University of Kaiserslautern

BACKGROUND: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS: When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. RESULTS: ), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. DISCUSSION: VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.

Coherent preparation by laser light of quantum states of atoms and molecules can lead to quantum interference in the amplitudes of optical transitions. In this way the optical properties of a medium can be dramatically modified, leading to electromagnetically induced transparency and related effects, which have placed gas-phase systems at the center of recent advances in the development of media with radically new optical properties. This article reviews these advances and the new possibilities they offer for nonlinear optics and quantum information science. As a basis for the theory of electromagnetically induced transparency the authors consider the atomic dynamics and the optical response of the medium to a continuous-wave laser. They then discuss pulse propagation and the adiabatic evolution of field-coupled states and show how coherently prepared media can be used to improve frequency conversion in nonlinear optical mixing experiments. The extension of these concepts to very weak optical fields in the few-photon limit is then examined. The review concludes with a discussion of future prospects and potential new applications.

In June 2005, a World Health Organization (WHO)-International Programme on Chemical Safety expert meeting was held in Geneva during which the toxic equivalency factors (TEFs) for dioxin-like compounds, including some polychlorinated biphenyls (PCBs), were reevaluated. For this reevaluation process, the refined TEF database recently published by Haws et al. (2006, Toxicol. Sci. 89, 4-30) was used as a starting point. Decisions about a TEF value were made based on a combination of unweighted relative effect potency (REP) distributions from this database, expert judgment, and point estimates. Previous TEFs were assigned in increments of 0.01, 0.05, 0.1, etc., but for this reevaluation, it was decided to use half order of magnitude increments on a logarithmic scale of 0.03, 0.1, 0.3, etc. Changes were decided by the expert panel for 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) (TEF = 0.3), 1,2,3,7,8-pentachlorodibenzofuran (PeCDF) (TEF = 0.03), octachlorodibenzo-p-dioxin and octachlorodibenzofuran (TEFs = 0.0003), 3,4,4',5-tetrachlorbiphenyl (PCB 81) (TEF = 0.0003), 3,3',4,4',5,5'-hexachlorobiphenyl (PCB 169) (TEF = 0.03), and a single TEF value (0.00003) for all relevant mono-ortho-substituted PCBs. Additivity, an important prerequisite of the TEF concept was again confirmed by results from recent in vivo mixture studies. Some experimental evidence shows that non-dioxin-like aryl hydrocarbon receptor agonists/antagonists are able to impact the overall toxic potency of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds, and this needs to be investigated further. Certain individual and groups of compounds were identified for possible future inclusion in the TEF concept, including 3,4,4'-TCB (PCB 37), polybrominated dibenzo-p-dioxins and dibenzofurans, mixed polyhalogenated dibenzo-p-dioxins and dibenzofurans, polyhalogenated naphthalenes, and polybrominated biphenyls. Concern was expressed about direct application of the TEF/total toxic equivalency (TEQ) approach to abiotic matrices, such as soil, sediment, etc., for direct application in human risk assessment. This is problematic as the present TEF scheme and TEQ methodology are primarily intended for estimating exposure and risks via oral ingestion (e.g., by dietary intake). A number of future approaches to determine alternative or additional TEFs were also identified. These included the use of a probabilistic methodology to determine TEFs that better describe the associated levels of uncertainty and "systemic" TEFs for blood and adipose tissue and TEQ for body burden.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR(2), http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

The authors discuss the technique of stimulated Raman adiabatic passage (STIRAP), a method of using partially overlapping pulses (from pump and Stokes lasers) to produce complete population transfer between two quantum states of an atom or molecule. The procedure relies on the initial creation of a coherence (a population-trapping state) with subsequent adiabatic evolution. The authors present the basic theory, with some extensions, and then describe examples of experimental utilization. They note some applications of the technique not only to preparation of selected states for reaction studies, but also to quantum optics and atom optics.

Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

METIS is the EU flagship 5G project with the objective of laying the foundation for 5G systems and building consensus prior to standardization. The METIS overall approach toward 5G builds on the evolution of existing technologies complemented by new radio concepts that are designed to meet the new and challenging requirements of use cases today's radio access networks cannot support. The integration of these new radio concepts, such as massive MIMO, ultra dense networks, moving networks, and device-to-device, ultra reliable, and massive machine communications, will allow 5G to support the expected increase in mobile data volume while broadening the range of application domains that mobile communications can support beyond 2020. In this article, we describe the scenarios identified for the purpose of driving the 5G research direction. Furthermore, we give initial directions for the technology components (e.g., link level components, multinode/multiantenna, multi-RAT, and multi-layer networks and spectrum handling) that will allow the fulfillment of the requirements of the identified 5G scenarios.

Sequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour-intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High-throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers-the variable V4 and V9 regions-from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long-tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.

In this paper, we present a patch-based land use and land cover classification approach using Sentinel-2 satellite images. The Sentinel-2 satellite images are openly and freely accessible, and are provided in the earth observation program Copernicus. We present a novel dataset, based on these images that covers 13 spectral bands and is comprised of ten classes with a total of 27 000 labeled and geo-referenced images. Benchmarks are provided for this novel dataset with its spectral bands using state-of-the-art deep convolutional neural networks. An overall classification accuracy of 98.57% was achieved with the proposed novel dataset. The resulting classification system opens a gate toward a number of earth observation applications. We demonstrate how this classification system can be used for detecting land use and land cover changes, and how it can assist in improving geographical maps. The geo-referenced dataset EuroSAT is made publicly available at https://github.com/phelber/eurosat.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

We describe a technique for manipulating quantum information stored in collective states of mesoscopic ensembles. Quantum processing is accomplished by optical excitation into states with strong dipole-dipole interactions. The resulting "dipole blockade" can be used to inhibit transitions into all but singly excited collective states. This can be employed for a controlled generation of collective atomic spin states as well as nonclassical photonic states and for scalable quantum logic gates. An example involving a cold Rydberg gas is analyzed.

As of today, the fifth generation (5G) mobile communication system has been rolled out in many countries and the number of 5G subscribers already reaches a very large scale. It is time for academia and industry to shift their attention towards the next generation. At this crossroad, an overview of the current state of the art and a vision of future communications are definitely of interest. This article thus aims to provide a comprehensive survey to draw a picture of the sixth generation (6G) system in terms of drivers, use cases, usage scenarios, requirements, key performance indicators (KPIs), architecture, and enabling technologies. First, we attempt to answer the question of “Is there any need for 6G?” by shedding light on its key driving factors, in which we predict the explosive growth of mobile traffic until 2030, and envision potential use cases and usage scenarios. Second, the technical requirements of 6G are discussed and compared with those of 5G with respect to a set of KPIs in a quantitative manner. Third, the state-of-the-art 6G research efforts and activities from representative institutions and countries are summarized, and a tentative roadmap of definition, specification, standardization, and regulation is projected. Then, we identify a dozen of potential technologies and introduce their principles, advantages, challenges, and open research issues. Finally, the conclusions are drawn to paint a picture of “What 6G may look like?.” This survey is intended to serve as an enlightening guideline to spur interests and further investigations for subsequent research and development of 6G communications systems.

About 10% to 15% of the nuclear genes of eukaryotic organisms encode mitochondrial proteins. These proteins are synthesized in the cytosol and recognized by receptors on the surface of mitochondria. Translocases in the outer and inner membrane of mitochondria mediate the import and intramitochondrial sorting of these proteins; ATP and the membrane potential are used as energy sources. Chaperones and auxiliary factors assist in the folding and assembly of mitochondrial proteins into their native, three-dimensional structures. This review summarizes the present knowledge on the import and sorting of mitochondrial precursor proteins, with a special emphasis on unresolved questions and topics of current research.

This critical review examines transition metal-catalyzed decarboxylative couplings that have emerged within recent years as a powerful strategy to form carbon-carbon or carbon-heteroatom bonds starting from carboxylic acids. In these reactions, C-C bonds to carboxylate groups are cleaved, and in their place, new carbon-carbon bonds are formed. Decarboxylative cross-couplings constitute advantageous alternatives to traditional cross-coupling or addition reactions involving preformed organometallic reagents. Decarboxylative reaction variants are also known for Heck reactions, direct arylation processes, and carbon-heteroatom bond forming reactions.

Spintronics is one of the emerging fields for the next-generation nanoelectronic devices to reduce their power consumption and to increase their memory and processing capabilities. Such devices utilise the spin degree of freedom of electrons and/or holes, which can also interact with their orbital moments. In these devices, the spin polarisation is controlled either by magnetic layers used as spin-polarisers or analysers or via spin–orbit coupling. Spin waves can also be used to carry spin current. In this review, the fundamental physics of these phenomena is described first with respect to the spin generation methods as detailed in Sections 2 ~ 9. The recent development in their device applications then follows in Sections 10 and 11. Future perspectives are provided at the end.

Recovery and reuse of expensive catalysts after catalytic reactions are important factors for sustainable process management. The aim of this Review is to highlight the progress in the formation and catalytic applications of magnetic nanoparticles and magnetic nanocomposites. Directed functionalization of the surfaces of nanosized magnetic materials is an elegant way to bridge the gap between heterogeneous and homogeneous catalysis. The introduction of magnetic nanoparticles in a variety of solid matrices allows the combination of well-known procedures for catalyst heterogenization with techniques for magnetic separation.

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

The origin and interpretation of the Raman features of amorphous (hydrogenated) carbon films deposited at room temperature in the region of 1000–1700 cm−1 is discussed in this paper. Possible interpretations of the linewidths, positions of the ‘‘G’’ graphite peak and ‘‘D’’ disordered peak, and their intensity ratios are examined using results obtained from magnetron sputtered and magnetic field enhanced plasma deposited films. It is shown that even small ‘‘clusters’’ of condensed benzene rings (cluster size below 20 Å) in carbon films can explain the observed Raman scattering. Besides the care that should be taken in the correct interpretation of Raman results, the utility of Raman scattering in obtaining an estimate of cluster sizes in amorphous (hydrogenated) carbon films is discussed. Carbon films prepared by magnetron sputtering show two additional Raman features at 1180 and 1490 cm−1 in addition to the G and D peaks. It is shown that a correlation exists between the 1180 cm−1 peak and the sp3 content in the films.

In recent years, there has been a resurgence of interest in the value construct among both marketing researchers and practitioners. Despite a growing body of research, it is still not clear how value interacts with related marketing constructs. Researchers have called for an investigation of the interrelationship between customer satisfaction and customer value to reduce the ambiguities surrounding both concepts. Investigates whether customer value and satisfaction represent two theoretically and empirically distinct concepts. Also addresses whether value is a better predictor of behavioral outcomes than satisfaction in a business marketing context. Two alternative models are developed and empirically tested in a cross‐sectional survey with purchasing managers in Germany. The first model suggests a direct impact of perceived value on the purchasing managers’ intentions. In the second model, perceived value is mediated by satisfaction. This research suggests that value and satisfaction can be conceptualized and measured as two distinct, yet complementary constructs.