Showing papers by "University of Vienna published in 2007"
Ewan Birney, John A. Stamatoyannopoulos1, Anindya Dutta2, Roderic Guigó3 +317 more•Institutions (44)
TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
5,091 citations
TL;DR: The ecology of sponge-microbe associations is examined, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution.
Abstract: Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations.
1,262 citations
Duke University1, Johns Hopkins University2, University of Florence3, Leiden University4, Stanford University5, University of Vienna6, University of California, San Francisco7, University of Texas Health Science Center at Houston8, University of Barcelona9, University of Wisconsin-Madison10, University of Zurich11, University of Helsinki12, Yale University13, Mayo Clinic14, University of Turin15, Humboldt University of Berlin16, University of Paris17, St Thomas' Hospital18
TL;DR: These revisions are made to incorporate advances related to tumor cell biology and diagnostic techniques as pertains to mycosis fungoides and Sézary syndrome to clarify certain variables that currently impede effective interinstitution and interinvestigator communication and/or the development of standardized clinical trials in MF and SS.
1,167 citations
TL;DR: Four protocols for sample preparation (suspensions of intact cell nuclei) and the analysis of nuclear DNA amounts using FCM are presented and the most frequent problems encountered with plant material such as the interference of secondary metabolites are described.
Abstract: Flow cytometry (FCM) using DNA-selective fluorochromes is now the prevailing method for the measurement of nuclear DNA content in plants. Ease of sample preparation and high sample throughput make it generally better suited than other methods such as Feulgen densitometry to estimate genome size, level of generative polyploidy, nuclear replication state and endopolyploidy (polysomaty). Here we present four protocols for sample preparation (suspensions of intact cell nuclei) and describe the analysis of nuclear DNA amounts using FCM. We consider the chemicals and equipment necessary, the measurement process, data analysis, and describe the most frequent problems encountered with plant material such as the interference of secondary metabolites. The purpose and requirement of internal and external standardization are discussed. The importance of using a correct terminology for DNA amounts and genome size is underlined, and its basic principles are explained.
1,143 citations
TL;DR: In this article, the authors demonstrate entanglement-based quantum key distribution over 144 km in a free-space link between the Canary Island of La Palma and the European Space Station of Tenerife.
Abstract: Quantum entanglement is the main resource to endow the field of quantum information processing with powers that exceed those of classical communication and computation. In view of applications such as quantum cryptography or quantum teleportation, extension of quantum-entanglement-based protocols to global distances is of considerable practical interest. Here we experimentally demonstrate entanglement-based quantum key distribution over 144 km. One photon is measured locally at the Canary Island of La Palma, whereas the other is sent over an optical free-space link to Tenerife, where the Optical Ground Station of the European Space Agency acts as the receiver. This exceeds previous free-space experiments by more than an order of magnitude in distance, and is an essential step towards future satellite-based quantum communication and experimental tests on quantum physics in space.
1,065 citations
TL;DR: The freedom in representations with and without translation symmetry are determined, derive respective canonical forms and provide efficient methods for obtaining them.
Abstract: This work gives a detailed investigation of matrix product state (MPS) representations for pure multipartite quantum states. We determine the freedom in representations with and without translation symmetry, derive respective canonical forms and provide efficient methods for obtaining them. Results on frustration free Hamiltonians and the generation of MPS are extended, and the use of the MPS-representation for classical simulations of quantum systems is discussed.
942 citations
01 Aug 2007
TL;DR: A candidate list of desirable qualities for a parallel programming language is offered, and how these qualities are addressed in the design of the Chapel language is described, providing an overview of Chapel's features and how they help address parallel productivity.
Abstract: In this paper we consider productivity challenges for parallel programmers and explore ways that parallel language design might help improve end-user productivity. We offer a candidate list of desirable qualities for a parallel programming language, and describe how these qualities are addressed in the design of the Chapel language. In doing so, we provide an overview of Chapel's features and how they help address parallel productivity. We also survey current techniques for parallel programming and describe ways in which we consider them to fall short of our idealized productive programming model.
905 citations
Bradley University1, University of Tartu2, National Institutes of Health3, University of California4, Pontifical Catholic University of Chile5, University of Louisville6, University of Latvia7, Pennsylvania State University8, Slovak Academy of Sciences9, University of San Carlos10, University of Malta11, Ghent University12, Clemson University13, Laval University14, University of Buenos Aires15, Osaka University16, Illinois State University17, National Autonomous University of Mexico18, University of Brasília19, University of Western Australia20, University of Lima21, Boğaziçi University22, University of Kassel23, York University24, University of Queensland25, Åbo Akademi University26, Al Akhawayn University27, University of Hawaii at Manoa28, University of Catania29, University of Otago30, University of Dhaka31, Chemnitz University of Technology32, Knox College33, Comenius University in Bratislava34, University of Rijeka35, University of Malaya36, Vilnius University37, American University of Beirut38, Kwangju Health College39, University of Salzburg40, Utrecht University41, National Computerization Agency42, City University of Hong Kong43, University of Idaho44, University of Zimbabwe45, University of Lisbon46, University of Central Lancashire47, Loyola Marymount University48, University of KwaZulu-Natal49, University of Granada50, University of Botswana51, Babeș-Bolyai University52, University of Cyprus53, University of Belgrade54, KPMG55, University of Montpellier56, University of Zurich57, University of Alabama58, Baylor University59, Queen's University Belfast60, University of Ljubljana61, University of Haifa62, University of La Serena63, Florida Atlantic University64, University of California, Davis65, University of Dar es Salaam66, Ramapo College67, Cyprus College68, Middle East Technical University69, Nicolaus Copernicus University in Toruń70, University of the South Pacific71, Vrije Universiteit Brussel72, University at Albany, SUNY73, University of the Aegean74, University of Lethbridge75, University of Vienna76, University of Hong Kong77, Yuan Ze University78, Charles University in Prague79, Chonnam National University80, Indian Institutes of Technology81
TL;DR: The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness as discussed by the authors.
Abstract: The Big Five Inventory (BFI) is a self-report measure designed to assess the high-order personality traits of Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness. As part of the International Sexuality Description Project, the BFI was translated from English into 28 languages and administered to 17,837 individuals from 56 nations. The resulting cross-cultural data set was used to address three main questions: Does the factor structure of the English BFI fully replicate across cultures? How valid are the BFI trait profiles of individual nations? And how are personality traits distributed throughout the world? The five-dimensional structure was robust across major regions of the world. Trait levels were related in predictable ways to self-esteem, sociosexuality, and national personality profiles. People from the geographic regions of South America and East Asia were significantly different in openness from those inhabiting other world regions. The discussion focuses on limitations of t...
876 citations
17 Jun 2007
TL;DR: An experimental scheme to create and probe optomechanical entanglement between a light field and a mechanical oscillator is proposed using a bright laser field that resonates inside a cavity and couples to the position and momentum of a moving (micro)mirror.
Abstract: In this paper we propose an experimental scheme to create and probe optomechanical entanglement between a light field and a mechanical oscillator. This is achieved using a bright laser field that resonates inside a cavity and couples to the position and momentum of a moving (micro)mirror.
804 citations
TL;DR: In this paper, it was shown that the first approximation leads to excellent agreement with experiment, whereas an update of the eigenvalues in $G$ and $W$ gives too large band gaps for virtually all materials.
Abstract: We present $GW$ calculations for small and large gap systems comprising typical semiconductors (Si, SiC, GaAs, GaN, ZnO, ZnS, CdS, and AlP), small gap semiconductors (PbS, PbSe, and PbTe), insulators (C, BN, MgO, and LiF), and noble gas solids (Ar and Ne). It is shown that the ${G}_{0}{W}_{0}$ approximation always yields too small band gaps. To improve agreement with experiment, the eigenvalues in the Green's function $G$ $(G{W}_{0})$ and in the Green's function and the dielectric matrix $(GW)$ are updated until self-consistency is reached. The first approximation leads to excellent agreement with experiment, whereas an update of the eigenvalues in $G$ and $W$ gives too large band gaps for virtually all materials. From a pragmatic point of view, the $G{W}_{0}$ approximation thus seems to be an accurate and still reasonably fast method for predicting quasiparticle energies in simple $sp$-bonded systems. We furthermore observe that the band gaps in materials with shallow $d$ states (GaAs, GaN, and ZnO) are systematically underestimated. We propose that an inaccurate description of the static dielectric properties of these materials is responsible for the underestimation of the band gaps in $G{W}_{0}$, which is itself a result of the incomplete cancellation of the Hartree self-energy within the $d$ shell by local or gradient corrected density functionals.
728 citations
TL;DR: This link between the Canary islands of La Palma and Tenerife has a path length much longer than from LEO satellites to a ground station and serves as a realistic test bed for future quantum communication to space.
Abstract: We report on the experimental implementation of a Bennett-Brassard 1984 (BB84) protocol type quantum key distribution over a 144 km free-space link using weak coherent laser pulses. Optimization of the link transmission was achieved with bidirectional active telescope tracking, and the security was ensured by employing decoy-state analysis. This enabled us to distribute a secure key at a rate of 12.8 bit/s at an attenuation of about 35 dB. Utilizing a simple transmitter setup and an optical ground station capable of tracking a spacecraft in low earth orbit, this outdoor experiment demonstrates the feasibility of global key distribution via satellites.
European Bioinformatics Institute1, Wellcome Trust2, University of Manchester3, University of Cambridge4, Swiss Institute of Bioinformatics5, École Polytechnique Fédérale de Lausanne6, Institute for Systems Biology7, University College Dublin8, Utrecht University9, University of Vienna10, Max Planck Society11, New York University12, Amgen13, University of California, Los Angeles14, Applied Biosystems15, Semel Institute for Neuroscience and Human Behavior16, Flanders Institute for Biotechnology17, University of New South Wales18, Scripps Research Institute19
TL;DR: The processes and principles underpinning the development of guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry are described and the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector are discussed.
Abstract: Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling 'MIAPE-compliant' reporting.
Book•
21 Jun 2007TL;DR: In this article, Braithwaite discusses tax law, the shadow economy and tax non-compliance, and social representations of taxes in the context of self-employment and taxpaying.
Abstract: Foreword Valerie Braithwaite Preface 1. Introduction 2. Tax law, the shadow economy and tax non-compliance 3. Social representations of taxes 4. Tax compliance decisions 5. Self-employment and taxpaying 6. Interaction between tax authorities and taxpayers 7. Cautious conclusions.
TL;DR: It is shown that the inclusion of the attractive electron-hole interaction via an effective nonlocal exchange correlation kernel is required to obtain accurate band gaps in the framework of self-consistent GW calculations.
Abstract: Self-consistent GW calculations, maintaining only the quasiparticle part of the Green's function G, are reported for a wide class of materials, including small gap semiconductors and large gap insulators. We show that the inclusion of the attractive electron-hole interaction via an effective nonlocal exchange correlation kernel is required to obtain accurate band gaps in the framework of self-consistent GW calculations. If these are accounted for via vertex corrections in W, the band gaps are found to be within a few percent of the experimental values.
TL;DR: The KIDSCREEN-27 seems to be a valid measure of HRQoL in children and adolescents, and further research is needed to assess longitudinal validity and sensitivity to change.
Abstract: Objective: To assess the construct and criterion validity of the KIDSCREEN-27 health-related quality of life (HRQoL) questionnaire, a shorter version of the KIDSCREEN-52. Methods: The five-dimensional KIDSCREEN-27 was tested in a sample of 22,827. For criterion validity the correlation with and the percentage explained variance of the scores of the KIDSCREEN-52 instrument were examined. Construct validity was assessed by testing a priori expected associations with other generic HRQoL measures (YQOL-S, PedsQL, CHIP), indicators of physical and mental health, and socioeconomic status. Age and gender differences were investigated. Results: Correlation with corresponding scales of the KIDSCREEN-52 ranged from r = 0.63 to r = 0.96, and r2 ranged from 0.39 to 0.92. Correlations between other HRQoL questionnaires and KIDSCREEN-27 dimensions were moderate to high for those assessing similar constructs (r = 0.36 to 0.63). Statistically significant and sizeable differences between physically and mentally healthy and ill children were found in all KIDSCREEN-27 dimensions together with strong associations with psychosomatic complaints (r = -0.52). Most of the KIDSCREEN-27 dimensions showed a gradient according to socio-economic status, age and gender. Conclusions: The KIDSCREEN-27 seems to be a valid measure of HRQoL in children and adolescents. Further research is needed to assess longitudinal validity and sensitivity to change. © 2007 Springer Science+Business Media B.V.
Book•
27 Sep 2007TL;DR: This article examined teacher and student talk at secondary school level from different discourse-analytic angles, taking into account the interpersonal pragmatics of classroom discourse and how school subjects are talked into being during lessons.
Abstract: The label CLIL stands for classrooms where a foreign language (English) is used as a medium of instruction in content subjects. This book provides a first in-depth analysis of the kind of communicative abilities which are embodied in such CLIL classrooms. It examines teacher and student talk at secondary school level from different discourse-analytic angles, taking into account the interpersonal pragmatics of classroom discourse and how school subjects are talked into being during lessons. The analysis shows how CLIL classroom interaction is strongly shaped by its institutional context, which in turn conditions the ways in which students experience, use and learn the target language. The research presented here suggests that CLIL programmes require more explicit language learning goals in order to fully exploit their potential for furthering the learners’ appropriation of a foreign language as a medium of learning.
TL;DR: In this paper, periodic density functional theory (DFT) calculations for the ground state properties of ground state structures were performed using the Perdew-Burke-Ernzerhof (PBE0) and Heyd-Scuseria-Ernerhof (HSE) hybrid functionals that include nonlocal Fock exchange.
Abstract: We report periodic density functional theory (DFT) calculations for ${\mathrm{CeO}}_{2}$ and ${\mathrm{Ce}}_{2}{\mathrm{O}}_{3}$ using the Perdew-Burke-Ernzerhof (PBE0) and Heyd-Scuseria-Ernzerhof (HSE) hybrid functionals that include nonlocal Fock exchange. We study structural, electronic, and magnetic ground state properties. Hybrid functionals correctly predict ${\mathrm{Ce}}_{2}{\mathrm{O}}_{3}$ to be an insulator as opposed to the ferromagnetic metal predicted by the local spin density (LDA) and generalized gradient (GGA) approximations. The equilibrium volumes of both structures are in very good agreement with experiments, improving upon the description of the LDA and GGA. The calculated ${\mathrm{CeO}}_{2}$ (O $2p$--Ce $5d$) and ${\mathrm{Ce}}_{2}{\mathrm{O}}_{3}$ $(\mathrm{Ce}\phantom{\rule{0.3em}{0ex}}4f\text{\ensuremath{-}}5d4f)$ band gaps are larger by up to 45% (PBE0) and 15% (HSE) than found in experiments. Furthermore, we calculate atomization energies, heats of formation, and the reduction energy of $2{\mathrm{CeO}}_{2}\ensuremath{\rightarrow}{\mathrm{Ce}}_{2}{\mathrm{O}}_{3}+(1∕2){\mathrm{O}}_{2}$. The latter is underestimated by $\ensuremath{\sim}0.4--0.9\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$ with respect to available experimental data at room temperature. We compare our results with the more traditional DFT+$U$ (LDA$+U$ and PBE$+U$) approach and discuss the role played by the Hubbard $U$ parameter.
14 Mar 2007
TL;DR: ProbeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information that allows any user to add, modify or remove information or to report errors in real-time.
Abstract: probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at http://www.microbial-ecology.net/probebase. Email correspondence can be addressed to ten.ygoloce-laiborcim@esabeborp.
TL;DR: The theoretical lattice constants overestimate the experimental ones by approximately 1%, and hence behave similarly to the PBE gradient-corrected exchange-correlation functional, and theoretical values for heats of formation for both the B3LYP as well as the B 3PW91 functionals are presented.
Abstract: The B3LYP hybrid functional has shown to successfully predict a wide range of molecular properties. For periodic systems, however, the failure to attain the exact homogeneous electron gas limit as well as the semiempirical construction turns out to be a major drawback of the functional. We rigorously assess the B3LYP functional for solids through calculations of lattice parameters, bulk moduli, and thermochemical properties (atomization energies and reaction energies). The theoretical lattice constants overestimate the experimental ones by approximately 1%, and hence behave similarly to the PBE gradient-corrected exchange-correlation functional. B3LYP atomization energies of solids are drastically worse than those of nonempirical hybrid Hartree-Fock/density functionals (HF/DFT) such as PBE0 and HSE03. These large errors can be traced back to the lack of a proper description of "free-electron-like" systems with a significant itinerant character (metals and small gap semiconductors). Similar calculations using the popular semiempirical B3PW91 hybrid functional, which fulfills the uniform electron gas limit, show a clear improvement over B3LYP regarding atomization energies. Finally, theoretical values for heats of formation for both the B3LYP as well as the B3PW91 functionals are presented. These document a most likely fortuitously good agreement with experiment for the B3LYP hybrid functional.
TL;DR: Based upon a quasi-randomized trial and long-term observational follow-up, results indicate mindfulness intervention to be of potential long- term benefit for female fibromyalgia patients.
Abstract: Background: Mindfulness-based stress reduction (MBSR) proposes a systematic program for reduction of suffering associated with a wide range of medical conditions. Studies suggest improvements in general aspects of well-being, including quality of life (QoL), coping and positive affect, as well as decreased anxiety and depression. Methods: A quasi-experimental study examined effects of an 8-week MBSR intervention among 58 female patients with fibromyalgia (mean, 52 8 8 years) who underwent MBSR or an active social support procedure. Participants were assigned to groups by date of entry, and 6 subjects dropped out during the study. Self-report measures were validated German inventories and included the following scales: visual analog pain, pain perception, coping with pain, a symptom checklist and QoL. Pre- and postintervention measurements were made. Additionally, a 3-year follow-up was carried out on a subgroup of 26 participants. Results: Pre- to postintervention analyses indicated MBSR to provide significantly greater benefits than the control intervention on most dimensions, including visual analog pain, QoL subscales, coping with pain, anxiety, depression and somatic complaints (Cohen d
TL;DR: In this article, the authors investigated the effect of climate warming on plant species richness on high peaks of the European Alps and found an increase in species richness from 11.4 to 12.7 species per plot, an increase of 11.8% or of at least 10.6% at a 95% confidence level.
Abstract: High mountain ecosystems are defined by low temperatures and are therefore considered to react sensitively to climate warming. Responding to observed changes in plant species richness on high peaks of the European Alps, an extensive setup of 1 m � 1 m permanent plots was established at the alpine-nival ecotone (between 2900 and 3450 m) on Mount Schrankogel, a GLORIA master site in the central Tyrolean Alps, Austria, in 1994. Recording was repeated in a representative selection of 362 quadrats in 2004. Ten years after the first recording, we observed an average change in vascular plant species richness from 11.4 to 12.7 species per plot, an increase of 11.8% (or of at least 10.6% at a 95% confidence level). The increase in species richness involved 23 species (about 43% of all taxa found at the ecotone), comprising both alpine and nival species and was pronouncedly higher in plots with subnival/nival vegetation than in plots with alpine grassland vegetation. Only three species showed a decrease in plot occupancy: one was an annual species, one was rare, and one a common nival plant that decreased in one part of the area but increased in the uppermost part. Species cover changed in relation to altitudinal preferences of species, showing significant declines of all subnival to nival plants, whereas alpine pioneer species increased in cover. Recent climate warming in the Alps, which has been twice as high as the global average, is considered to be the primary driver of the observed differential changes in species cover. Our results indicate an ongoing range contraction of subnival to nival species at their rear (i.e. lower) edge and a concurrent expansion of alpine pioneer species at their leading edge. Although this was expected from predictive distribution models and different temperature-related habitat preferences of alpine and nival species, we provide first evidence on – most likely – warming-induced species declines in the high European Alps. The projected acceleration of climate warming raises concerns that this phenomenon could become the major threat to biodiversity in high mountains.
TL;DR: It is shown that a matrix, which is a composition of a random matrix of certain type and a deterministic dictionary, has small restricted isometry constants, and signals that are sparse with respect to the dictionary can be recovered via basis pursuit from a small number of random measurements.
Abstract: This article extends the concept of compressed sensing to signals that are not sparse in an orthonormal basis but rather in a redundant dictionary. It is shown that a matrix, which is a composition of a random matrix of certain type and a deterministic dictionary, has small restricted isometry constants. Thus, signals that are sparse with respect to the dictionary can be recovered via Basis Pursuit from a small number of random measurements. Further, thresholding is investigated as recovery algorithm for compressed sensing and conditions are provided that guarantee reconstruction with high probability. The different schemes are compared by numerical experiments.
TL;DR: An analysis of intra- and interspecific variation in the butterfly family Lycaenidae which includes a well-sampled clade with a peculiar characteristic that facilitates the recognition of species as reproductively isolated units even in allopatric populations indicates that the "barcoding gap" is an artifact of insufficient sampling across taxa.
Abstract: Background
DNA barcoding, i.e. the use of a 648 bp section of the mitochondrial gene cytochrome c oxidase I, has recently been promoted as useful for the rapid identification and discovery of species. Its success is dependent either on the strength of the claim that interspecific variation exceeds intraspecific variation by one order of magnitude, thus establishing a "barcoding gap", or on the reciprocal monophyly of species.
TL;DR: The problem of discriminating two different quantum states in the setting of asymptotically many copies is considered, and the minimal probability of error is determined, leading to the identification of the quantum Chernoff bound, thereby solving a long-standing open problem.
Abstract: We consider the problem of discriminating two different quantum states in the setting of asymptotically many copies, and determine the minimal probability of error. This leads to the identification of the quantum Chernoff bound, thereby solving a long-standing open problem. The bound reduces to the classical Chernoff bound when the quantum states under consideration commute. The quantum Chernoff bound is the natural symmetric distance measure between quantum states because of its clear operational meaning and because it does not seem to share some of the undesirable features of other distance measures.
TL;DR: In this article, a comparative full-potential study of generalized Kohn-Sham (gKS) schemes with explicit focus on their suitability as starting point for the solution of the quasiparticle equation is presented.
Abstract: We present a comparative full-potential study of generalized Kohn-Sham (gKS) schemes with explicit focus on their suitability as starting point for the solution of the quasiparticle equation. We compare ${G}_{0}{W}_{0}$ quasiparticle band structures calculated upon local-density approximation (LDA), screened-exchange, HSE03, PBE0, and Hartree-Fock functionals for exchange and correlation (XC) for Si, InN, and ZnO. Furthermore, the HSE03 functional is studied and compared to the generalized gradient approximation (GGA) for 15 nonmetallic materials for its use as a starting point in the calculation of quasiparticle excitation energies. For this case, the effects of self-consistency in the $GW$ self-energy are also analyzed. It is shown that the use of a gKS scheme as a starting point for a perturbative quasiparticle correction can improve upon the deficiencies found for LDA or GGA starting points for compounds with shallow $d$ bands. For these solids, the order of the valence and conduction bands is often inverted using local or semilocal approximations for XC, which makes perturbative ${G}_{0}{W}_{0}$ calculations unreliable. The use of a gKS starting point allows for the calculation of fairly accurate band gaps even in these difficult cases, and generally single-shot ${G}_{0}{W}_{0}$ calculations following calculations using the HSE03 functional are very close to experiment.
TL;DR: In this paper, a wavelength-tunable, fiber-coupled source of entangled photons with extremely high spectral brightness and quality of entanglement was demonstrated using a 25 mm PPKTP crystal inside a polarization Sagnac interferometer.
Abstract: We demonstrate a wavelength-tunable, fiber-coupled source of polarization- entangled photons with extremely high spectral brightness and quality of entanglement. Using a 25 mm PPKTP crystal inside a polarization Sagnac interferometer we detect a spectral brightness of 273000 pairs (s mW nm)(-1), a factor of 28 better than comparable previous sources while state tomography showed the two-photon state to have a tangle of T = 0.987. This improvement was achieved by use of a long crystal, careful selection of focusing parameters and single-mode fiber coupling. We demonstrate that, due to the particular geometry of the setup, the signal and idler wavelengths can be tuned over a wide range without loss of entanglement.
TL;DR: It is predicted that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.
Abstract: Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.
TL;DR: The N ewton -X program package as mentioned in this paper is based on Tully's surface hopping approach and can be used to perform both adiabatic and nonadiabatic simulations.
Abstract: The great importance of ultrafast phenomena in photochemistry and photobiology has made dynamics simulations an essential methodology in these areas. In this work, we present the N ewton -X program package containing a new implementation of a direct dynamics approach to perform adiabatic (Born–Oppenheimer) and nonadiabatic simulations. The nonadiabatic dynamics is based on Tully's surface hopping approach. The program has been developed with the aim of (1) to create a flexible tool to be used in connection with a multitude of third-party electronic-structure program packages and (2) to provide the most common options for excited-state dynamics simulations. Benchmark calculations on the nonadiabatic dynamics are presented for the methaniminium, butatriene and pentadieniminium cations. The simulation of UV absorption spectra is presented for the methaniminium cation and pyrazine.
University Hospital of Basel1, French Institute of Health and Medical Research2, Istanbul University3, Aristotle University of Thessaloniki4, University of Düsseldorf5, Charles University in Prague6, Karolinska University Hospital7, Ludwig Maximilian University of Munich8, Sapienza University of Rome9, Catholic University of Leuven10, University of Vienna11, Washington University in St. Louis12, University of California, San Francisco13, National Institutes of Health14, St. Michael's Hospital15, Brigham and Women's Hospital16, Ruhr University Bochum17, Royal Melbourne Hospital18
TL;DR: This Review revisits and update previous recommendations on natalizumab for treatment of patients with RRMS, based on additional long-term follow-up of clinical studies and post-marketing observations, including appropriate patient selection and management recommendations.
Abstract: Natalizumab, a highly specific α4-integrin antagonist, is approved for treatment of patients with active relapsing-remitting multiple sclerosis (RRMS). It is generally recommended for individuals who have not responded to a currently available first-line disease-modifying therapy or who have very active disease. The expected benefits of natalizumab treatment have to be weighed against risks, especially the rare but serious adverse event of progressive multifocal leukoencephalopathy. In this Review, we revisit and update previous recommendations on natalizumab for treatment of patients with RRMS, based on additional long-term follow-up of clinical studies and post-marketing observations, including appropriate patient selection and management recommendations.