA libraries with Pacific Bioscience Iso-Seq. 5' cap selection was performed on the embryo library to provide methodological comparison. From these Iso-Seq sequencing projects, we have identified 60 k transcripts and 29 k genes within the chicken transcriptome. Of these, more than 20 k are novel lncRNA transcripts with ~3 k classified as sense exonic overlapping lncRNA, which is a class that is underrepresented in many vertebrate annotations. The relative proportion of alternative transcription events revealed striking similarities between the chicken and human transcriptomes while also providing explanations for previously observed genomic differences. Conclusions: Our results indicate that the chicken transcriptome is similar in complexity compared to human, and provide insights into other vertebrate biology. Our methodology demonstrates the potential of Iso-Seq sequencing to rapidly expand our knowledge of transcriptomics