Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons

Background Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content. Results We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community. Conclusions A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.National Science Foundation [1640775]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Private Law and the European Constitutionalisation of Values

According to the CFREU, the EU is founded on the general values such as values of human dignity, freedom, equality and solidarity. In addition, the TEU refers to a more political set of foundational values, ie respect for human dignity, freedom, democracy, equality, the rule of law and respect for human rights. These references could be understood as purely ornamental, or as irrelevant in any case for private law. Indeed, it is true that the Court of Justice so far has never made any references to these values in private law cases. Still, the Court already has shown boldness before in the context of the interpretation and review of secondary EU law in private law cases, when it discovered general principles of EU law and general principles of civil law. Therefore, it should not be excluded that the Court may be tempted one day to follow the example of the German constitutional court that famously understands its national constitution as expressing an objective system of constitutional values. This paper explores what such an understanding of private law as an instrument for furthering common European values would entail and examines whether such an ethical reading of European private law would be desirable. It argues that the promotion by the EU of a set of official values through its laws is not compatible we the respect we owe each other in a society characterised by reasonable pluralism. In addition, it points to further difficulties, both of a moral and a practical nature, of the idea of advancing ethical values through private law. It concludes that although it is very well thinkable that the values to which the TEU and the Charter refer will one day be interpreted as an objective value system with (indirect) horizontal effects, the Court of Justice nevertheless should refrain from going down that road

Drafting a composite indicator of validity for regulatory models and legal systems

The aim of this paper is to lay the groundwork for the creation of a composite indicator of the validity of regulatory systems. The composite nature of the indicator implies a) that its construction is embedded in the long-standing theoretical debate and framework of legal validity; b) that it formally contains other sub-indicators whose occurrence is essential to the determination of validity. The paper suggests, in other words, that validity is a second-degree property, i.e., one that occurs only once the justice, efficiency, effectiveness, and enforceability of the system have been checked

Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5′ and 3′ UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org)

Balancing, Proportionality, and Constitutional Rights

In the theory and practice of constitutional adjudication, proportionality review plays a crucial role. At a theoretical level, it lies at core of the debate on rights adjudication; in judicial practice, it is a widespread decision-making model characterizing the action of constitutional, supra-national and international courts. Despite its circulation and centrality in contemporary legal discourse, proportionality in rights-adjudication is still extremely controversial. It raises normative questions—concerning its justification and limits—and descriptive questions—regarding its nature and distinctive features. The chapter addresses both orders of questions. Part I centres on the justification of proportionality review, the connection between proportionality, balancing and theories of rights and the critical aspects of this connection. Part II identifies and analyses the different forms of proportionality both in review, as a template for rights-adjudication, and of review, as a way of defining the scope and limits of adjudication

Bipartite Graphs and the Decomposition of Systems of Equations

Solving large systems of equations is a problem often encountered in engineering disciplines. However, as such systems grow, the effort required for finding a solution to them increases as well. In order to be able to cope with ever larger systems of equations, some form of decomposition is needed. By decomposing a large system into smaller subsystems, the total effort required for finding a solution may decrease. However, whether this is really the case of course depends on the additional effort required for obtaining the decomposition itself. In this thesis several aspects of the difficulty of obtaining such decompositions are explored

Stability of Velocity in the Major Industrial Countries: A Kalman Filter Approach

Forecasting models are estimated using annual data for the income velocity of money in seven major industrial countries. The predictions are conditional on the realized value of the long-term domestic government bond rate. These forecasts did not deteriorate over the period 1980-88, compared with the earlier postwar period. Velocity of M1 is found to be very interest elastic in almost all countries; velocity of M2, less so. The specifications (based on Kalman filters) point to a nonconstant trend in velocity, raising questions about the assumptions required for the cointegration techniques used in other research on money demand.