BadiRate: Estimating Family Turnover Rates by Likelihood-Based Methods

Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites. Results: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset.

Sea-level changes and ammonite faunal turnover during the Lias/Dogger transition in the western Tethys

The aim of this paper was to investigate the possible connections between ammonite faunal turnover and the eustatic events recorded in Tethyan sequences during the middle Toarcian/early Bajocian time interval. For this we have analysed the biostratigraphic ranges, at the subzone level, of approximately 600 ammonite species belonging to 160 genera from several selected sections of the western Tethys (Mediterranean and Submediterranean provinces). The analysis of taxon ranges enabled us to plot curves for ammonite faunal turnovers, inter-subzonal distance, and diversity. Comparing the mentioned curves with Tethyan sequences [Hardenbol et al., 19981, we find that sea-level changes correlate well with origination and extinction events and faunal diversity. Most of the faunal turnovers correlate with stratigraphic events. Extinction events with their corresponding decrease in diversity correlate with regressive intervals and with major or minor sequence boundaries. Origination events and their corresponding increase in diversity were clearly connected with transgressions in Tethyan sequences. In several cases, the major sequence boundary and the subsequent transgressive phase correlate with major ammonite faunal turnover, whereas minor or medium sequence boundaries generally gave rise to minor or medium turnovers.

BadiRate: estimating family turnover rates by likelihood-based methods

Motivation: The comparative analysis of gene gain and loss rates is critical for understanding the role of natural selection and adaptation in shaping gene family sizes. Studying complete genome data from closely related species allows accurate estimation of gene family turnover rates. Current methods and software tools, however, are not well designed for dealing with certain kinds of functional elements, such as microRNAs or transcription factor binding sites. Results: Here, we describe BadiRate, a new software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. It implements two stochastic population models, which provide the appropriate statistical framework for testing hypothesis, such as lineage-specific gene family expansions or contractions. We have assessed the accuracy of BadiRate by computer simulations, and have also illustrated its functionality by analyzing a representative empirical dataset.

Carbon-isotope stratigraphy and ammonite faunal turnover for the Middle Jurassic in the Southern Iberian palaeomargin

Variations in the stable carbon-isotope ratio of marine and continental sediments can reflect changes in sink and flux modifications of the palaeocarbon cycle. Here we report carbon-isotope compositions of Middle Jurassic marine carbonates from the Betic Cordillera (southern Spain), which represents an ideal region to link the stable carbon-isotope curves directly to ammonite zones and subzones, and thereby for the first time achieve an accurate chronostratigraphic calibration. The five sections studied represent basin and high swell deposits of the Southern Iberian palaeomargin. We find a similar delta C-13 of carbonates between different oceanic areas, suggesting a homogeneous carbon-isotope oceanic reservoir through the Middle Jurassic. The Aalenian-Bajocian transition is a critical period in ammonite evolution; hence the Early Jurassic fauna are replaced by new ammonite families which become dominant throughout the Middle and Late Jurassic. For this reason, we compared the delta C-13 values of carbonates with ammonite diversity and extinction rates at different taxonomical levels in order to explore the possible relationship between the carbon cycle and ammonite evolution. The carbon-isotope values of carbonates are not exactly linearly correlated with the extinction rate and ammonite diversity, but the main faunal turnovers follow minimum delta C-13 values, where extinct taxa are replaced by new ones. Likewise, radiation episodes are associated with increasing delta C-13 values and with transgressive sea-level rise. All these data support the idea that perturbations in the global carbon cycle reflect rapid palaeoenvironmental changes. We made detailed analyses of these faunal turnovers, using them as a proxy to identify major palaeoenvironmental crises in their ecosystems forced by modification in the carbon cycle. (c) 2006 Elsevier B.V All rights reserved.

Context-dependent dual role of SKI8 homologs in mRNA synthesis and turnover.

Eukaryotic mRNA transcription and turnover is controlled by an enzymatic machinery that includes RNA polymerase II and the 3' to 5' exosome. The activity of these protein complexes is modulated by additional factors, such as the nuclear RNA polymerase II-associated factor 1 (Paf1c) and the cytoplasmic Superkiller (SKI) complex, respectively. Their components are conserved across uni- as well as multi-cellular organisms, including yeast, Arabidopsis, and humans. Among them, SKI8 displays multiple facets on top of its cytoplasmic role in the SKI complex. For instance, nuclear yeast ScSKI8 has an additional function in meiotic recombination, whereas nuclear human hSKI8 (unlike ScSKI8) associates with Paf1c. The Arabidopsis SKI8 homolog VERNALIZATION INDEPENDENT 3 (VIP3) has been found in Paf1c as well; however, whether it also has a role in the SKI complex remains obscure so far. We found that transgenic VIP3-GFP, which complements a novel vip3 mutant allele, localizes to both nucleus and cytoplasm. Consistently, biochemical analyses suggest that VIP3-GFP associates with the SKI complex. A role of VIP3 in the turnover of nuclear encoded mRNAs is supported by random-primed RNA sequencing of wild-type and vip3 seedlings, which indicates mRNA stabilization in vip3. Another SKI subunit homolog mutant, ski2, displays a dwarf phenotype similar to vip3. However, unlike vip3, it displays neither early flowering nor flower development phenotypes, suggesting that the latter reflect VIP3's role in Paf1c. Surprisingly then, transgenic ScSKI8 rescued all aspects of the vip3 phenotype, suggesting that the dual role of SKI8 depends on species-specific cellular context.

Effect of physical exercise on glycogen turnover and net substrate utilization according to the nutritional state.

To determine the metabolic effects of a single bout of exercise performed after a meal or in the fasting state, nine healthy subjects were studied over two 8-h periods during which net substrate oxidation was monitored by indirect calorimetry. On one occasion, exercise was performed 90 min after ingestion of a meal labeled with [U-13C]glucose [protocol meal-exercise (M-E)]. On the second occasion, exercise was performed after an overnight fast and was followed 30 min later by ingestion of an identical meal [protocol exercise-meal (E-M)]. Energy balances were similar in both protocols, but carbohydrate balance was positive (42.2 +/- 5.1 g), and lipid balance was negative (-11.1 +/- 2.0) during E-M, whereas they were nearly even during M-E. Total glycogen synthesis was calculated as carbohydrate intake minus oxidation of exogenous 13C-labeled carbohydrate (calculated from 13CO2 production). Total glycogen synthesis was increased by 90% (from 47.6 +/- 3.8 to 90.7 +/- 5.4 g, P < 0.0001) during E-M vs. M-E. Endogenous glycogen breakdown was calculated as net carbohydrate oxidation minus oxidation of exogenous carbohydrate and was increased by 44% (from 35.8 +/- 5.6 to 51.7 +/- 6.6 g, P < 0.004) during E-M. It is concluded that exercise performed in the fasting state stimulates glycogen turnover and fat oxidation.

Origins of production errors and significance of employee empowerment in reducing production error amount in sheet metal fabricating industry

The market place of the twenty-first century will demand that manufacturing assumes a crucial role in a new competitive field. Two potential resources in the area of manufacturing are advanced manufacturing technology (AMT) and empowered employees. Surveys in Finland have shown the need to invest in the new AMT in the Finnish sheet metal industry in the 1990's. In this run the focus has been on hard technology and less attention is paid to the utilization of human resources. In manymanufacturing companies an appreciable portion of the profit within reach is wasted due to poor quality of planning and workmanship. The production flow production error distribution of the sheet metal part based constructions is inspectedin this thesis. The objective of the thesis is to analyze the origins of production errors in the production flow of sheet metal based constructions. Also the employee empowerment is investigated in theory and the meaning of the employee empowerment in reducing the overall production error amount is discussed in this thesis. This study is most relevant to the sheet metal part fabricating industrywhich produces sheet metal part based constructions for electronics and telecommunication industry. This study concentrates on the manufacturing function of a company and is based on a field study carried out in five Finnish case factories. In each studied case factory the most delicate work phases for production errors were detected. It can be assumed that most of the production errors are caused in manually operated work phases and in mass production work phases. However, no common theme in collected production error data for production error distribution in the production flow can be found. Most important finding was still that most of the production errors in each case factory studied belong to the 'human activity based errors-category'. This result indicates that most of the problemsin the production flow are related to employees or work organization. Development activities must therefore be focused to the development of employee skills orto the development of work organization. Employee empowerment gives the right tools and methods to achieve this.

On-Line Analytical Processing of Inventory Turnover

Operatiivisen tiedon tuottaminen loppukäyttäjille analyyttistä tarkastelua silmällä pitäen aiheuttaa ongelmia useille yrityksille. Diplomityö pyrkii ratkaisemaan ko. ongelman Teleste Oyj:ssä. Työ on jaettu kolmeen pääkappaleeseen. Kappale 2 selkiyttää On-Line Analytical Processing (OLAP)- käsitteen. Kappale 3 esittelee muutamia OLAP-tuotteiden valmistajia ja heidän arkkitehtuurejaan sekä tyypillisten sovellusalueiden lisäksi huomioon otettavia asioita OLAP käyttöönoton yhteydessä. Kappale 4, tuo esille varsinaisen ratkaisun. Teknisellä arkkitehtuurilla on merkittävä asema ratkaisun rakenteen kannalta. Tässä on sovellettu Microsoft:n tietovarasto kehysrakennetta. Kappaleen 4 edetessä, tapahtumakäsittelytieto muutetaan informaatioksi ja edelleen loppukäyttäjien tiedoksi. Loppukäyttäjät varustetaan tehokkaalla ja tosiaikaisella analysointityökalulla moniulotteisessa ympäristössä. Vaikka kiertonopeus otetaan työssä sovellusesimerkiksi, työ ei pyri löytämään optimaalista tasoa Telesten varastoille. Siitä huolimatta eräitä parannusehdotuksia mainitaan.

Management Control for Corporate Sustainability Execution: The Role of Employee Compensation

The research described in this thesis examines the characteristics, the benefits and the challenges associated with the implementation of management accounting systems in the field of Corporate Social Responsibility (CSR). Applied to the CSR context, management accounting relates to the identification, elaboration and communication of information about an organization's interactions with the society and the environment. Based on this information, firms are able to make decisions to achieve social and environmental objectives and provide evidence justifying the benefits and the costs of such actions. The study begins by focusing on green management and exploring the characteristics of Environmental Management Accounting (EMA) systems within firms. The first chapter informs the reader about the growing body of EMA research and reveals unexplored relevant aspects that need to be further investigated. The work also emphasizes the importance of developing new theoretical hypotheses and appropriate research designs to empirically tackle new aspects of EMA and gain understanding on the use of these practices. Subsequently, given the acknowledged importance of control systems in influencing the behaviour of individuals within organizations, the remaining two chapters of the dissertation focus on the functioning of CSR-linked incentives assigned to employees in the form of compensation plans. The second chapter examines the determinants influencing corporate provision of incentives for the attainment of environmental targets. Empirical analysis of a sample of international firms reveals that companies are likely to use green incentives as mechanisms to increase the efficacy in contracting with their employees as well as to respond to social influences. Finally, the third chapter investigates the effectiveness of contracting associated with the use of CSR-linked executive compensation. Empirical analysis of a sample of US-based companies shows that corporate choice to tie senior executives' pay to CSR targets promotes the firm's CSR performance. Cette thèse examine les caractéristiques, avantages et défis associés à l'utilisation des systèmes de contrôle de gestion dans le domaine de la Responsabilité Sociale des Entreprises (RSE). Dans le contexte de la RSE, les activités du contrôle de gestion impliquent l'identification, l'élaboration et la communication d'informations qui concernent les interactions des organisations avec la société et l'environnement. Avec ces informations les entreprises sont en mesure de prendre des décisions visant à atteindre les objectifs sociaux et environnementaux de l'organisation et de documenter les bénéfices et coûts de ces actions. Dès le début, la thèse se concentre sur les caractéristiques des systèmes de contrôle de gestion environnementale au sein des entreprises. Le premier chapitre passe en revue la littérature existante et révèle des aspects inexplorés. Pour ce faire, le travail suggère le développement de nouvelles théories ainsi que l'utilisation de méthodes appropriées. Ces dernières doivent permettre d'aborder empiriquement de nouveaux aspects des systèmes de contrôle environnemental et faciliter la compréhension sur l'utilisation de ces pratiques. Considérant l'importance des systèmes de contrôle pour influencer le comportement des individus au sein des organisations, la suite du travail se concentre sur le fonctionnement des contrats de rémunération des employées liées aux résultats de la RSE. Plus particulièrement, le deuxième chapitre examine les facteurs qui influencent la décision des entreprises d'assigner des objectifs environnementaux aux employées. L'analyse empirique d'un échantillon d'entreprises internationales montre que les entreprises sont susceptibles d'utiliser des mécanismes incitatifs écologiques pour augmenter l'efficacité des contrats ainsi que pour répondre aux influences sociales. Finalement, le troisième chapitre analyse l'efficacité des contrats de rémunération des dirigeants liés aux résultats de la RSE. L'analyse empirique d'un échantillon de sociétés américaines indique que le choix de l'entreprise de lier la rémunération des dirigeants à des objectifs de la RSE favorise la performance RSE de l'organisation.

Reggie-1/Flotillin-2 regulates integrin trafficking and focal adhesion turnover via Rab11a.

Reggies/flotillins are implicated in trafficking of membrane proteins to their target sites and in the regulation of the Rab11a-dependent targeted recycling of E-cadherin to adherens junctions (AJs). Here we demonstrate a function of reggies in focal adhesion (FA) formation and α5- and β1-integrin recycling to FAs. Downregulation of reggie-1 in HeLa and A431 cells by siRNA and shRNA increased the number of FAs, impaired their distribution and modified FA turnover. This was coupled to enhanced focal adhesion kinase (FAK) and Rac1 signaling and gain in plasma membrane motility. Wild type and constitutively-active (CA) Rab11a rescued the phenotype (normal number of FAs) whereas dominant-negative (DN) Rab11a mimicked the loss-of-reggie phenotype in control cells. That reggie-1 affects integrin trafficking emerged from the faster loss of internalized antibody-labeled β1-integrin in reggie-deficient cells. Moreover, live imaging using TIRF microscopy revealed vesicles containing reggie-1 and α5- or β1-integrin, trafficking close to the substrate-near membrane and making kiss-and-run contacts with FAs. Thus, reggie-1 in interaction with Rab11a controls Rac1 and FAK activation and coordinates the targeted recycling of α5- and β1-integrins to FAs to regulate FA formation and membrane dynamics.

The age of the"Grande Coupure" mammal turnover: New constraints from the Eocene Oligocene record of the Eastern Ebro Basin (NE Spain.)

The Grande Coupure represents a major terrestrial faunal turnover recorded in Eurasia associated with the overall climate shift at the Eocene-Oligocene transition. During this event, a large number of European Eocene endemic mammals became extinct and new Asian immigrants appeared. The absolute age of the Grande Coupure, however, has remained controversial for decades. The Late Eocene-Oligocene continental record of the Eastern Ebro Basin (NE Spain) constitutes a unique opportunity to build a robust magnetostratigraphy- based chronostratigraphy which can contribute with independent age constraints for this important turnover. This study presents new magnetostratigraphic data of a 495-m-thick section (Moià-Santpedor) that ranges from 36.1 Ma to 33.3 Ma. The integration of the new results with previous litho- bio- and magnetostratigraphic records of the Ebro Basin yields accurate ages for the immediately pre- and post-Grand Coupure mammal fossil assemblages found in the study area, bracketing the Grande Coupure to an age embracing the Eocene-Oligocene transition, with a maximum allowable lag of 0.5 Myr with respect to this boundary. The shift to drier conditions that accompanied the global cooling at the Eocene-Oligocene transition probably determined the sedimentary trends in the Eastern Ebro Basin. The occurrence and expansion of an amalgamated-channel sandstone unit is interpreted as the forced response of the fluvial fan system to the transient retraction of the central-basin lake systems. The new results from the Ebro Basin allow us to revisit correlations for the controversial Eocene-Oligocene record of the Hampshire Basin (Isle of Wight, UK), and their implications for the calibration of the Mammal Palaeogene reference levels MP18 to MP21.

Labour segregation and immigrant and native-born wage distributions in Spain: an analysis using matched employer-employee data

This article carries out an empirical examination of the origin of the differences between immigrant and native-born wage structures in the Spanish labour market. Especial attention is given in the analysis to the role played by occupational and workplace segregation of immigrants. Legal immigrants from developing countries exhibit lower mean wages and a more compressed wage structure than native-born workers. By contrast, immigrants from developed countries display higher mean wages and a more dispersed wage structure. The main empirical finding is that the disparities in the wage distributions for the native-born and both groups of immigrants are largely explained by their different observed characteristics, with a particularly important influence in this context of workplace and, particularly, occupational segregation.

Workplace Social Capital and Employee Health

Työyhteisön sosiaalinen pääoma ja työntekijöiden terveys Monien tutkimusten mukaan sosiaalinen pääoma vaikuttaa terveyteen. Vaikka työssä käyvä väestönosa on merkittävän osan valveillaoloajastaan työyhteisössä, siellä kertyvää sosiaalista pääomaa on toistaiseksi tutkittu vähän. Tässä tutkimuksessa selvitettiin työyhteisön sosiaalisen pääoman ja kuntatyöntekijöiden terveyden välistä yhteyttä pitkittäisasetelmassa hyödyntäen Kuntasektorin henkilöstön seurantatutkimuksen aineistoa vuosilta 2000–2005. Yhteensä 48592 kuntatyöntekijää vastasi kyselyyn vuosina 2000–02 (vastausprosentti 68 %). Heistä 35914 (77 %) osallistui myös seurantatutkimukseen vuosina 2004–05. Tutkimuksessa kehitettiin kyselyyn perustuva työyhteisön sosiaalisen pääoman mittausmenetelmä. Työntekijän omaan arvioon perustuvan sosiaalisen pääoman lisäksi mitattiin työyhteisön sosiaalista pääomaa käyttämällä samassa työyhteisössä työskentelevien muiden työntekijöiden keskimääräistä arviota sosiaalisesta pääomasta. Terveyttä mitattiin kysymyksellä koetusta terveydestä. Masennusta arvioitiin sekä kysymällä lääkärin toteamasta masennuksesta että masennuslääkeostoilla Kelan lääkerekistereistä. Analyyseihin otettiin mukaan vain ne kuntatyöntekijät, jotka olivat lähtötilanteissa terveitä eli kokivat terveytensä hyväksi tai heillä ei ollut aiempaa diagnosoitua tai lääkehoitoa vaatinutta masennusta. Tulosten analysointiin käytettiin monitasomallinnusta. Tulokset vakioitiin sosiodemografisten tekijöiden ja terveyskäyttäytymisen suhteen. Neljän vuoden seurannassa sekä jatkuvasti vähäinen että vähenevä yksilön sosiaalinen pääoma työssä lisäsi riskiä koetun terveyden heikkenemiseen niillä kuntatyöntekijöillä, jotka eivät vaihtaneet työpaikkaa seurannan aikana ja jotka seurannan alussa kokivat terveytensä hyväksi. Tulos ei selittynyt sosiodemografisilla tekijöillä tai terveyskäyttäytymisen eroilla. Tuloksen merkittävyyttä tuki havainto, että myös työtoverien arvioon perustuva sosiaalinen pääoma ennusti oman terveyden huononemista seuranta-aikana. Niillä työntekijöillä, jotka työskentelivät sellaisissa työyhteisöissä, joissa koko seurannan ajan oli vähiten sosiaalista pääomaa, oli lähes 1.3 -kertainen riski terveyden heikentymiseen. Vähäinen omaan arvioon perustuva sosiaalinen pääoma työssä ennusti myös masennuksen ilmaantuvuutta lähtötilanteessa ei-masentuneilla lähes neljän vuoden seurannassa. Matalaan sosiaaliseen pääomaan liittyi 20–50 % suurempi todennäköisyys sairastua masennukseen seurannan aikana niin itseraportoidun lääkärin totea-man masennuksen kuin masennuslääkeostojen perusteella. Tätä tulosta ei kuitenkaan pystytty toistamaan käyttämällä oman arvion sijasta työtoverien arviota työyhteisön sosiaalisesta pääomasta. Tutkimusta sosiaalisen pääoman vaikutusta masennuksen ilmaantumiseen jatkettiin selvittämällä miten sosiaalisen pääoman eri ulottuvuudet vaikuttivat masennuksen ilmaantumiseen. Tulosten mukaan sosiaalisen pääoman vertikaalinen komponentti (työntekijöiden ja esimiesten välinen luottamus, vastavuoroisuus ja jaetut arvot ja normit, jotka edesauttavat yhteistyötä) sekä horisontaalinen komponentti (työntekijöiden välisissä suhteissa yhteistyöstä, luottamuksesta ja vastavuoroisuudesta syntyvä sosiaalinen pääoma) vaikuttivat itsenäisesti masennusriskiin. Tutkimuksen perusteella korkea työyhteisön sosiaalinen pääoma saattaa vaikuttaa edullisesti työntekijöiden terveyteen. Jos näin on, olisi tärkeää edistää työyhteisöjen sosiaalista pääomaa ja kannustaa sellaiseen toimintaan, joka lisää suvaitsevaisuutta, luottamusta ja vastavuoroisuutta sekä työntekijöiden kesken että työntekijöiden ja esimiesten välillä.