Integrated multiple sequence alignment

Sammeth M. Integrated multiple sequence alignment. Bielefeld (Germany): Bielefeld University; 2005.The thesis presents enhancements for automated and manual multiple sequence alignment: existing alignment algorithms are made more easily accessible and new algorithms are designed for difficult cases. Firstly, we introduce the QAlign framework, a graphical user interface for multiple sequence alignment. It comprises several state-of-the-art algorithms and supports their parameters by convenient dialogs. An alignment viewer with guided editing functionality can also highlight or print regions of the alignment. Also phylogenetic features are provided, e.g., distance-based tree reconstruction methods, corrections for multiple substitutions and a tree viewer. The modular concept and the platform-independent implementation guarantee an easy extensibility. Further, we develop a constrained version of the divide-and-conquer alignment such that it can be restricted by anchors found earlier with local alignments. It can be shown that this method shares attributes of both, local and global aligners, in the quality of results as well as in the computation time. We further modify the local alignment step to work on bipartite (or even multipartite) sets for sequences where repeats overshadow valuable sequence information. In the end a technique is established that can accurately align sequences containing eventually repeated motifs. Finally, another algorithm is presented that allows to compare tandem repeat sequences by aligning them with respect to their possible repeat histories. We describe an evolutionary model including tandem duplications and excisions, and give an exact algorithm to compare two sequences under this model

Beyond the Fruit Tree: A Proposal for Revision of the Assignment of Income Doctrine—Caruth Corp. v. United States, 865 F.2d 644 (5th Cir. 1989)

The Supreme Court developed the assignment of income doctrine to solve the question of who the proper taxpayer is under section 61 of the Internal Revenue Code. The question arises when individuals transfer income that rightly belongs to them without declaring the income for federal tax purposes. The assignment doctrine attributes income, for tax purposes, to the earner or practical owner of the income notwithstanding that person\u27s assignment of the income. However, the Supreme Court\u27s development of the doctrine has been inadequate, as exemplified by the recent decision of the Fifth Circuit Court of Appeals in Caruth Corp. v. United State. Caruth demonstrates the improper focus of the traditional doctrine on form rather than substance. The doctrine should be redefined to attribute assigned income to taxpayers based upon who controls and enjoys that income rather than upon the form of the transaction in which the income was transferred

ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets

In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon–intron structure between transcript variants and the need for computational tools to address ‘complex’ AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events. The method extracts AS events dynamically from custom gene annotations, classifies them into groups of common types and visualizes a comprehensive picture of the resulting AS landscape. Thus, ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected by the user according to common functional/structural attributes of interest: http://genome.imim.es/astalavist

Assessing the impact of future CAP reforms on the demand of production factors

The CAP reform process has been a central issue for agricultural economics research in recent years, and is gaining further attention in view of the post-2013 perspectives. The objective of this paper is to assess ex-ante the effect of different post-2013 CAP and market scenarios on the demand of productions factors. The paper is based on the use of farm household dynamic programming models maximising the net present value with a time horizon until 2030. A representative model has been implemented for 18 different farming systems in 8 EU countries. Changes in marginal values of selected resource constraints (land, labour and capital) are used to assess the potential effect of different scenarios on farm-household demand of production factors. Results highlight that both policy and market conditions change strongly the demand of productive factors.CAP reform, Investment behaviour, Farm Household model, Factor markets, Agricultural and Food Policy, Q12,

Impact of rural poverty reduction strategies: The case of smallholders in Sierra Leone

The present analysis, which exploits one of the first empirical data collected from smallholders in Sierra Leone since the end of the civil war, compares the impact of two poverty reduction strategies targeting smallholders in Sierra Leone: support to rice production is compared with support to coffee and cocoa production in terms of sustainable income generation and contributing to macroeconomic stability and growth. Supporting rice production is intended to help the country regain self-sufficiency in its traditional principle staple. This will help towards improving food security and reducing dependency on volatile world market prices which, for example, with respect to the recent global spike has had dramatic effects on the lowest incomes. Support to cocoa and coffee production on the other hand aims to create and increase income by producing exportable commodities with higher value added. This research addresses strategic options most successful in improving food security and accelerating economic development. Additionally, bottlenecks in terms of inputs, infrastructure and social and economic factors are identified and analysed in order to isolate those which once improved will impact most on productivity. The results are discussed within a broader economic and socio-economic context in particular with respect to enhanced targeting and impact of Official Development Assistance.Agriculture, Poverty, Official Development Assistance, Sierra Leone, Food Security and Poverty, O1, Q1,

OpenDSU: Digital Sovereignty in PharmaLedger

Distributed ledger networks, chiefly those based on blockchain technologies, currently are heralding a next generation of computer systems that aims to suit modern users' demands. Over the recent years, several technologies for blockchains, off-chaining strategies, as well as decentralised and respectively self-sovereign identity systems have shot up so fast that standardisation of the protocols is lagging behind, severely hampering the interoperability of different approaches. Moreover, most of the currently available solutions for distributed ledgers focus on either home users or enterprise use case scenarios, failing to provide integrative solutions addressing the needs of both. Herein we introduce the OpenDSU platform that allows to interoperate generic blockchain technologies, organised - and possibly cascaded in a hierarchical fashion - in domains. To achieve this flexibility, we seamlessly integrated a set of well conceived OpenDSU components to orchestrate off-chain data with granularly resolved and cryptographically secure access levels that are nested with sovereign identities across the different domains. Employing our platform to PharmaLedger, an inter-European network for the standardisation of data handling in the pharmaceutical industry and in healthcare, we demonstrate that OpenDSU can cope with generic demands of heterogeneous use cases in both, performance and handling substantially different business policies. Importantly, whereas available solutions commonly require a pre-defined and fixed set of components, no such vendor lock-in restrictions on the blockchain technology or identity system exist in OpenDSU, making systems built on it flexibly adaptable to new standards evolving in the future.Comment: 18 pages, 8 figure

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

Background: The quantity of transcriptome data is rapidly increasing for non-model organisms. As sequencing technology advances, focus shifts towards solving bioinformatic challenges, of which sequence read assembly is the first task. Recent studies have compared the performance of different software to establish a best practice for transcriptome assembly. Here, we adapted a simulation approach to evaluate specific features of assembly programs on 454 data. The novelty of our study is that the simulation allows us to calculate a model assembly as reference point for comparison. Findings: The simulation approach allows us to compare basic metrics of assemblies computed by different software applications (CAP3, MIRA, Newbler, and Oases) to a known optimal solution. We found MIRA and CAP3 are conservative in merging reads. This resulted in comparably high number of short contigs. In contrast, Newbler more readily merged reads into longer contigs, while Oases produced the overall shortest assembly. Due to the simulation approach, reads could be traced back to their correct placement within the transcriptome. Together with mapping reads onto the assembled contigs, we were able to evaluate ambiguity in the assemblies. This analysis further supported the conservative nature of MIRA and CAP3, which resulted in low proportions of chimeric contigs, but high redundancy. Newbler produced less redundancy, but the proportion of chimeric contigs was higher. Conclusion: Our evaluation of four assemblers suggested that MIRA and Newbler slightly outperformed the othe

Assessing the impact of future CAP reforms on the demand of production factors

The CAP reform process has been a central issue for agricultural economics research in recent years, and is gaining further attention in view of the post-2013 perspectives. The objective of this paper is to assess ex-ante the effect of different post-2013 CAP and market scenarios on the demand of productions factors. The paper is based on the use of farm household dynamic programming models maximising the net present value with a time horizon until 2030. A representative model has been implemented for 18 different farming systems in 8 EU countries. Changes in marginal values of selected resource constraints (land, labour and capital) are used to assess the potential effect of different scenarios on farm-household demand of production factors. Results highlight that both policy and market conditions change strongly the demand of productive factors.JRC.J.4-Agriculture and Life Sciences in the Econom

Farm Investment Beahviour in the EU: An Ex Post Analysis through Panel Data

Farm investment behaviour is the result of the complex interplay of several variables and is strictly connected to expectations by farmers. The main objective of this paper is to investigate the determinants of investment behaviour in EU farming systems, based on a panel analysis of 178 farm households in 6 EU countries. The analysis focuses in particular on the changes occurred between 2006 and 2009 in terms of stated intention to invest. The results confirm the role of major structural (location, farm size) and demographic (farmers age) variables in affecting farm investment as already known from the literature. However the panel analysis emphasises the changes in investment attitude occurred in the period 2006-2009, likely as a combined effect of the economic crisis and of the dynamics of agricultural costs and prices.JRC.DDG.J.5-Agriculture and Life Sciences in the Econom

Assessing the impact of future CAP reforms on the demand of production factors

The CAP reform process has been a central issue for agricultural economics research in recent years, and is gaining further attention in view of the post-2013 perspectives. The objective of this paper is to assess ex-ante the effect of different post-2013 CAP and market scenarios on the demand of productions factors. The paper is based on the use of farm household dynamic programming models maximising the net present value with a time horizon until 2030. A representative model has been implemented for 18 different farming systems in 8 EU countries. Changes in marginal values of selected resource constraints (land, labour and capital) are used to assess the potential effect of different scenarios on farm-household demand of production factors. Results highlight that both policy and market conditions change strongly the demand of productive factors