The origins, evolution, and functional potential of alternative splicing in vertebrates.

Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.

EsPal: One-stop shopping for Spanish word properties

This article introduces EsPal: a Web-accessible repository containing a comprehensive set of properties of Spanish words. EsPal is based on an extensible set of data sources, beginning with a 300 million token written database and a 460 million token subtitle database. Properties available include word frequency, orthographic structure and neighborhoods, phonological structure and neighborhoods, and subjective ratings such as imageability. Subword structure properties are also available in terms of bigrams and trigrams, bi-phones, and bi-syllables. Lemma and part-of-speech information and their corresponding frequencies are also indexed. The website enables users to either upload a set of words to receive their properties, or to receive a set of words matching constraints on the properties. The properties themselves are easily extensible and will be added over time as they become available. It is freely available from the following website: http://www.bcbl.eu/databases/espal

Forward Looking Banking Stress in EMU Countries

Based on contingent claims analysis, CCA, this paper tries to estimate the systemic risk build-up in the European Economic and Monetary Union, EMU countries using a market based measure distance-to-default, DtD. It analyzes the individual and aggregated series for a comprehensive set of banks in each eurozone country over the period 2004-Q4 to 2013-Q2. Given the structural differences in financial sector and banking regulations at national level, the indices provide a useful indicator for monitoring country specific banking vulnerability and stress. We find that average DtD indicators are intuitive, forward-looking and timely risk indicators. The underlying trend, fluctuations and correlations among indices help us analyze the interdependence while cross-sectional differences in DtD prior to crisis suggest banking sector fragility in peripheral EMU countries.

Reference intervals for 24 laboratory parameters determined in 24-hour urine collections.

BACKGROUND: Reference intervals for many laboratory parameters determined in 24-h urine collections are either not publicly available or based on small numbers, not sex specific or not from a representative sample. METHODS: Osmolality and concentrations or enzymatic activities of sodium, potassium, chloride, glucose, creatinine, citrate, cortisol, pancreatic α-amylase, total protein, albumin, transferrin, immunoglobulin G, α1-microglobulin, α2-macroglobulin, as well as porphyrins and their precursors (δ-aminolevulinic acid and porphobilinogen) were determined in 241 24-h urine samples of a population-based cohort of asymptomatic adults (121 men and 120 women). For 16 of these 24 parameters creatinine-normalized ratios were calculated based on 24-h urine creatinine. The reference intervals for these parameters were calculated according to the CLSI C28-A3 statistical guidelines. RESULTS: By contrast to most published reference intervals, which do not stratify for sex, reference intervals of 12 of 24 laboratory parameters in 24-h urine collections and of eight of 16 parameters as creatinine-normalized ratios differed significantly between men and women. For six parameters calculated as 24-h urine excretion and four parameters calculated as creatinine-normalized ratios no reference intervals had been published before. For some parameters we found significant and relevant deviations from previously reported reference intervals, most notably for 24-h urine cortisol in women. Ten 24-h urine parameters showed weak or moderate sex-specific correlations with age. CONCLUSIONS: By applying up-to-date analytical methods and clinical chemistry analyzers to 24-h urine collections from a large population-based cohort we provide as yet the most comprehensive set of sex-specific reference intervals calculated according to CLSI guidelines for parameters determined in 24-h urine collections.

Enhancing the development of military capabilities by a systems approach

The political environment of security and defence has changed radically in the Western industrialised world since the Cold War. As a response to these changes, since the beginning of the twenty-first century, most Western countries have adopted a ‘capabilities-based approach’ to developing and operating their armed forces. More responsive and versatile military capabilities must be developed to meet the contemporary challenges. The systems approach is seen as a beneficial means of overcoming traps in resolving complex real -world issues by conventional thinking. The main objectives of this dissertation are to explore and assess the means to enhance the development of military capabilities both in concept development and experimentation (CD&E) and in national defence materiel collaboration issues. This research provides a unique perspective, a systems approach, to the development areas of concern in resolving complex real-world issues. This dissertation seeks to increase the understanding of the military capability concept both as a whole and with in its life cycle. The dissertation follows the generic functionalist systems methodology by Jackson. The methodology applies a comprehensive set of constitutive rules to examine the research objectives. This dissertation makes contribution to current studies about military capability. It presents two interdepen dent conceptual capability models: the comprehensive capability meta-model (CCMM) and the holistic capability life cycle model (HCLCM). These models holistically and systematically complement the existing, but still evolving, understanding of military capability and its life cycle. In addition, this dissertation contributes to the scientific discussion of defence procurement in its broad meaning by introducing the holistic model about the national defence materiel collaboration between the defence forces, defence industry and academia. The model connects the key collaborative mechanisms, which currently work in isolation from each other, and take into consideration the unique needs of each partner. This dissertation contributes empirical evidence regarding the benefits of enterprise architectures (EA) to CD&E. The EA approach may add value to traditional concept development by increasing the clarity, consistency and completeness of the concept. The most important use considered for EA in CD&E is that it enables further utilisation of the concept created in the case project.

Thermal Properties of Dicalcium Lead Propionate Across the Prominent Transition Temperatures

The thermal transport properties, thermal diffusivity, thermal conductivity and specific heat capacity of Dicalcium Lead Propionate (DLP) crystal have been measured following a modified photopyroelectric thermal wave method. The measurements have been carried out with thermal waves propagating along the three principal symmetry directions, so as to bring out the anisotropy in these parameters. The variations of the above parameters through two prominent phase transition temperatures of this crystal have also been measured to understand the variation of these parameters as it undergoes ferroelectric phase transitions. In addition, complete thermal analysis and FTIR measurements have been done on the crystal to bring out the correlation of these results with the corresponding thermal transport properties. All these results are presented and discussed. The data presented in this paper form a comprehensive set of results on the thermal transport properties of this crystal.

The European organic food market - how to increase its transparency?

Der Europäische Markt für ökologische Lebensmittel ist seit den 1990er Jahren stark gewachsen. Begünstigt wurde dies durch die Einführung der EU-Richtlinie 2092/91 zur Zertifizierung ökologischer Produkte und durch die Zahlung von Subventionen an umstellungswillige Landwirte. Diese Maßnahmen führten am Ende der 1990er Jahre für einige ökologische Produkte zu einem Überangebot auf europäischer Ebene. Die Verbrauchernachfrage stieg nicht in gleichem Maße wie das Angebot, und die Notwendigkeit für eine Verbesserung des Marktgleichgewichts wurde offensichtlich. Dieser Bedarf wurde im Jahr 2004 von der Europäischen Kommission im ersten „Europäischen Aktionsplan für ökologisch erzeugte Lebensmittel und den ökologischen Landbau“ formuliert. Als Voraussetzung für ein gleichmäßigeres Marktwachstum wird in diesem Aktionsplan die Schaffung eines transparenteren Marktes durch die Erhebung statistischer Daten über Produktion und Verbrauch ökologischer Produkte gefordert. Die Umsetzung dieses Aktionsplans ist jedoch bislang nicht befriedigend, da es auf EU-Ebene noch immer keine einheitliche Datenerfassung für den Öko-Sektor gibt. Ziel dieser Studie ist es, angemessene Methoden für die Erhebung, Verarbeitung und Analyse von Öko-Marktdaten zu finden. Geeignete Datenquellen werden identifiziert und es wird untersucht, wie die erhobenen Daten auf Plausibilität untersucht werden können. Hierzu wird ein umfangreicher Datensatz zum Öko-Markt analysiert, der im Rahmen des EU-Forschungsprojektes „Organic Marketing Initiatives and Rural Development” (OMIaRD) erhoben wurde und alle EU-15-Länder sowie Tschechien, Slowenien, Norwegen und die Schweiz abdeckt. Daten für folgende Öko-Produktgruppen werden untersucht: Getreide, Kartoffeln, Gemüse, Obst, Milch, Rindfleisch, Schaf- und Ziegenfleisch, Schweinefleisch, Geflügelfleisch und Eier. Ein zentraler Ansatz dieser Studie ist das Aufstellen von Öko-Versorgungsbilanzen, die einen zusammenfassenden Überblick von Angebot und Nachfrage der jeweiligen Produktgruppen liefern. Folgende Schlüsselvariablen werden untersucht: Öko-Produktion, Öko-Verkäufe, Öko-Verbrauch, Öko-Außenhandel, Öko-Erzeugerpreise und Öko-Verbraucherpreise. Zudem werden die Öko-Marktdaten in Relation zu den entsprechenden Zahlen für den Gesamtmarkt (öko plus konventionell) gesetzt, um die Bedeutung des Öko-Sektors auf Produkt- und Länderebene beurteilen zu können. Für die Datenerhebung werden Primär- und Sekundärforschung eingesetzt. Als Sekundärquellen werden Publikationen von Marktforschungsinstituten, Öko-Erzeugerverbänden und wissenschaftlichen Instituten ausgewertet. Empirische Daten zum Öko-Markt werden im Rahmen von umfangreichen Interviews mit Marktexperten in allen beteiligten Ländern erhoben. Die Daten werden mit Korrelations- und Regressionsanalysen untersucht, und es werden Hypothesen über vermutete Zusammenhänge zwischen Schlüsselvariablen des Öko-Marktes getestet. Die Datenbasis dieser Studie bezieht sich auf ein einzelnes Jahr und stellt damit einen Schnappschuss der Öko-Marktsituation der EU dar. Um die Marktakteure in die Lage zu versetzen, zukünftige Markttrends voraussagen zu können, wird der Aufbau eines EU-weiten Öko-Marktdaten-Erfassungssystems gefordert. Hierzu wird eine harmonisierte Datenerfassung in allen EU-Ländern gemäß einheitlicher Standards benötigt. Die Zusammenstellung der Marktdaten für den Öko-Sektor sollte kompatibel sein mit den Methoden und Variablen der bereits existierenden Eurostat-Datenbank für den gesamten Agrarmarkt (öko plus konventionell). Eine jährlich aktualisierte Öko-Markt-Datenbank würde die Transparenz des Öko-Marktes erhöhen und die zukünftige Entwicklung des Öko-Sektors erleichtern. ---------------------------

Controlling the transport of an ion: classical and quantum mechanical solutions

The accurate transport of an ion over macroscopic distances represents a challenging control problem due to the different length and time scales that enter and the experimental limitations on the controls that need to be accounted for. Here, we investigate the performance of different control techniques for ion transport in state-of-the-art segmented miniaturized ion traps. We employ numerical optimization of classical trajectories and quantum wavepacket propagation as well as analytical solutions derived from invariant based inverse engineering and geometric optimal control. The applicability of each of the control methods depends on the length and time scales of the transport. Our comprehensive set of tools allows us make a number of observations. We find that accurate shuttling can be performed with operation times below the trap oscillation period. The maximum speed is limited by the maximum acceleration that can be exerted on the ion. When using controls obtained from classical dynamics for wavepacket propagation, wavepacket squeezing is the only quantum effect that comes into play for a large range of trapping parameters. We show that this can be corrected by a compensating force derived from invariant based inverse engineering, without a significant increase in the operation time.

The EU-EFIGE/Bruegel-unicredit dataset. Bruegel Working Paper 2012/13, October 2012

This paper describes the EU-EFIGE/Bruegel-UniCredit dataset (in short the EFIGE dataset), a database recently collected within the EFIGE project (European Firms in a Global Economy: internal policies for external competitiveness) supported by the Directorate General Research of the European Commission through its 7th Framework Programme and coordinated by Bruegel. • The database, for the first time in Europe, combines measures of firms’ international activities (eg exports, outsourcing, FDI, imports) with quantitative and qualitative information on about 150 items ranging from R&D and innovation, labour organisation, financing and organisational activities, and pricing behaviour. Data consists of a representative sample (at the country level for the manufacturing industry) of almost 15,000 surveyed firms (above 10 employees) in seven European economies (Germany, France, Italy, Spain, United Kingdom, Austria, Hungary). Data was collected in 2010, covering the years from 2007 to 2009. Special questions related to the behaviour of firms during the crisis were also included in the survey. • We illustrate the construction and usage of the dataset, capitalising on the experience of researchers who have exploited the data within the EFIGE project. Importantly, the document also reports a comprehensive set of validation measures that have been used to assess the comparability of the survey data with official statistics. A set of descriptive statistics describing the EFIGE variables within (and across) countries and industries is also provided.

The addition reaction between silylene and ethyne: further isotope studies, pressure dependence studies, and quantum chemical calculations

Time-resolved kinetic studies of the reaction of dideutero-silylene, SiD2, generated by laser flash photolysis of phenylsilane-d(3), have been carried out to obtain rate constants for its bimolecular reaction with C2H2. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at five temperatures in the range 297-600 K. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equation log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.05 +/- 0.05) + (3.43 +/- 0.36 kJ mol(-1))/RT ln 10. The rate constants were used to obtain a comprehensive set of isotope effects by comparison with earlier obtained rate constants for the reactions of SiH2 with C2H2 and C2D2. Additionally, pressure-dependent rate constants for the reaction of SiH2 with C2H2 in the presence of He (1-100 Tort) were obtained at 300, 399, and 613 K. Quantum chemical (ab initio) calculations of the SiC2H4 reaction system at the G3 level support the initial formation of silirene, which rapidly isomerizes to ethynylsilane as the major pathway. Reversible formation of vinylsilylene is also an important process. The calculations also indicate the involvement of several other intermediates, not previously suggested in the mechanism. RRKM calculations are in semiquantitative agreement with the pressure dependences and isotope effects suggested by the ab initio calculations, but residual discrepancies suggest the possible involvement of the minor reaction channel, SiH2 + C2H2 - SWPO + C2H4. The results are compared and contrasted with previous studies of this reaction system.

Palaeovegetation in China during the late Quaternary: Biome reconstructions based on a global scheme of plant functional types

Two previous reconstructions of palaeovegetation across the whole of China were performed using a simple classification of plant functional types (PFTs). Now a more explicit, global PFT classification scheme has been developed, and a substantial number of additional pollen records have become available. Here we apply the global scheme of PFTs to a comprehensive set of pollen records available from China to test the applicability of the global scheme of PFTs in China, and to obtain a well-founded reconstruction of changing palaeovegetation patterns. A total of 806 pollen surface samples, 188 mid-Holocene (MH, 6000 14C yr BP) and 50 last glacial maximum (LGM, 18,000 14C yr BP) pollen records were used to reconstruct vegetation patterns in China, based on a new global classification system of PFTs and a standard numerical technique for biome assignment (biomization). The biome reconstruction based on pollen surface samples showed convincing agreement with present potential natural vegetation. Coherent patterns of change in biome distribution between MH, LGM and present are observed. In the MH, cold and cool-temperate evergreen needleleaf forests and mixed forests, temperate deciduous broadleaf forest, and warm-temperate evergreen broadleaf and mixed forest in eastern China were shifted northward by 200–500 km. Cold-deciduous forest in northeastern China was replaced by cold evergreen needleleaf forest while in central northern China, cold-deciduous forest was present at some sites now occupied by temperate grassland and desert. The forest–grassland boundary was 200–300 km west of its present position. Temperate xerophytic shrubland, temperate grassland and desert covered a large area on the Tibetan Plateau, but the area of tundra was reduced. Treeline was 300–500 m higher than present in Tibet. These changes imply generally warmer winters, longer growing seasons and more precipitation during the MH. Westward shifts of the forest–shrubland–grassland and grassland–desert boundaries imply greater moisture availability in the MH, consistent with a stronger summer monsoon. During the LGM, in contrast, cold-deciduous forest, cool-temperate evergreen needleleaf forest, cool mixed forests, warm-temperate evergreen broadleaf and mixed forest in eastern China were displaced to the south by 300–1000 km, while temperate deciduous broadleaf forest, pure warm-temperate evergreen forest, tropical semi-evergreen and evergreen broadleaf forests were restricted or absent from the mainland of southern China, implying colder winters than present. Strong shifts of temperate xerophytic shrubland, temperate grassland and desert to the south and east in northern and western China and on the Tibetan Plateau imply drier conditions than present.

Getting the measure of derivational morphology in adult speech a corpus analysis using MorphoQuantics

This paper describes the methodology used to compile a corpus called MorphoQuantics that contains a comprehensive set of 17,943 complex word types extracted from the spoken component of the British National Corpus (BNC). The categorisation of these complex words was derived primarily from the classification of Prefixes, Suffixes and Combining Forms proposed by Stein (2007). The MorphoQuantics corpus has been made available on a website of the same name; it lists 554 word-initial and 281 word-final morphemes in English, their etymology and meaning, and records the type and token frequencies of all the associated complex words containing these morphemes from the spoken element of the BNC, together with their Part of Speech. The results show that, although the number of word-initial affixes is nearly double that of word-final affixes, the relative number of each observed in the BNC is very similar; however, word-final affixes are more productive in that, on average, the frequency with which they attach to different bases is three times that of word-initial affixes. Finally, this paper considers how linguists, psycholinguists and psychologists may use MorphoQuantics to support their empirical work in first and second language acquisition, and clinical and educational research.

Micro Far-Infrared Reflectivity of CaNb(2)O(6) Single Crystal Fibers Grown by the Laser-Heated Pedestal Growth Technique

CaNb(2)O(6) single crystal fibers were grown by the laser-heated pedestal growth technique, directly from the starting reagents. Optically transparent fibers were obtained in the form of rods with elliptical cross-section, free from cracks, impurities, and secondary phases, with an average diameter of 0.4 mm and about 20 mm of length. The fibers grew within the orthorhombic Pbcn columbite structure, with the growth axis nearly parallel to the crystallographic a-direction. The parameters b and c were parallel to the shorter and larger ellipsis axes. A special setup using a microscope was developed to obtain the far-infrared reflectivity spectra of these micrometer-sized fibers, allowing the identification and assignment of 34 of the 38 polar phonons foreseen for the material. From these phonons, the intrinsic dielectric constant ( = 18.2) and quality factor ( of 185 THz) could be estimated, showing the potential of the material for applications in microwave circuitry. These results, along with previous polarized Raman data (Cryst. Growth Des. 2010, 10, 1569), allow us to present a comprehensive set of optical phonon modes and to discuss the potential use of designed CaNb(2)O(6) microcrystals in compact optical devices.

Measures of the welfare cost of inflation: a complete ordering

This paper presents three contributions to the literature on the welfare cost of ináation. First, it introduces a new sensible way of measuring this cost - that of a compensating variation in consumption or income, instead of the equivalent variation notion that has been extensively used in empirical and theoretical research during the past fiftt years. We Önd this new measure to be interestingly related to the proxy measure of the shopping-time welfare cost of ináation introduced by Simonsen and Cysne (2001). Secondly, it discusses for which money-demand functions this and the shopping-time measure can be evaluated in an economically meaningful way. And, last but not least, it completely orders a comprehensive set of measures of the welfare cost of ináation for these money-demand specification. All of our results are extended to an economy in which there are many types of monies present, and are illustrated with the log-log money-demand specification.

Common factors in Latin America's business cycles

This paper constructs new business cycle indices for Argentina, Brazil, Chile, and Mexico based on common dynamic factors extracted from a comprehensive set of sectoral output, external trade, fiscal and financial variables. The analysis spans the 135 years since the insertion of these economies into the global economy in the 1870s. The constructed indices are used to derive a business cyc1e chronology for these countries and characterize a set of new stylized facts. In particular, we show that ali four countries have historically displayed a striking combination of high business cyc1e volatility and persistence relative to advanced country benchmarks. Volatility changed considerably over time, however, being very high during early formative decades through the Great Depression, and again during the 1970s and ear1y 1980s, before declining sharply in three of the four countries. We also identify a sizeable common factor across the four economies which variance decompositions ascribe mostly to foreign interest rates and shocks to commodity terms of trade.