Saccharomyces cerevisiae as a model organism: a comparative study

Background: Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking. Methodology/Principal Findings: In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes. Conclusions/Significance: The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.

Interviewer and Respondent Survey Quality Effects in a CATI Panel

Especially in panel surveys, respondent attrition, respondent learning, and interviewer experience effects play a crucial role with respect to data quality. We examine three interview survey quality indicators in the same survey in a cross sectional as well as in a longitudinal way. In the cross sectional analysis we compare data quality in the mature original sample with that in a refreshment sample, surveyed in the same wave. Because in the same wave an interviewer survey was conducted, collecting attitudes on their socio demography, survey attitudes and burden measures, we are able to consider interviewer fixed effects as well. The longitudinal analysis gives more insight in the respondent learning effects with respect to the quality indicators considered by considering the very same respondents across waves. The Swiss Household Panel, a CATI survey representative of the Swiss residential population, forms an ideal modelling database: the interviewer - respondent assignment is random, both within and across waves. This design avoids possible confusion with other effects stemming from a non-random assignment of interviewers, e.g. area effects or effects from assigning the best interviewers to the hard cases. In order to separate interviewer, respondent and wave effects, we build cross-classified multilevel models.

The profile of general practitioners (GPs) who publish in selected family practice journals

Background: Providing support for research is one of the key issues in the ongoing attempts to improve Primary Care. However, when patient care takes up a significant part of a GP's time, conducting research is difficult. In this study we examine the working conditions and profile of GPs who publish in three leading medical journals and propose possible remedial policy actions. Findings: The authors of all articles published in 2006 and 2007 in three international Family Medicine journals - Annals of Family Medicine, Family Practice, and Journal of Family Practice - were contacted by E-mail. They were asked to complete a questionnaire investigating the following variables: availability of specific time for research, time devoted to research, number of patients attended, and university affiliation. Only GPs were included in the study. Three hundred and ten relevant articles published between 2006 and 2007 were identified and the authors contacted using a survey tool. 124 researchers responded to our questionnaire; 45% of respondents who were not GPs were excluded. On average GPs spent 2.52 days per week and 6.9 hours per day on patient care, seeing 45 patients per week. Seventy-five per cent of GPs had specific time assigned to research, on average 13 hours per week; 79% were affiliated to a university and 69% held teaching positions. Conclusions: Most GPs who publish original articles in leading journals have time specifically assigned to research as part of their normal working schedule. They see a relatively small number of patients. Improving the working conditions of family physicians who intend to investigate is likely to lead to better research results.

Can smartphones and tablets improve the management of childhood illness in Tanzania? A qualitative study from a primary health care worker's perspective.

BACKGROUND: The impact of the Integrated Management of Childhood Illness (IMCI) strategy has been less than anticipated because of poor uptake. Electronic algorithms have the potential to improve quality of health care in children. However, feasibility studies about the use of electronic protocols on mobile devices over time are limited. This study investigated constraining as well as facilitating factors that influence the uptake of a new electronic Algorithm for Management of Childhood Illness (ALMANACH) among primary health workers in Dar es Salaam, Tanzania. METHODS: A qualitative approach was applied using in-depth interviews and focus group discussions with altogether 40 primary health care workers from 6 public primary health facilities in the three municipalities of Dar es Salaam, Tanzania. Health worker's perceptions related to factors facilitating or constraining the uptake of the electronic ALMANACH were identified. RESULTS: In general, the ALMANACH was assessed positively. The majority of the respondents felt comfortable to use the devices and stated that patient's trust was not affected. Most health workers said that the ALMANACH simplified their work, reduced antibiotic prescription and gave correct classification and treatment for common causes of childhood illnesses. Few HWs reported technical challenges using the devices and complained about having had difficulties in typing. Majority of the respondents stated that the devices increased the consultation duration compared to routine practice. In addition, health system barriers such as lack of staff, lack of medicine and lack of financial motivation were identified as key reasons for the low uptake of the devices. CONCLUSIONS: The ALMANACH built on electronic devices was perceived to be a powerful and useful tool. However, health system challenges influenced the uptake of the devices in the selected health facilities.

Agile Methods in Small Software Projects

Agile software development methods are attempting to provide an answer to the software development industry's need of lighter weight, more agile processes that offer the possibility to react to changes during the software development process. The objective of this thesis is to analyze and experiment the possibility of using agile methods or practices also in small software projects, even in projects containing only one developer. In the practical part of the thesis a small software project was executed with some agile methods and practices that in the theoretical part of the thesis were found possible to be applied to the project. In the project a Bluetooth proxy application that is run in the S60 smartphone platform and PC was developed further to contain some new features. As a result it was found that certain agile practices can be useful even in the very small projects. The selection of the suitable practices depends on the project and the size of the project team.

BDNF promoter I methylation correlates between post-mortem human peripheral and brain tissues.

Several psychiatric disorders have been associated with CpG methylation changes in CG rich promoters of the brain-derived neurotrophic factor (BDNF) mainly by extracting DNA from peripheral blood cells. Whether changes in peripheral DNA methylation can be used as a proxy for brain-specific alterations remains an open question. In this study we aimed to compare DNA methylation levels in BDNF promoter regions in human blood cells, muscle and brain regions using bisulfite-pyrosequencing. We found a significant correlation between the levels of BDNF promoter I methylation measured in quadriceps and vPFC tissues extracted from the same individuals (n = 98, Pearson, r = 0.48, p = 4.5 × 10(-7)). In the hippocampus, BDNF promoter I and IV methylation levels were strongly correlated (Pearson, n = 37, r = 0.74, p = 1.4 × 10(-7)). We found evidence for sex-dependent effect on BDNF promoter methylation levels in the various tissues and blood samples. Taken together, these data indicate a strong intra-individual correlation between peripheral and brain tissue. They also suggest that sex determines methylation patterns in BDNF promoter region across different types of tissue, including muscle, brain, and blood.

Regional determinants of firm entry in a developing country

We analyse the determinants of firm entry in developing countries using Argentina as an illustrative case. Our main finding is that although most of the regional determinants used in previous studies analysing developed countries are also relevant here, there is a need for additional explanatory variables that proxy for the specificities of developing economies (e.g., poverty, informal economy and idle capacity).We also find evidence of a core-periphery pattern in the spatial structure of entry that seems to be mostly driven by differences in agglomeration economies. Since regional policies aiming to attract new firms are largely based on evidence from developed countries, our results raise doubts about the usefulness of such policies when applied to developing economies. JEL classification: R12, R30, C33. Key words: Firm entry, Argentina, count data models.

Functional error modeling for uncertainty quantification in hydrogeology

Approximate models (proxies) can be employed to reduce the computational costs of estimating uncertainty. The price to pay is that the approximations introduced by the proxy model can lead to a biased estimation. To avoid this problem and ensure a reliable uncertainty quantification, we propose to combine functional data analysis and machine learning to build error models that allow us to obtain an accurate prediction of the exact response without solving the exact model for all realizations. We build the relationship between proxy and exact model on a learning set of geostatistical realizations for which both exact and approximate solvers are run. Functional principal components analysis (FPCA) is used to investigate the variability in the two sets of curves and reduce the dimensionality of the problem while maximizing the retained information. Once obtained, the error model can be used to predict the exact response of any realization on the basis of the sole proxy response. This methodology is purpose-oriented as the error model is constructed directly for the quantity of interest, rather than for the state of the system. Also, the dimensionality reduction performed by FPCA allows a diagnostic of the quality of the error model to assess the informativeness of the learning set and the fidelity of the proxy to the exact model. The possibility of obtaining a prediction of the exact response for any newly generated realization suggests that the methodology can be effectively used beyond the context of uncertainty quantification, in particular for Bayesian inference and optimization.

Ilmastointikojeen uuden rakenneratkaisun markkinaselvitys

Työssä selvitetään korjaus- ja uudisrakentamista Suomessa sekä ilmastointikojeen valintaan vaikuttavia tekijöitä. Korjausrakentamisen osuus on kasvamassa ja tilan puute on korjausrakentamisessa usein ongelma. Lähtökohtana on tilaavan tahon idea uudesta ilmastointikojeesta, jonka rakenne soveltuu erityisesti korjausrakentamiseen. Tutkimuksessa halutaan selvittää ilmastointikojeen markkinaympäristöä ja uuden kojeen rakenneratkaisu. Tarkoitus on selvittää idean jatkokehitysmahdollisuus ja mielenkiinto asiakasympäristössä. Tietoja IV-kojeen rakenneratkaisuun ja korjausrakentamisen ongelmiin hankittiin empiirisellä kyselytutkimuksella. Kyselytutkimus koostui joukosta väittämiä. Kyselytutkimus suunnattiin rakennuttajille, urakoitsijoille ja iv-suunnittelijoille, joista suunnittelijoiden osuus on merkittävin. Tutkimus toteutettiin sähköpostikyselynä ja haastatteluina. Kaikkiaan saatiin 124 analysoitavaa vastausta. Tutkimuksessa kävi selville, että uudelle rakenneratkaisulle on kysyntää. Vastaajat olivat erityisen kiinnostuneita kojeesta, joka saastaa tilaa ja on helppo asentaa. Työ tuotti selvityksen yrityksen tuotekehitysprojektin paatoksenteon tueksi perustuen kyselytutkimuksen vastauksiin.

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In this chapter, we examine the multiple dimensions of declarations of fertility in-tention in order to provide a critical reading of currently used indicators of the childbearing decision-making process. Using a qualitative approach, we pay atten-tion to the complexity of the process through which individuals make (or fail to make) plans regarding their reproductive future. The data are a series of compara-ble in-depth interviews conducted in a number of European countries with varying fertility levels, and differing normative and institutional contexts. First, we ana-lyze the meanings that respondents attribute to their childbearing intentions, pay-ing particular attention to uncertain intentions that are often underanalyzed. Se-cond, we study the ways in which individuals vary in holding to their intentions over time, and consider why they might change their minds, even over relatively short periods of time. Third, we examine how several aspects of the larger social context (attitudes towards having children, family policy, norms related to the di-vision of labor, norms about the timing of children) shape fertility intentions.

Differential monocular vs. binocular pupil responses from melanopsin-based photoreception in patients with anterior ischemic optic neuropathy.

We examined the effect of anterior ischemic optic neuropathy (AION) on the activity of intrinsically photosensitive retinal ganglion cells (ipRGCs) using the pupil as proxy. Eighteen patients with AION (10 unilateral, 8 bilateral) and 29 age-matched control subjects underwent chromatic pupillometry. Red and blue light stimuli increasing in 0.5 log steps were presented to each eye independently under conditions of dark and light adaptation. The recorded pupil contraction was plotted against stimulus intensity to generate scotopic and photopic response curves for assessment of synaptically-mediated ipRGC activity. Bright blue light stimuli presented monocularly and binocularly were used for melanopsin activation. The post-stimulus pupil size (PSPS) at the 6th second following stimulus offset was the marker of intrinsic ipRGC activity. Finally, questionnaires were administered to assess the influence of ipRGCs on sleep. The pupil response and PSPS to all monocularly-presented light stimuli were impaired in AION eyes, indicating ipRGC dysfunction. To binocular light stimulation, the PSPS of AION patients was similar to that of controls. There was no difference in the sleep habits of the two groups. Thus after ischemic injury to one or both optic nerves, the summated intrinsic ipRGC activity is preserved when both eyes receive adequate light exposure.

A territorial approach to R&D subsidies: Empirical evidence for Catalonian firms

Using a database of 2,263 responses to R&D public calls in Catalonia, during the period 2007–2010, this paper proceeds to analyse the potential interaction of the territorial and policy dimensions with the propensity to apply for, and be awarded, a public R&D subsidy. Controlling for characteristics at the firm and project level, we estimate models using a twostep procedure. In the first step, our results suggest that large firms which export and which belong to high-tech manufactures are more likely to participate in a public R&D call. Furthermore, both urban location and past experience of such calls have a positive effect. Our territorial proxy of information spillovers shows a positive sign, but this is only significant at intra-industry level. Membership of one of the sectors prioritized by the Catalan government, perhaps surprisingly, does not have a significant impact. In the second step, our results show that cooperative projects, SMEs or old firms shows a positive effect on the probability of obtaining a public subsidy. Finally, the cluster policy does not show a clear relationship with the public R&D call, suggesting that cluster policies and R&D subsidies follow different goals. Our results are in line with previous results in the literature, but they highlight the unequal territorial distribution of the firms which apply and the fact that policymakers should interlink the decision criteria for their public call with other policies.

Assessing trends in insured losses from floods in Spain 1971-2008

Economic impacts from floods have been increasing over recent decades, a fact often attributed to a changing climate. On the other hand, there is now a significant body of scientific scholarship all pointing towards increasing concentrations and values of assets as the principle cause of the increasing cost of natural disasters. This holds true for a variety of perils and across different jurisdictions. With this in mind, this paper examines the time history of insured losses from floods in Spain between 1971 and 2008. It as- sesses whether any discernible residual signal remains after adjusting the data for the increase in the number and value of insured assets over this period of time. Data on insured losses from floods were sourced from Consorcio de Com- pensacíon de Seguros (CCS). Although a public institution, CCS compensates homeowners for the damage produced by floods, and thus plays a role similar to that of a private insurance company. Insured losses were adjusted using two proxy measures: first, changes in the total amount of annual surcharges (premiums) paid by customers to CCS, and secondly, changes in the total value of dwellings per year. The adjusted data reveals no significant trend over the period 1971-2008 and serves again to confirm that at this juncture, societal in- fluences remain the prime factors driving insured and economic losses from natural disasters.

Organizational change - the personnel perpective Case: Nordea - Financial Institutions

Tutkimuksen tavoite Tutkimuksen tavoite oli kerätä FI:n johdolle tietoa henkilöstön suhtautumisesta organisaatiomuutokseen. Tutkimus toimii pohjana muutosprosessin kriittiselle tarkastelulle ja mahdollisille muutoksille resurssien kohdentamisessa. Tutkimusmenetelmä Organisaatiomuutosta käsittelevä kirjallisuus muodosti tutkielman teoriapohjan. Tutkimuksen aineisto kerättiin kyselylomakkeella FI:n henkilöstölle ja neljällä haastattelulla henkilöstön ja johdon kanssa. Johtopäätökset Yleisesti tuloksista on nähtävissä, että vastaajat ovat aluksi vastustaneet muutosta, vaikka muutos itsessään onkin nähty positiivisena kehityksenä. Vastarintaa ovat aiheuttaneet pääasiallisesti muutoksen johtamisen tyyli ja tiedotuksen kokeminen riittämättömänä.

Mortality risk associated with underweight : a census-linked cohort of 31,578 individuals with up to 32 years of follow-up

BACKGROUND: In contrast to obesity, information on the health risks of underweight is sparse. We examined the long-term association between underweight and mortality by considering factors possibly influencing this relationship. METHODS: We included 31,578 individuals aged 25-74 years, who participated in population based health studies between 1977 and 1993 and were followed-up for survival until 2008 by record linkage with the Swiss National Cohort (SNC). Body Mass Index (BMI) was calculated from measured (53% of study population) or self-reported height and weight. Underweight was defined as BMI < 18.5 kg/m2. Cox regression models were used to determine mortality Hazard Ratios (HR) of underweight vs. normal weight (BMI 18.5- < 25.0 kg/m2). Covariates were study, sex, smoking, healthy eating proxy, sports frequency, and educational level. RESULTS: Underweight individuals represented 3.0% of the total study population (n = 945), and were mostly women (89.9%). Compared to normal weight, underweight was associated with increased all-cause mortality (HR: 1.37; 95% CI: 1.14-1.65). Increased risk was apparent in both sexes, regardless of smoking status, and mainly driven by excess death from external causes (HR: 3.18; 1.96-5.17), but not cancer, cardiovascular or respiratory diseases. The HR were 1.16 (0.88-1.53) in studies with measured BMI and 1.59 (1.24-2.05) with self-reported BMI. CONCLUSIONS: The increased risk of dying of underweight people was mainly due to an increased mortality risk from external causes. Using self-reported BMI may lead to an overestimation of mortality risk associated with underweight.