Towards sharing in lazy computation systems

Work on proving congruence of bisimulation in functional programming languages often refers to [How89,How96], where Howe gave a highly general account on this topic in terms of so-called lazy computation systems . Particularly in implementations of lazy functional languages, sharing plays an eminent role. In this paper we will show how the original work of Howe can be extended to cope with sharing. Moreover, we will demonstrate the application of our approach to the call-by-need lambda-calculus lambda-ND which provides an erratic non-deterministic operator pick and a non-recursive let. A definition of a bisimulation is given, which has to be based on a further calculus named lambda-~, since the na1ve bisimulation definition is useless. The main result is that this bisimulation is a congruence and contained in the contextual equivalence. This might be a step towards defining useful bisimulation relations and proving them to be congruences in calculi that extend the lambda-ND-calculus

On equivalences and standardization in a non-deterministic call-by-need lambda calculus

The goal of this report is to prove correctness of a considerable subset of transformations w.r.t. contextual equivalence in a an extended lambda-calculus with case, constructors, seq, let, and choice, with a simple set of reduction rules. Unfortunately, a direct proof appears to be impossible. The correctness proof is by defining another calculus comprising the complex variants of copy, case-reduction and seq-reductions that use variablebinding chains. This complex calculus has well-behaved diagrams and allows a proof that of correctness of transformations, and also that the simple calculus defines an equivalent contextual order

How to prove similarity a precongruence in non-deterministic call-by-need lambda calculi

Extending the method of Howe, we establish a large class of untyped higher-order calculi, in particular such with call-by-need evaluation, where similarity, also called applicative simulation, can be used as a proof tool for showing contextual preorder. The paper also demonstrates that Mann’s approach using an intermediate “approximation” calculus scales up well from a basic call-by-need non-deterministic lambdacalculus to more expressive lambda calculi. I.e., it is demonstrated, that after transferring the contextual preorder of a non-deterministic call-byneed lambda calculus to its corresponding approximation calculus, it is possible to apply Howe’s method to show that similarity is a precongruence. The transfer is not treated in this paper. The paper also proposes an optimization of the similarity-test by cutting off redundant computations. Our results also applies to deterministic or non-deterministic call-by-value lambda-calculi, and improves upon previous work insofar as it is proved that only closed values are required as arguments for similaritytesting instead of all closed expressions

Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

Background: Eggshell mineralization in commercially important species such as chicken, turkey or quail is of interest as a general model of calcium carbonate biomineralization. Knowledge of proteins and molecular mechanisms in eggshell assembly may also pave the way to manipulation of thickness of the calcified layer or other features. Comparison of eggshell matrix proteomes of different species may contribute to a better understanding of the mineralization process. The recent publication of the quail genome sequence now enables the proteomic analysis of the quail shell matrix and this comparison with those of chicken and turkey. Results: The quail eggshell proteome comprised 622 identified proteins, 311 of which were shared with chicken and turkey eggshell proteomes. Forty-eight major proteins (iBAQ-derived abundance higher than 0.1 % of total identified proteome) together covered 94 % of total proteome mass. Fifteen of these are also among the most abundant proteins in chicken and turkey eggshell matrix. Only three proteins with a percentage higher than 1.0 % of the total had not previously been identified as eggshell matrix proteins. These were an uncharacterized member of the latexin family, an uncharacterized protease inhibitor containing a Kunitz domain, and gastric intrinsic factor. The most abundant proteins were ovocleidin-116, ovalbumin and ovocalyxin-36 representing approximately 31, 13 and 8 % of the total identified proteome, respectively. The major phosphoproteins were ovocleidin-116 and osteopontin. While osteopontin phosphorylation sites were predominantly conserved between chicken and quail sequences, conservation was less in ovocleidin-116. Conclusions: Ovocleidin-116 and ovocalyxin-36 are among the most abundant eggshell matrix proteins in all three species of the family Phasianidae analyzed so far, indicating that their presently unknown function is essential for eggshell mineralization. Evidence for other chicken eggshell-specific proteins in quail was inconclusive. Therefore measurement of additional eggshell proteomes, especially from species of different families and preferentially from outside the order Galliformes, will be necessary

In-depth analysis of the chicken egg white proteome using an LTQ Orbitrap Velos

Abstract Background Hen's egg white has been the subject of intensive chemical, biochemical and food technological research for many decades, because of its importance in human nutrition, its importance as a source of easily accessible model proteins, and its potential use in biotechnological processes. Recently the arsenal of tools used to study the protein components of egg white has been complemented by mass spectrometry-based proteomic technologies. Application of these fast and sensitive methods has already enabled the identification of a large number of new egg white proteins. Recent technological advances may be expected to further expand the egg white protein inventory. Results Using a dual pressure linear ion trap Orbitrap instrument, the LTQ Orbitrap Velos, in conjunction with data analysis in the MaxQuant software package, we identified 158 proteins in chicken egg white with two or more sequence unique peptides. This group of proteins identified with very high confidence included 79 proteins identified in egg white for the first time. In addition, 44 proteins were identified tentatively. Conclusions Our results, apart from identifying many new egg white components, indicate that current mass spectrometry technology is sufficiently advanced to permit direct identification of minor components of proteomes dominated by a few major proteins without resorting to indirect techniques, such as chromatographic depletion or peptide library binding, which change the composition of the proteome.</p

The ever expanding scope of electrospray mass spectrometry-a 30 year journey

John Fenn's electrospray mass spectrometry (ESMS) was awarded the chemistry Nobel Prize in 2002 and is now the basis of the entire field of MS-based proteomics. Technological progress continues unabated, enabling single cell sensitivity and clinical applications

Aid for trade facilitation

Does foreign aid spent on trade facilitation increase trade flows of developing countries? There is an on-going and high profile discussion of aid-for-trade associated with the Doha negotiations of the World Trade Organization. There continue also questions about how best to achieve the Millennium Development Goals. The analysis in this paper explicitly considers how to target aid most effectively to increase trade – a fundamental question related to the crisis and policy debate over restarting the world trading system. Using detailed data on aid flows from the OECD, the analysis here estimates the responsiveness of trade flows to specific types of foreign aid. The findings indicate that aid directed toward promoting trade enhances the trade performance of recipient countries: a 1 percent increase in aid directed toward trade policy and regulatory reform (amounting to about US$11.7 million more such aid) could generate an increase in global trade of about US$818 million. This yields a"rate of return"on every dollar of this type of aid of about US$697 in additional trade. As the dollar aid flow is relatively small, such targeted aid mitigates concerns about absorptive capacity and real exchange rate appreciation, which may accompany larger disbursements.

In-depth, high-accuracy proteomics of sea urchin tooth organic matrix

<p>Abstract</p> <p>Background</p> <p>The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the <it>Strongylocentrotus purpuratus </it>genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis.</p> <p>Results</p> <p>We identified 138 proteins in the matrix of tooth powder. Only 56 of these proteins were previously identified in the matrices of test (shell) and spine. Among the novel components was an interesting group of five proteins containing alanine- and proline-rich neutral or basic motifs separated by acidic glycine-rich motifs. In addition, four of the five proteins contained either one or two predicted Kazal protease inhibitor domains. The major components of tooth matrix were however largely identical to the set of spicule matrix proteins and MSP130-related proteins identified in test (shell) and spine matrix. Comparison of the matrices of crushed teeth to intact teeth revealed a marked dilution of known intracrystalline matrix proteins and a concomitant increase in some intracellular proteins.</p> <p>Conclusion</p> <p>This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Knowledge of the components of this model system may stimulate further experiments aiming at the elucidation of structure, function, and interaction of biomineral matrix components.</p

In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea

<p>Abstract</p> <p>Background</p> <p>Invertebrate biominerals are characterized by their extraordinary functionality and physical properties, such as strength, stiffness and toughness that by far exceed those of the pure mineral component of such composites. This is attributed to the organic matrix, secreted by specialized cells, which pervades and envelops the mineral crystals. Despite the obvious importance of the protein fraction of the organic matrix, only few in-depth proteomic studies have been performed due to the lack of comprehensive protein sequence databases. The recent public release of the gastropod <it>Lottia gigantea</it> genome sequence and the associated protein sequence database provides for the first time the opportunity to do a state-of-the-art proteomic in-depth analysis of the organic matrix of a mollusc shell.</p> <p>Results</p> <p>Using three different sodium hypochlorite washing protocols before shell demineralization, a total of 569 proteins were identified in <it>Lottia gigantea</it> shell matrix. Of these, 311 were assembled in a consensus proteome comprising identifications contained in all proteomes irrespective of shell cleaning procedure. Some of these proteins were similar in amino acid sequence, amino acid composition, or domain structure to proteins identified previously in different bivalve or gastropod shells, such as BMSP, dermatopontin, nacrein, perlustrin, perlucin, or Pif. In addition there were dozens of previously uncharacterized proteins, many containing repeated short linear motifs or homorepeats. Such proteins may play a role in shell matrix construction or control of mineralization processes.</p> <p>Conclusions</p> <p>The organic matrix of <it>Lottia gigantea</it> shells is a complex mixture of proteins comprising possible homologs of some previously characterized mollusc shell proteins, but also many novel proteins with a possible function in biomineralization as framework building blocks or as regulatory components. We hope that this data set, the most comprehensive available at present, will provide a platform for the further exploration of biomineralization processes in molluscs.</p

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes

<p>Abstract</p> <p>Background</p> <p>The organic matrix of biominerals plays an important role in biomineral formation and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin, which is an important model organism for developmental biology and biomineralization, only few matrix components have been identified and characterized at the protein level. The recent publication of the <it>Strongylocentrotus purpuratus </it>genome sequence rendered possible not only the identification of possible matrix proteins at the gene level, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy, proteomic analysis.</p> <p>Results</p> <p>We identified 110 proteins as components of sea urchin test and spine organic matrix. Fourty of these proteins occurred in both compartments while others were unique to their respective compartment. More than 95% of the proteins were detected in sea urchin skeletal matrices for the first time. The most abundant protein in both matrices was the previously characterized spicule matrix protein SM50, but at least eight other members of this group, many of them only known as conceptual translation products previously, were identified by mass spectrometric sequence analysis of peptides derived from <it>in vitro </it>matrix degradation. The matrices also contained proteins implicated in biomineralization processes previously by inhibition studies using antibodies or specific enzyme inhibitors, such as matrix metalloproteases and members of the mesenchyme-specific MSP130 family. Other components were carbonic anhydrase, collagens, echinonectin, a α2-macroglobulin-like protein and several proteins containing scavenger receptor cysteine-rich domains. A few possible signal transduction pathway components, such as GTP-binding proteins, a semaphorin and a possible tyrosine kinase were also identified.</p> <p>Conclusion</p> <p>This report presents the most comprehensive list of sea urchin skeletal matrix proteins available at present. The complex mixture of proteins identified in matrices of the sea urchin skeleton may reflect many different aspects of the mineralization process. Because LC-MS/MS-based methods directly measures peptides our results validate many predicted genes and confirm the existence of the corresponding proteins. Considering the many newly identified matrix proteins, this proteomic study may serve as a road map for the further exploration of biomineralization processes in an important model organism.</p