Maximally incompatible quantum observables

The existence of maximally incompatible quantum observables in the sense of a minimal joint measurability region is investigated. Employing the universal quantum cloning device it is argued that only infinite dimensional quantum systems can accommodate maximal incompatibility. It is then shown that two of the most common pairs of complementary observables (position and momentum; number and phase) are maximally incompatible

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

<p>Abstract</p> <p>Background</p> <p>Methods of determining whether or not any particular HIV-1 sequence stems - completely or in part - from some unknown HIV-1 subtype are important for the design of vaccines and molecular detection systems, as well as for epidemiological monitoring. Nevertheless, a single algorithm only, the Branching Index (BI), has been developed for this task so far. Moving along the genome of a query sequence in a sliding window, the BI computes a ratio quantifying how closely the query sequence clusters with a subtype clade. In its current version, however, the BI does not provide predicted boundaries of unknown fragments.</p> <p>Results</p> <p>We have developed <it>Unknown Subtype Finder </it>(USF), an algorithm based on a probabilistic model, which automatically determines which parts of an input sequence originate from a subtype yet unknown. The underlying model is based on a simple profile hidden Markov model (pHMM) for each <it>known </it>subtype and an additional pHMM for an <it>unknown </it>subtype. The emission probabilities of the latter are estimated using the emission frequencies of the known subtypes by means of a (position-wise) probabilistic model for the emergence of new subtypes. We have applied USF to SIV and HIV-1 sequences formerly classified as having emerged from an unknown subtype. Moreover, we have evaluated its performance on artificial HIV-1 recombinants and non-recombinant HIV-1 sequences. The results have been compared with the corresponding results of the BI.</p> <p>Conclusions</p> <p>Our results demonstrate that USF is suitable for detecting segments in HIV-1 sequences stemming from yet unknown subtypes. Comparing USF with the BI shows that our algorithm performs as good as the BI or better.</p

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

BACKGROUND: Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events. RESULTS: We developed a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach. Given a partition of the aligned input sequence family into known sequence subtypes, our model can jump between states corresponding to these different subtypes, depending on which subtype is locally most similar to a database sequence. Jumps between different subtypes are indicative of intersubtype recombinations. We applied our method to a large set of genome sequences from human immunodeficiency virus (HIV) and hepatitis C virus (HCV) as well as to simulated recombined genome sequences. CONCLUSION: Our results demonstrate that jumps in our jumping profile HMM often correspond to recombination breakpoints; our approach can therefore be used to detect recombinations in genomic sequences. The recombination breakpoints identified by jpHMM were found to be significantly more accurate than breakpoints defined by traditional methods based on comparing single representative sequences

Utilizing ISS Camera Systems for Scientific Analysis of Lightning Characteristics and Comparison with ISS-LIS and GLM

Video and still frame images from cameras aboard the International Space Station (ISS) are used to inspire, educate, and provide a unique vantage point from low-Earth orbit that is second to none; however, these cameras have overlooked capabilities for contributing to scientific analysis of the Earth and near-space environment. The goal of this project is to study how geo referenced video/images from available ISS camera systems can be useful for scientific analysis, using lightning properties as a demonstration

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al. The input data for our server is a partial or complete genome sequence from HIV-1; our tool assigns regions of the input sequence to known subtypes of HIV-1 and predicts phylogenetic breakpoints. jpHMM is available online at

Is Demonstrating the Concept of Multi-Use Too Soon for the North Sea?:Barriers and Opportunities from a Stakeholder Perspective

Multi-use (MU) has been promoted as a viable approach to the effective planning and mitigation of user-conflicts in the marine realm. Despite several research and pilot projects demonstrating the approach’s feasibility and benefits, commercially viable MU applications remain patchy and few. Further, MU is neither systematically applied nor purposively planned for even in the imminent event of incompatible and conflicting use of marine space. This paper seeks to identify barriers and opportunities for mainstreaming MU based on desktop study and iterative stakeholder consultation. The findings reveal that the MU concept was frequently framed as ‘co-location’ or ‘co-existence’ and aimed toward mitigating conflict among users. Practice was ahead of theory with little attention to synergistic and efficiency aspects. Barriers for MU application include shortcomings in legislation, sectoral thinking, and burdensome administrative procedures. The main opportunity lies in creating a conducive policy environment where MU risks and transaction costs become low and competitive, respectively. Solutions at the sea basin and national level, upon which further MU application can be anchored, are proposed

Eemian landscape response to climatic shifts and evidence for northerly neanderthal occupation at a palaeolake margin in northern germany

The prevailing view suggests that the Eemian interglacial on the European Plain was characterized by largely negligible geomorphic activity beyond the coastal areas. However, systematic geomorphological studies are sparse. Here we present a detailed reconstruction of Eemian to Early Weichselian landscape evolution in the vicinity of a small fingerlake on the northern margin of the Salzwedel Palaeolake in Lower Saxony (Germany). We apply a combination of seismics, sediment coring, pollen analysis and luminescence dating on a complex sequence of colluvial, paludal and lacustrine sediments. Results suggest two pronounced phases of geomorphic activity, directly before the onset and at the end of the Eemian period, with an intermediate period of pronounced landscape stability. The dynamic phases were largely driven by incomplete vegetation cover, but likely accentuated by fluvial incision in the neighbouring Elbe Valley. Furthermore, we discovered Neanderthal occupation at the lakeshore during Eemian pollen zone (PZ) E IV, which is chronologically in line with other known Eemian sites of central Europe. Our highly‐resolved spatio‐temporal data substantially contribute to the understanding of climate‐induced geomorphic processes throughout and directly after the last interglacial period. It helps unraveling the landscape dynamics between the coastal areas to the north and the loess belt to the south

Eemian landscape response to climatic shifts and evidence for northerly Neanderthal occupation at a palaeolake margin in northern Germany

The prevailing view suggests that the Eemian interglacial on the European Plain was characterized by largely negligible geomorphic activity beyond the coastal areas. However, systematic geomorphological studies are sparse. Here we present a detailed reconstruction of Eemian to Early Weichselian landscape evolution in the vicinity of a small fingerlake on the northern margin of the Salzwedel Palaeolake in Lower Saxony (Germany). We apply a combination of seismics, sediment coring, pollen analysis and luminescence dating on a complex sequence of colluvial, paludal and lacustrine sediments. Results suggest two pronounced phases of geomorphic activity, directly before the onset and at the end of the Eemian period, with an intermediate period of pronounced landscape stability. The dynamic phases were largely driven by incomplete vegetation cover, but likely accentuated by fluvial incision in the neighbouring Elbe Valley. Furthermore, we discovered Neanderthal occupation at the lakeshore during Eemian pollen zone (PZ) E IV, which is chronologically in line with other known Eemian sites of central Europe. Our highly-resolved spatio-temporal data substantially contribute to the understanding of climate-induced geomorphic processes throughout and directly after the last interglacial period. It helps unraveling the landscape dynamics between the coastal areas to the north and the loess belt to the south