Falsification and corroboration of conceptual hydrological models using geophysical data

Geophysical data may provide crucial information about hydrological properties, states, and processes that are difficult to obtain by other means. Large data sets can be acquired over widely different scales in a minimally invasive manner and at comparatively low costs, but their effective use in hydrology makes it necessary to understand the fidelity of geophysical models, the assumptions made in their construction, and the links between geophysical and hydrological properties. Geophysics has been applied for groundwater prospecting for almost a century, but it is only in the last 20 years that it is regularly used together with classical hydrological data to build predictive hydrological models. A largely unexplored venue for future work is to use geophysical data to falsify or rank competing conceptual hydrological models. A promising cornerstone for such a model selection strategy is the Bayes factor, but it can only be calculated reliably when considering the main sources of uncertainty throughout the hydrogeophysical parameter estimation process. Most classical geophysical imaging tools tend to favor models with smoothly varying property fields that are at odds with most conceptual hydrological models of interest. It is thus necessary to account for this bias or use alternative approaches in which proposed conceptual models are honored at all steps in the model building process.

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software.

Two-dimensional probabilistic inversion of plane-wave electromagnetic data: Methodology, model constraints and joint inversion with electrical resistivity data

Probabilistic inversion methods based on Markov chain Monte Carlo (MCMC) simulation are well suited to quantify parameter and model uncertainty of nonlinear inverse problems. Yet, application of such methods to CPU-intensive forward models can be a daunting task, particularly if the parameter space is high dimensional. Here, we present a 2-D pixel-based MCMC inversion of plane-wave electromagnetic (EM) data. Using synthetic data, we investigate how model parameter uncertainty depends on model structure constraints using different norms of the likelihood function and the model constraints, and study the added benefits of joint inversion of EM and electrical resistivity tomography (ERT) data. Our results demonstrate that model structure constraints are necessary to stabilize the MCMC inversion results of a highly discretized model. These constraints decrease model parameter uncertainty and facilitate model interpretation. A drawback is that these constraints may lead to posterior distributions that do not fully include the true underlying model, because some of its features exhibit a low sensitivity to the EM data, and hence are difficult to resolve. This problem can be partly mitigated if the plane-wave EM data is augmented with ERT observations. The hierarchical Bayesian inverse formulation introduced and used herein is able to successfully recover the probabilistic properties of the measurement data errors and a model regularization weight. Application of the proposed inversion methodology to field data from an aquifer demonstrates that the posterior mean model realization is very similar to that derived from a deterministic inversion with similar model constraints.

Työpisteiden tiedonkäyttö ja hyödyntäminen osana palveluyhtiön johtamisjärjestelmää

Tutkimuksen tavoitteena oli etsiä kohdeorganisaation taustalla olevia tekijöitä, jotka joko edesauttavat tai estävät nykyisen johtamisjärjestelmän soveltamista, tiedon käyttöä ja hyödyntämistä organisaation työpisteissä. Kohdeorganisaatio on Varenso Oy, Tekniset tuotantopalvelut. Teoriaosiossa käsitellään tietojohtamiseen liittyvää käsitteistöä sekä tiedon luomiseen, johtamiseen ja hyödyntämiseen liittyviä tekijöitä. Johtamista lähestytään myös perustehtävän, strategian ja muutosvalmiuden, valta- ja organisaatiorakenteiden sekä informaatio- ohjauksen näkökulmasta. Lopuksi käsitellään suorituskykyä, tavoitteiden asettamista, mittaamista funktionaalisissa- ja prosessijohdetuissa organisaatioissa. Empiirisessä osiossa tehtiin kyselytutkimus. Tulokset analysoitiin monimuuttujamenetelmiä soveltaen ja löydettiin faktorit, joiden avulla on mahdollista vaikuttaa kohdeorganisaation toimintaan. Kyselytutkimuksen avulla tulkittiin organisaation tämän hetkistä suorituskykyä ja asemaa suhteessa tavoitteisiin. Tuloksena syntyi myös toimenpideehdotuksia.

Mapping the diagnosis axis of an interface terminology to the NANDA International Taxonomy

Background: Nursing terminologies are designed to support nursing practice but, as with any other clinical tool, they should be evaluated. Cross-mapping is a formal method for examining the validity of the existing controlled vocabularies. Objectives: The study aims to assess the inclusiveness and expressiveness of the nursing diagnosis axis of a newly implemented interface terminology by cross-mapping with the NANDA-I taxonomy. Design/Methods: The study applied a descriptive design, using a cross-sectional, bidirectional mapping strategy. The sample included 728 concepts from both vocabularies. Concept cross-mapping was carried out to identify one-to-one, negative, and hierarchical connections. The analysis was conducted using descriptive statistics. Results: Agreement of the raters" mapping achieved 97%. More than 60% of the nursing diagnosis concepts in the NANDA-I taxonomy were mapped to concepts in the diagnosis axis of the new interface terminology; 71.1% were reversely mapped. Conclusions: Main results for outcome measures suggest that the diagnosis axis of this interface terminology meets the validity criterion of cross-mapping when mapped from and to the NANDA-I taxonomy.

Psychotherapy for Personality Disorders in a Natural Setting: A Pilot Study over Two Years of Treatment.

Long-term assessment of the effects of psychotherapy for personality disorders (PDs) in a natural environment is an important task. Such research contributes to enlarge the practice-based evidence, embedded in broad collaborations between clinicians and researchers in psychotherapy for PDs. The present pilot study used rigorous assessment procedures and incorporated feedback loops of outcome information to the therapists in demonstrating the effects of psychotherapy for PD in a natural setting. The number of Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV), criteria for any PD was the primary outcome (along with psychological distress, depression, impulsiveness, and quality of life as secondary measures), assessed at intake, 6, 12, 18, and 24 months of psychotherapy for N = 13 patients with PD. Data were analyzed using hierarchical linear modeling. Results demonstrated a large pre-post effect (d = 2.22) for the observer-rated measure (primary outcome), and small to medium effects for the secondary outcomes; these results were corroborated by a steady decrease of symptoms over all five time points, which was significant for several outcomes. These results add a piece to the literature by demonstrating the effects of long-term psychotherapy for PDs in increasingly diverse contexts and suggest that practice-oriented research can be carried out in a collaborative and systematic manner.

Organisaation sisäinen yhteistyökyvykkyys. Case: Metso Paper, Jyväskylä

Tutkielman tarkoituksena oli yleisesti ymmärtää sisäistä yhteistyökyvykkyyttä ja sen roolia yrityksen menestystekijänä. Empiirisesti sisäistä yhteistyökyvykkyyttä tarkasteltiin case-organisaation, Metso Paper Jyväskylän, avulla. Tavoitteena oli selvittää, mistä sisäinen yhteistyökyvykkyys koostuu sekä siihen vaikuttavia kriittisiä tekijöitä. Myös käytännön keinoja ja sovelluksia etsittiin edistämään sisäistä yhteistyötä. Tutkielmassa käytettiin kvalitatiivista tutkimusotetta. Tiedon hankinnan strategiana oli tapaustutkimus ja tutkimusaineisto kerättiin teemahaastattelujen avulla. Saatu aineisto analysoitiin teemoittelun avulla. Teemoja etsittiin tekstistä teoriasta johdettujen oletusten ja empiriasta löydettyjen tekijöiden perusteella. Tutkimuksen tuloksena oli, että yhteistyökyvykkyys koostuu sekä yksilöön että organisaatioon liittyvistä tekijöistä. Yhteistyökyvykkyyden kriittisiä ja sitä estäviä tekijöitä olivat toiminnan painottuminen ulkoisiin suhteisiin, muodollinen ja monitasoinen organisaatiorakenne, organisaatiorakenteiden nopea muutostahti, toimintamallin yksisuuntaisuus, organisaatio- ja johtamiskulttuuri, joka ei tue yhteistyötä, ylimmän johdon ja operatiivisten toimintojen välinen kuilu, tiedon painottuminen tietojärjestelmiin, dialogin puute, kommunikoinnin yksisuuntaisuus ja erilaisista työkulttuureista aiheutuvat kommunikaatioesteet, yhteistyösuhteiden puute ja transaktiosuhteiden painottuminen sekä ryhmien sisäisen yhtenäisyyden vahvuus. Näiden tekijöiden esiin tuominen tuo uusia näkökulmia organisaation sisäisen yhteistyökyvykkyyden ymmärtämiseen ja kehittämiseen.

Polymorphisms in DNA-repair genes in a cohort of prostate cancer patients from different areas in Spain: heterogeneity between populations as a confounding factor in association studies

Background: Differences in the distribution of genotypes between individuals of the same ethnicity are an important confounder factor commonly undervalued in typical association studies conducted in radiogenomics. Objective: To evaluate the genotypic distribution of SNPs in a wide set of Spanish prostate cancer patients for determine the homogeneity of the population and to disclose potential bias. Design, Setting, and Participants: A total of 601 prostate cancer patients from Andalusia, Basque Country, Canary and Catalonia were genotyped for 10 SNPs located in 6 different genes associated to DNA repair: XRCC1 (rs25487, rs25489, rs1799782), ERCC2 (rs13181), ERCC1 (rs11615), LIG4 (rs1805388, rs1805386), ATM (rs17503908, rs1800057) and P53 (rs1042522). The SNP genotyping was made in a Biotrove OpenArrayH NT Cycler. Outcome Measurements and Statistical Analysis: Comparisons of genotypic and allelic frequencies among populations, as well as haplotype analyses were determined using the web-based environment SNPator. Principal component analysis was made using the SnpMatrix and XSnpMatrix classes and methods implemented as an R package. Non-supervised hierarchical cluster of SNP was made using MultiExperiment Viewer. Results and Limitations: We observed that genotype distribution of 4 out 10 SNPs was statistically different among the studied populations, showing the greatest differences between Andalusia and Catalonia. These observations were confirmed in cluster analysis, principal component analysis and in the differential distribution of haplotypes among the populations. Because tumor characteristics have not been taken into account, it is possible that some polymorphisms may influence tumor characteristics in the same way that it may pose a risk factor for other disease characteristics. Conclusion: Differences in distribution of genotypes within different populations of the same ethnicity could be an important confounding factor responsible for the lack of validation of SNPs associated with radiation-induced toxicity, especially when extensive meta-analysis with subjects from different countries are carried out.

The SwissLipids knowledgebase for lipid biology.

MOTIVATION: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it. RESULTS: To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology-SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge. AVAILABILITY: SwissLipids is freely available at http://www.swisslipids.org/. CONTACT: alan.bridge@isb-sib.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species. RESULTS: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence. CONCLUSION: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection. REVIEWERS: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

What Role Does Sleep Play in Weight Gain in the First Semester of University?

We hypothesized that shorter sleep durations and greater variability in sleep patterns are associated with weight gain in the first semester of university. Students (N = 132) completed daily sleep diaries for 9 weeks, completed the MEQ (chronotype) and CES-D (depressed mood) at week 9, and self-reported weight/height (weeks 1 & 9). Mean and variability scores were calculated for sleep duration (TST, TSTv), bedtime (BT, BTv), and wake time (WT, WTv). An initial hierarchical regression evaluated (block 1) sex, ethnicity; (block 2) depressed mood, chronotype; (block 3) TST; (block 4) BT, WT; and (block 5; R(2) change = 0.09, p = 0.005) TSTv, BTv, WTv with weight change. A sex-by-TSTv interaction was found. A final model showed that ethnicity, TST, TSTv, and BTv accounted for 31% of the variance in weight change for males; TSTv was the most significant contributor (R(2) change = 0.21, p < 0.001). Daily variability in sleep duration contributes to males' weight gain. Further investigation needs to examine sex-specific outcomes for sleep and weight.

Aasian toinen todellisuus - Suomen suurlähetystöjen monikulttuurisen johtamisen haasteet

Monikulttuurinen johtaminen on globalisaation ja nopean kansainvälistymisen takia erittäin ajankohtainen aihe. Suomessa sitä on kuitenkin tutkittu vasta vähän. Tämän tutkimuksen tarkoituksena on tutkia Suomen suurlähetystöjenmonikulttuurista johtamista Aasian eri kohdemaissa ja kulttuureissa sekä ottaa osaa tieteelliseen keskusteluun monikulttuurisesta johtamisesta. Tutkimuksen kohdemaiksi on valittu neljä Aasian maata, jotka ovat tällä hetkellä hyvin ajankohtaisia nopean talouskasvunsa takia. Itä-Aasiasta mukana ovat Etelä-Korea (Korean tasavalta), Japani ja Kiinan kansantasavalta sekä Kaakkois-Aasiasta tutkimuksessa mukana on Malesia. Tämä tutkimus on laadullinen tutkimus, jonka aineisto koostuu kahdesta laadulliselle tutkimukselle poikkeuksellisesta avoimesta kyselystä, jotka on lähetetty edellä mainittujen maiden suurlähettiläille eri kohdemaihin. Analyysissä menetelmänä on käytetty teemoittelua, jonka avulla on voitu jäsentää saatua aineistoa. Näin teemojen vertailu on myös ollut helpompaa. Tutkimuksen tuloksista kävi ilmi, että monikulttuurinen johtaminen on erittäin haasteellista kansallisten kulttuurien eroista johtuen. Arvot ovat hyvin keskeisessä osassa kulttuuria tutkittaessa ja niiden erot voivat vaikeuttaa kanssakäymistä eri kulttuureista tulevien ihmisten kesken, koska asioiden merkitykset jäävät usein arvoituksiksi vieraasta kulttuurista tuleville henkilöille. Kansallisen kulttuurin tekijöistä kieli, arvot ja uskonto ovat merkittäviä monikulttuurisen johtamisen kannalta. Tutkimuksesta kävi myös ilmi, että Itä- Aasian maissa konfutselaisuudella on suuri merkitys yhteiskuntafilosofiana. Se on muokannut yhteiskunnan arvoja, tapoja ja rakenteita. Vanhempien ja ylempiarvoisten ihmisten arvostus ja vahvasti hierarkkinen yhteiskuntarakenne ovat tyypillisiä konfutselaisuuden piirteitä. Kulttuurin ulottuvuuksista merkityksellisempiä tämän tutkimuksen kannalta ovat yksilöllisyys vs. kollektiivisuus, valtaetäisyys ja konfutselaisuuden dynamiikka (lyhyen vs. pitkän aikavälin suuntautuminen). Kaikki tämän tutkimuksen maat ovat kollektiivisia sekä niissä valtaetäisyys on myös korkea. Tämä tuo haasteita monikulttuuriseen johtamiseen Suomen suurlähetystöissä, koska suomalainen kulttuuri on useimpien länsimaiden tapaan yksilöllinen ja valtaetäisyys on suhteellisen matala. Konfutselaisuuden dynamiikka vaikuttaa lähinnä vain Itä-Aasian maissa tuoden mukanaan erittäin vahvan hierarkian, jota ei voi sivuuttaa. Tutkimuksen aineistoa käsitellään näytenäkökulmasta, eikä sitä ei voisuoraan verrata muihin organisaatioihin tai kulttuureihin. Toisaalta jokaisen kansallisen kulttuurin ihmiset toimivat tietyllä tavalla tietyssä kontekstissa, riippumatta siitä, missä organisaatiossa he työskentelevät. Kulttuuri ohjaa ihmisen toimintaa ja kansallinen kulttuuri on yrityskulttuuria voimakkaampi tekijä.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

BACKGROUND: Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. RESULTS: Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. CONCLUSIONS: Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.

Measuring Intermediary Determinants of Early Childhood Health: A Composite Index Comparing Colombian Departments

In recent years there has been growing interest in composite indicators as an efficient tool of analysis and a method of prioritizing policies. This paper presents a composite index of intermediary determinants of child health using a multivariate statistical approach. The index shows how specific determinants of child health vary across Colombian departments (administrative subdivisions). We used data collected from the 2010 Colombian Demographic and Health Survey (DHS) for 32 departments and the capital city, Bogotá. Adapting the conceptual framework of Commission on Social Determinants of Health (CSDH), five dimensions related to child health are represented in the index: material circumstances, behavioural factors, psychosocial factors, biological factors and the health system. In order to generate the weight of the variables, and taking into account the discrete nature of the data, principal component analysis (PCA) using polychoric correlations was employed in constructing the index. From this method five principal components were selected. The index was estimated using a weighted average of the retained components. A hierarchical cluster analysis was also carried out. The results show that the biggest differences in intermediary determinants of child health are associated with health care before and during delivery.