Implicit methods for qualitative modeling of gene regulatory networks.

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

Detecting, quantifying and adjusting for publication bias in meta-analyses: protocol of a systematic review on methods.

BACKGROUND: Health professionals and policymakers aspire to make healthcare decisions based on the entire relevant research evidence. This, however, can rarely be achieved because a considerable amount of research findings are not published, especially in case of 'negative' results - a phenomenon widely recognized as publication bias. Different methods of detecting, quantifying and adjusting for publication bias in meta-analyses have been described in the literature, such as graphical approaches and formal statistical tests to detect publication bias, and statistical approaches to modify effect sizes to adjust a pooled estimate when the presence of publication bias is suspected. An up-to-date systematic review of the existing methods is lacking. METHODS/DESIGN: The objectives of this systematic review are as follows:âeuro¢ To systematically review methodological articles which focus on non-publication of studies and to describe methods of detecting and/or quantifying and/or adjusting for publication bias in meta-analyses.âeuro¢ To appraise strengths and weaknesses of methods, the resources they require, and the conditions under which the method could be used, based on findings of included studies.We will systematically search Web of Science, Medline, and the Cochrane Library for methodological articles that describe at least one method of detecting and/or quantifying and/or adjusting for publication bias in meta-analyses. A dedicated data extraction form is developed and pilot-tested. Working in teams of two, we will independently extract relevant information from each eligible article. As this will be a qualitative systematic review, data reporting will involve a descriptive summary. DISCUSSION: Results are expected to be publicly available in mid 2013. This systematic review together with the results of other systematic reviews of the OPEN project (To Overcome Failure to Publish Negative Findings) will serve as a basis for the development of future policies and guidelines regarding the assessment and handling of publication bias in meta-analyses.

Steganalytic Methods for the Detection of Histogram Shifting Data Hiding Schemes

Peer-reviewed

In conspectu prope totius urbis: an application of different visual methods at the ager Tarraconensis landscape

We present in this paper the results of the application of several visual methods on a group of locations, dated between VI and I centuries BC, of the ager Tarraconensis (Tarragona, Spain) a Hinterland of the roman colony of Tarraco. The difficulty in interpreting the diverse results in a combined way has been resolved by means of the use of statistical methods, such as Principal Components Analysis (PCA) and K-means clustering analysis. These methods have allowed us to carry out site classifications in function of the landscape's visual structure that contains them and of the visual relationships that could be given among them.

Combining hypoxic methods for peak performance.

New methods and devices for pursuing performance enhancement through altitude training were developed in Scandinavia and the USA in the early 1990s. At present, several forms of hypoxic training and/or altitude exposure exist: traditional 'live high-train high' (LHTH), contemporary 'live high-train low' (LHTL), intermittent hypoxic exposure during rest (IHE) and intermittent hypoxic exposure during continuous session (IHT). Although substantial differences exist between these methods of hypoxic training and/or exposure, all have the same goal: to induce an improvement in athletic performance at sea level. They are also used for preparation for competition at altitude and/or for the acclimatization of mountaineers. The underlying mechanisms behind the effects of hypoxic training are widely debated. Although the popular view is that altitude training may lead to an increase in haematological capacity, this may not be the main, or the only, factor involved in the improvement of performance. Other central (such as ventilatory, haemodynamic or neural adaptation) or peripheral (such as muscle buffering capacity or economy) factors play an important role. LHTL was shown to be an efficient method. The optimal altitude for living high has been defined as being 2200-2500 m to provide an optimal erythropoietic effect and up to 3100 m for non-haematological parameters. The optimal duration at altitude appears to be 4 weeks for inducing accelerated erythropoiesis whereas <3 weeks (i.e. 18 days) are long enough for beneficial changes in economy, muscle buffering capacity, the hypoxic ventilatory response or Na(+)/K(+)-ATPase activity. One critical point is the daily dose of altitude. A natural altitude of 2500 m for 20-22 h/day (in fact, travelling down to the valley only for training) appears sufficient to increase erythropoiesis and improve sea-level performance. 'Longer is better' as regards haematological changes since additional benefits have been shown as hypoxic exposure increases beyond 16 h/day. The minimum daily dose for stimulating erythropoiesis seems to be 12 h/day. For non-haematological changes, the implementation of a much shorter duration of exposure seems possible. Athletes could take advantage of IHT, which seems more beneficial than IHE in performance enhancement. The intensity of hypoxic exercise might play a role on adaptations at the molecular level in skeletal muscle tissue. There is clear evidence that intense exercise at high altitude stimulates to a greater extent muscle adaptations for both aerobic and anaerobic exercises and limits the decrease in power. So although IHT induces no increase in VO(2max) due to the low 'altitude dose', improvement in athletic performance is likely to happen with high-intensity exercise (i.e. above the ventilatory threshold) due to an increase in mitochondrial efficiency and pH/lactate regulation. We propose a new combination of hypoxic method (which we suggest naming Living High-Training Low and High, interspersed; LHTLHi) combining LHTL (five nights at 3000 m and two nights at sea level) with training at sea level except for a few (2.3 per week) IHT sessions of supra-threshold training. This review also provides a rationale on how to combine the different hypoxic methods and suggests advances in both their implementation and their periodization during the yearly training programme of athletes competing in endurance, glycolytic or intermittent sports.

Oops! Another medication error : a literature review of contributing factors and methods to prevent medication errors

The purpose of this bachelor's thesis was to chart scientific research articles to present contributing factors to medication errors done by nurses in a hospital setting, and introduce methods to prevent medication errors. Additionally, international and Finnish research was combined and findings were reflected in relation to the Finnish health care system. Literature review was conducted out of 23 scientific articles. Data was searched systematically from CINAHL, MEDIC and MEDLINE databases, and also manually. Literature was analysed and the findings combined using inductive content analysis. Findings revealed that both organisational and individual factors contributed to medication errors. High workload, communication breakdowns, unsuitable working environment, distractions and interruptions, and similar medication products were identified as organisational factors. Individual factors included nurses' inability to follow protocol, inadequate knowledge of medications and personal qualities of the nurse. Developing and improving the physical environment, error reporting, and medication management protocols were emphasised as methods to prevent medication errors. Investing to the staff's competence and well-being was also identified as a prevention method. The number of Finnish articles was small, and therefore the applicability of the findings to Finland is difficult to assess. However, the findings seem to fit to the Finnish health care system relatively well. Further research is needed to identify those factors that contribute to medication errors in Finland. This is a necessity for the development of methods to prevent medication errors that fit in to the Finnish health care system.

Protective effect and economic impact of insecticide application methods on barley

The objective of this work was to evaluate the protective effect of different forms of insecticide application on the transmission of yellow dwarf disease in barley cultivars, as well as to determine the production costs and the net profit of these managements. The experiments were carried out during 2011 and 2012 growing seasons, using the following managements at main plots: T1, seed treatment with insecticide (ST) + insecticide on shoots at 15-day interval; T2, just ST; T3, insecticide applied on shoots, when aphid control level (CL) was reached; T4, without insecticide; and T5, ST + insecticide on shoots when CL was reached. Different barley cultivars - BRS Cauê, BRS Brau and MN 6021 - were arranged in the subplots. Insecticides lambda cyhalothrin (pyrethroid) and thiamethoxam (neonicotinoid) were used. There were differences on yellow dwarf disease index in both seasons for the different treatments, while damage to grain yield was influenced by year and aphid population. Production costs and net profit were different among treatments. Seed treatment with insecticide is sufficient to reduce the transmission of yellow dwarf disease in years with low aphid population pressure, while in years with larger populations, the application of insecticide on shoots is also required.

Average performance analysis of circular and hyperbolic geolocation

A comparative performance analysis of four geolocation methods in terms of their theoretical root mean square positioning errors is provided. Comparison is established in two different ways: strict and average. In the strict type, methods are examined for a particular geometric configuration of base stations(BSs) with respect to mobile position, which determines a givennoise profile affecting the respective time-of-arrival (TOA) or timedifference-of-arrival (TDOA) estimates. In the average type, methodsare evaluated in terms of the expected covariance matrix ofthe position error over an ensemble of random geometries, so thatcomparison is geometry independent. Exact semianalytical equationsand associated lower bounds (depending solely on the noiseprofile) are obtained for the average covariance matrix of the positionerror in terms of the so-called information matrix specific toeach geolocation method. Statistical channel models inferred fromfield trials are used to define realistic prior probabilities for therandom geometries. A final evaluation provides extensive resultsrelating the expected position error to channel model parametersand the number of base stations.

Spatial predictions of land-use transitions and associated threats to biodiversity: the case of forest regrowth in mountain grasslands

Question Can we predict where forest regrowth caused by abandonment of agricultural activities is likely to occur? Can we assess how it may conflict with grassland diversity hotspots? Location Western Swiss Alps (4003210m a.s.l.). Methods We used statistical models to predict the location of land abandonment by farmers that is followed by forest regrowth in semi-natural grasslands of the Western Swiss Alps. Six modelling methods (GAM, GBM, GLM, RF, MDA, MARS) allowing binomial distribution were tested on two successive transitions occurring between three time periods. Models were calibrated using data on land-use change occurring between 1979 and 1992 as response, and environmental, accessibility and socio-economic variables as predictors, and these were validated for their capacity to predict the changes observed from 1992 to 2004. Projected probabilities of land-use change from an ensemble forecast of the six models were combined with a model of plant species richness based on a field inventory, allowing identification of critical grassland areas for the preservation of biodiversity. Results Models calibrated over the first land-use transition period predicted the second transition with reasonable accuracy. Forest regrowth occurs where cultivation costs are high and yield potential is low, i.e. on steeper slopes and at higher elevations. Overlaying species richness with land-use change predictions, we identified priority areas for the management and conservation of biodiversity at intermediate elevations. Conclusions Combining land-use change and biodiversity projections, we propose applied management measures for targeted/identified locations to limit the loss of biodiversity that could otherwise occur through loss of open habitats. The same approach could be applied to other types of land-use changes occurring in other ecosystems.

Fluid flow and dispersion predictions in porous media by utilizing advanced numerical methods

Diplomityön tavoitteena oli tarkastella numeerisen virtauslaskennan avulla virtaukseen liittyviä ilmiöitä ja kaasun dispersiota. Diplomityön sisältö on jaettu viiteen osaan; johdantoon, teoriaan, katsaukseen virtauksen mallinnukseen huokoisessa materiaalissa liittyviin tutkimusselvityksiin, numeeriseen mallinnukseen sekä tulosten esittämiseen ja johtopäätöksiin. Diplomityön alussa kiinnitettiin huomiota erilaisiin kokeellisiin, numeerisiin ja teoreettisiin mallinnusmenetelmiin, joilla voidaan mallintaa virtausta huokoisessa materiaalissa. Kirjallisuusosassa tehtiin katsaus aikaisemmin julkaistuihin puoliempiirisiin ja empiirisiin tutkimusselvityksiin, jotka liittyvät huokoisen materiaalin aiheuttamaan painehäviöön. Numeerisessa virtauslaskenta osassa rakennettiin ja esitettiin huokoista materiaalia kuvaavat numeeriset mallit käyttäen kaupallista FLUENT -ohjelmistoa. Työn lopussa arvioitiin teorian, numeerisen virtauslaskennan ja kokeellisten tutkimusselvitysten tuloksia. Kolmiulotteisen huokoisen materiaalinnumeerisessa mallinnuksesta saadut tulokset vaikuttivat lupaavilta. Näiden tulosten perusteella tehtiin suosituksia ajatellen tulevaa virtauksen mallinnusta huokoisessa materiaalissa. Osa tässä diplomityössä esitetyistä tuloksista tullaan esittämään 55. Kanadan Kemiantekniikan konferenssissa Torontossa 1619 Lokakuussa 2005. ASME :n kansainvälisessä tekniikan alan julkaisussa. Työ on hyväksytty esitettäväksi esitettäväksi laskennallisen virtausmekaniikan (CFD) aihealueessa 'Peruskäsitteet'. Lisäksi työn yksityiskohtaiset tulokset tullaan lähettämään myös CES:n julkaisuun.

Methods for the analysis of two dimensional measurement data of paper web

This work is devoted to the problem of reconstructing the basis weight structure at paper web with black{box techniques. The data that is analyzed comes from a real paper machine and is collected by an o®-line scanner. The principal mathematical tool used in this work is Autoregressive Moving Average (ARMA) modelling. When coupled with the Discrete Fourier Transform (DFT), it gives a very flexible and interesting tool for analyzing properties of the paper web. Both ARMA and DFT are independently used to represent the given signal in a simplified version of our algorithm, but the final goal is to combine the two together. Ljung-Box Q-statistic lack-of-fit test combined with the Root Mean Squared Error coefficient gives a tool to separate significant signals from noise.

Modélisation par automate cellulaire des phénomènes diagénétiques des plateformes carbonatées : calibration et paramétrage à partir de deux cas d'études : l'Urgonien du Vercors (Crétacé inférieur, SE France) et les Calcaires Gris du Mont Compomolon (Lias, NE Italie)

Une fois déposé, un sédiment est affecté au cours de son enfouissement par un ensemble de processus, regroupé sous le terme diagenèse, le transformant parfois légèrement ou bien suffisamment pour le rendre méconnaissable. Ces modifications ont des conséquences sur les propriétés pétrophysiques qui peuvent être positives ou négatives, c'est-à-dire les améliorer ou bien les détériorer. Une voie alternative de représentation numérique des processus, affranchie de l'utilisation des réactions physico-chimiques, a été adoptée et développée en mimant le déplacement du ou des fluides diagénétiques. Cette méthode s'appuie sur le principe d'un automate cellulaire et permet de simplifier les phénomènes sans sacrifier le résultat et permet de représenter les phénomènes diagénétiques à une échelle fine. Les paramètres sont essentiellement numériques ou mathématiques et nécessitent d'être mieux compris et renseignés à partir de données réelles issues d'études d'affleurements et du travail analytique effectué. La représentation des phénomènes de dolomitisation de faible profondeur suivie d'une phase de dédolomitisation a été dans un premier temps effectuée. Le secteur concerne une portion de la série carbonatée de l'Urgonien (Barrémien-Aptien), localisée dans le massif du Vercors en France. Ce travail a été réalisé à l'échelle de la section afin de reproduire les géométries complexes associées aux phénomènes diagénétiques et de respecter les proportions mesurées en dolomite. De plus, la dolomitisation a été simulée selon trois modèles d'écoulement. En effet, la dédolomitisation étant omniprésente, plusieurs hypothèses sur le mécanisme de dolomitisation ont été énoncées et testées. Plusieurs phases de dolomitisation per ascensum ont été également simulées sur des séries du Lias appartenant aux formations du groupe des Calcaire Gris, localisées au nord-est de l'Italie. Ces fluides diagénétiques empruntent le réseau de fracturation comme vecteur et affectent préférentiellement les lithologies les plus micritisées. Cette étude a permis de mettre en évidence la propagation des phénomènes à l'échelle de l'affleurement. - Once deposited, sediment is affected by diagenetic processes during their burial history. These diagenetic processes are able to affect the petrophysical properties of the sedimentary rocks and also improve as such their reservoir capacity. The modelling of diagenetic processes in carbonate reservoirs is still a challenge as far as neither stochastic nor physicochemical simulations can correctly reproduce the complexity of features and the reservoir heterogeneity generated by these processes. An alternative way to reach this objective deals with process-like methods, which simplify the algorithms while preserving all geological concepts in the modelling process. The aim of the methodology is to conceive a consistent and realistic 3D model of diagenetic overprints on initial facies resulting in petrophysical properties at a reservoir scale. The principle of the method used here is related to a lattice gas automata used to mimic diagenetic fluid flows and to reproduce the diagenetic effects through the evolution of mineralogical composition and petrophysical properties. This method developed in a research group is well adapted to handle dolomite reservoirs through the propagation of dolomitising fluids and has been applied on two case studies. The first study concerns a mid-Cretaceous rudist and granular platform of carbonate succession (Urgonian Fm., Les Gorges du Nan, Vercors, SE France), in which several main diagenetic stages have been identified. The modelling in 2D is focused on dolomitisation followed by a dédolomitisation stage. For the second study, data collected from outcrops on the Venetian platform (Lias, Mont Compomolon NE Italy), in which several diagenetic stages have been identified. The main one is related to per ascensum dolomitisation along fractures. In both examples, the evolution of the effects of the mimetic diagenetic fluid on mineralogical composition can be followed through space and numerical time and help to understand the heterogeneity in reservoir properties. Carbonates, dolomitisation, dédolomitisation, process-like modelling, lattice gas automata, random walk, memory effect.

Methods of Telecommunication Technology Forecasting

This master's thesis coversthe concepts of knowledge discovery, data mining and technology forecasting methods in telecommunications. It covers the various aspects of knowledge discoveryin data bases and discusses in detail the methods of data mining and technologyforecasting methods that are used in telecommunications. Main concern in the overall process of this thesis is to emphasize the methods that are being used in technology forecasting for telecommunications and data mining. It tries to answer to some extent to the question of do forecasts create a future? It also describes few difficulties that arise in technology forecasting. This thesis was done as part of my master's studies in Lappeenranta University of Technology.

Monte Carlo Methods in Parameter Estimation of Nonlinear Models

Yksi keskeisimmistä tehtävistä matemaattisten mallien tilastollisessa analyysissä on mallien tuntemattomien parametrien estimointi. Tässä diplomityössä ollaan kiinnostuneita tuntemattomien parametrien jakaumista ja niiden muodostamiseen sopivista numeerisista menetelmistä, etenkin tapauksissa, joissa malli on epälineaarinen parametrien suhteen. Erilaisten numeeristen menetelmien osalta pääpaino on Markovin ketju Monte Carlo -menetelmissä (MCMC). Nämä laskentaintensiiviset menetelmät ovat viime aikoina kasvattaneet suosiotaan lähinnä kasvaneen laskentatehon vuoksi. Sekä Markovin ketjujen että Monte Carlo -simuloinnin teoriaa on esitelty työssä siinä määrin, että menetelmien toimivuus saadaan perusteltua. Viime aikoina kehitetyistä menetelmistä tarkastellaan etenkin adaptiivisia MCMC menetelmiä. Työn lähestymistapa on käytännönläheinen ja erilaisia MCMC -menetelmien toteutukseen liittyviä asioita korostetaan. Työn empiirisessä osuudessa tarkastellaan viiden esimerkkimallin tuntemattomien parametrien jakaumaa käyttäen hyväksi teoriaosassa esitettyjä menetelmiä. Mallit kuvaavat kemiallisia reaktioita ja kuvataan tavallisina differentiaaliyhtälöryhminä. Mallit on kerätty kemisteiltä Lappeenrannan teknillisestä yliopistosta ja Åbo Akademista, Turusta.