Simulation of growth and development of irrigated cowpea in Piauí State by CROPGRO model

The objective of this work was to adapt the CROPGRO model, which is part of the DSSAT system, for simulating the cowpea (Vigna unguiculata) growth and development under soil and climate conditions of the Baixo Parnaíba region, Piauí State, Brazil. In the CROPGRO, only input parameters that define crop species, cultivars, and ecotype were changed in order to characterize the cowpea crop. Soil and climate files were created for the considered site. Field experiments without water deficit were used to calibrate the model. In these experiments, dry matter (DM), leaf area index (LAI), yield components and grain yield of cowpea (cv. BR 14 Mulato) were evaluated. The results showed good fit for DM and LAI estimates. The medium values of R² and medium absolute error (MAE) were, respectively, 0.95 and 264.9 kg ha-1 for DM, and 0.97 and 0.22 for LAI. The difference between observed and simulated values of plant phenology varied from 0 to 3 days. The model also presented good performance for yield components simulation, excluding 100-grain weight, for which the error ranged from 20.9% to 34.3%. Considering the medium values of crop yield in two years, the model presented an error from 5.6%.

ADME pharmacogenetics: investigation of the pharmacokinetics of the antiretroviral agent lopinavir coformulated with ritonavir.

BACKGROUND: An ADME (absorption, distribution, metabolism and excretion)-pharmacogenetics association study may identify functional variants relevant to the pharmacokinetics of lopinavir co-formulated with ritonavir (LPV/r), a first-line anti-HIV agent. METHODS: An extensive search of literature and web resources helped select ADME genes and single nucleotide polymorphisms (SNPs, functional and HapMap tagging SNPs) with a proven or potentially relevant role in LPV/r pharmacokinetics. The study followed a two-stage design. Stage 1 (discovery) considered a Caucasian population (n=638) receiving LPV/r, where we selected 117 individuals with low LPV clearance (cases) and 90 individuals with high clearance (controls). Genotyping was performed by a 1536-SNP customized GoldenGate Illumina BeadArray. Stage 2 (confirmation) represented a replication study of candidate SNPs from the stage 1 in 148 individuals receiving LPV/r. The analysis led to formal population pharmacokinetic-pharmacogenetic modeling of demographic, environmental and candidate SNP effects. RESULTS: One thousand three hundred and eighty SNPs were successfully genotyped. Nine SNPs prioritized by the stage 1 analysis were brought to replication. Stage 2 confirmed the contribution of two functional SNPs in SLCO1B1, one functional SNP in ABCC2 and a tag SNP of the CYP3A locus in addition to body weight effect and ritonavir coadministration. According to the population pharmacokinetic-pharmacogenetic model, genetic variants explained 5% of LPV variability. Individuals homozygous rs11045819 (SLCO1B1*4) had a clearance of 12.6 l/h, compared with 5.4 l/h in the reference group, and 3.9 l/h in individuals with two or more variant alleles of rs4149056 (SLCO1B1*5), rs717620 (ABCC2) or rs6945984 (CYP3A). A subanalysis confirmed that although a significant part of the variance in LPV clearance was attributed to fluctuation in ritonavir levels, genetic variants had an additional effect on LPV clearance. CONCLUSION: The two-stage strategy successfully identified genetic variants affecting LPV/r pharmacokinetics. Such a general approach of ADME pharmacogenetics should be generalized to other drugs.

Hydraulisen kuristinmallin ja liikealustan ohjauksen kehittäminen reaaliaikasimulointiin

Diplomityön ensimmäisessä vaiheessa tutkittiin hydraulisen kuristimen ominaisuuksia ja esiteltiin numeerisesti tehokas kuristinmalli käyttäenpolynomifunktiota virtauksen laminaarisen ja transitioalueen kuvaukseen. Puoliempiirisen mallin paremmuus tulee esille siinä, että kuristimen geometriatietoja ei tarvita laskettaessa virtausta paine-eron perusteella. Reaaliaikasimuloinnissa esiintyy kompromisseja tarkkuuden ja laskentanopeuden välillä. Tätä asiaa tutkittiin kahden virtausalueen kuristinmallilla. Transition paine-eron ja integrointiaika-askelen valinnan vaikutus tarkkuuteen ja laskentanopeuteen tutkittiin. Toisessa vaiheessa tutkittiin mahdollisimman hyvän liiketuntuman tuottamista liikealustalla ohjaussignaalia kehittämällä. Liikealustan liikeradan rajallisuudesta johtuen ohjauksessa on perinteisesti käytetty washout-suodatusta, joka erottelee simuloitavan järjestelmän kiihtyvyyssignaalista vain nopeatkiihtyvyydet. Tässä työssä tutkittiin hitaiden kiihtyvyyksien ottamista mukaan liikealustan ohjaukseen liikealustan liikeradan puitteissa. Tämä toteutettiin kuvaamalla hitaat kiihtyvyydet kallistamalla liikealustaa, jolloin käyttäjään kohdistuva voima saatiin kuvattua gravitaatiota hyväksi käyttäen.

Contribution of early detection and adjuvant treatments to breast cancer mortality reduction in Catalonia, Spain

Background: Reductions in breast cancer (BC) mortality in Western countries have been attributed to the use of screening mammography and adjuvant treatments. The goal of this work was to analyze the contributions of both interventions to the decrease in BC mortality between 1975 and 2008 in Catalonia. Methodology/Principal Findings: A stochastic model was used to quantify the contribution of each intervention. Age standardized BC mortality rates for calendar years 1975-2008 were estimated in four hypothetical scenarios: 1) Only screening, 2) Only adjuvant treatment, 3) Both interventions, and 4) No intervention. For the 30-69 age group, observed Catalan BC mortality rates per 100,000 women-year rose from 29.4 in 1975 to 38.3 in 1993, and afterwards continuously decreased to 23.2 in 2008. If neither of the two interventions had been used, in 2008 the estimated BC mortality would have been 43.5, which, compared to the observed BC mortality rate, indicates a 46.7% reduction. In 2008 the reduction attributable to screening was 20.4%, to adjuvant treatments was 15.8% and to both interventions 34.1%. Conclusions/Significance: Screening and adjuvant treatments similarly contributed to reducing BC mortality in Catalonia. Mathematical models have been useful to assess the impact of interventions addressed to reduce BC mortality that occurred over nearly the same periods.

Determinants of school efficiency : The case of primary schools in the State of Geneva, Switzerland

Purpose The purpose of this paper is (1) to measure school technical efficiency and (2) to identify the determinants of primary school performance. Design/methodology/approach A two-stage Data Envelopment Analysis (DEA) of school efficiency is conducted. At the first stage, DEA is employed to calculate an individual efficiency score for each school. At the second stage, efficiency is regressed on school characteristics and environmental variables. Findings The mean technical efficiency of schools in the State of Geneva is equal to 93%. By improving the operation of schools, 7% (100 - 93) of inputs could be saved, representing 17'744'656.2 Swiss francs in 2010. School efficiency is negatively influenced by (1) operations being held on multiple sites, (2) the proportion of disadvantaged pupils enrolled at the school and (3) the provision of special education, but positively influenced by school size (captured by the number of pupils). Practical implications Technically, the determinants of school efficiency are outside of the control of the headteachers. However, it is still possible to either boost the positive impact or curb the negative impact. Potential actions are discussed. Originality/value Unlike most similar studies, the model in this study is tested for multicollinearity, heteroskedasticity and endogeneity. It is therefore robust. Moreover, one explanatory variable of school efficiency (operations being held on multiple sites) is a truly original variable as it has never been tested so far.

Cost-effectivness in a DRG system for two-step exchange of infected total joint arthroplasty

The costs related to the treatment of infected total joint arthroplasties represent an ever groving burden to the society. Different patient-adapted therapeutic options like débridement and retention, 1- or 2-step exchange can be used. If a 2-step exchange is used we have to consider short (2-4 weeks) or long (>4-6 weeks) interval treatment. The Swiss DRG (Diagnose related Groups) determines the reimboursement the hopsital receives for the treatment of an infected total arthroplasty. The review assesses the cost-effectiveness of hospitalisation practices linked to surgical treatment in the two-stage exchange of a prosthetic-joint infection. The aim of this retrospectiv study is to compare the economical impact between a short (2 to 4 weeks) versus a long (6 weeks and above) interval during a two-satge procedure to determine the financial impact. Retrospectiv study of the patients with a two-stage procedure for a hip or knee prosthetic joint infection at CHUV hospital Lausanne (Switzerland) between 2012 and 2013. The review analyses the correlation between the interval length and the length of the hospital stay as well as with the costs and revenues per hospital stay. In average there is a loss of 40′000 Euro per hospitalisation for the treatment of prosthetic joint infection. Revenues never cover all the costs, even with a short interval procedure. This economical loss increases with the length of the hospital stay if a long-term intervall is choosen. The review explores potential for improvement in reimbourement practices and hospitalisation practices in the current Swiss healthcare setting. There should be alternative setups to decrease the burden of medical costs by a) increase the reimboursment for the treatment of infected total joints or by b) splitting the hospital stay with partners (rapid transfer after first operation from center hospital to level 2 hospital and retransfer for second operation to center) in order to increase revenues.

Genesis and Emplacement of Carbonatites and Lamprophyres in the Svecofennian Domain

A small carbonatite dyke swarm has been identified at Naantali, southwest Finland. Several swarms of shoshonitic lamprophyres are also known along the Archean-Proterozoic boundary in eastern Finland and northwest Russia. These intrusions, along with the carbonatite intrusion at Halpanen, eastern Finland, represent a stage of widespread low-volume mantle-sourced alkaline magmatism in the Svecofennian Domain. Using trace element and isotope geochemistry coupled with precise geochronology from these rocks, a model is presented for the Proterozoic metasomatic evolution of the Fennoscandian subcontinental lithospheric mantle. At ~2.2-2.06 Ga, increased biological production in shallow seas linked to continental rifting, resulted in increased burial rates of organic carbon. Subduction between ~1.93-1.88 Ga returned organic carbon-enriched sediments of mixed Archean and Proterozoic provenance to the mantle. Dehydration reactions supplied water to the mantle wedge, driving arc volcanism, while mica, amphibole and carbonate were brought deeper into the mantle with the subducting slab. The cold subducted slab was heated conductively from the surrounding warm mantle, while pressures continued to gradually increase as a result of crustal thickening. The sediments began to melt in a two stage process, first producing a hydrous alkaline silicate melt, which infiltrated the mantle wedge and crystallised as metasomatic veins. At higher temperatures, carbonatite melt was produced, which preferentially infiltrated the pre-existing metasomatic vein network. At the onset of post-collisional extension, deep fault structures formed, providing conduits for mantle melts to reach the upper crust. Low-volume partial melting of the enriched mantle at depths of at least 110 km led to the formation of first carbonatitic magma and subsequently lamprophyric magma. Carbonatite was emplaced in the upper crust at Naantali at 1795.7 ± 6.8 Ma; lamprophyres along the Archean-Proterozoic boundary were emplaced between 1790.1 ± 3.3 Ma and 1781 ± 20 Ma.

Recovery and refining of manganese as by-product from hydrometallurgical processes

The consumption of manganese is increasing, but huge amounts of manganese still end up in waste in hydrometallurgical processes. The recovery of manganese from multi-metal solutions at low concentrations may not be economical. In addition, poor iron control typically prevents the production of high purity manganese. Separation of iron from manganese can be done with chemical precipitation or solvent extraction methods. Combined carbonate precipitation with air oxidation is a feasible method to separate iron and manganese due to the fast kinetics, good controllability and economical reagents. In addition the leaching of manganese carbonate is easier and less acid consuming than that of hydroxide or sulfide precipitates. Selective iron removal with great efficiency from MnSO4 solution is achieved by combined oxygen or air oxidation and CaCO3 precipitation at pH > 5.8 and at a redox potential of > 200 mV. In order to avoid gypsum formation, soda ash should be used instead of limestone. In such case, however, extra attention needs to be paid on the reagents mole ratios in order to avoid manganese coprecipitation. After iron removal, pure MnSO4 solution was obtained by solvent extraction using organophosphorus reagents, di-(2-ethylhexyl)phosphoric acid (D2EHPA) and bis(2,4,4- trimethylpentyl)phosphinic acid (CYANEX 272). The Mn/Ca and Mn/Mg selectivities can be increased by decreasing the temperature from the commonly used temperatures (40 –60oC) to 5oC. The extraction order of D2EHPA (Ca before Mn) at low temperature remains unchanged but the lowering of temperature causes an increase in viscosity and slower phase separation. Of these regents, CYANEX 272 is selective for Mn over Ca and, therefore, it would be the better choice if there is Ca present in solution. A three-stage Mn extraction followed by a two-stage scrubbing and two-stage sulfuric acid stripping is an effective method of producing a very pure MnSO4 intermediate solution for further processing. From the intermediate MnSO4 some special Mn- products for ion exchange applications were synthesized and studied. Three types of octahedrally coordinated manganese oxide materials as an alternative final product for manganese were chosen for synthesis: layer structured Nabirnessite, tunnel structured Mg-todorokite and K-kryptomelane. As an alternative source of pure MnSO4 intermediate, kryptomelane was synthesized by using a synthetic hydrometallurgical tailings. The results show that the studied OMS materials adsorb selectively Cu, Ni, Cd and K in the presence of Ca and Mg. It was also found that the exchange rates were reasonably high due to the small particle dimensions. Materials are stable in the studied conditions and their maximum Cu uptake capacity was 1.3 mmol/g. Competitive uptake of metals and acid was studied using equilibrium, batch kinetic and fixed-bed measurements. The experimental data was correlated with a dynamic model, which also accounts for the dissolution of the framework manganese. Manganese oxide micro-crystals were also bound onto silica to prepare a composite material having a particle size large enough to be used in column separation experiments. The MnOx/SiO2 ratio was found to affect significantly the properties of the composite. The higher the ratio, the lower is the specific surface area, the pore volume and the pore size. On the other hand, higher amount of silica binder gives composites better mechanical properties. Birnesite and todorokite can be aggregated successfully with colloidal silica at pH 4 and with MnO2/SiO2 weight ratio of 0.7. The best gelation and drying temperature was 110oC and sufficiently strong composites were obtained by additional heat-treatment at 250oC for 2 h. The results show that silica–supported MnO2 materials can be utilized to separate copper from nickel and cadmium. The behavior of the composites can be explained reasonably well with the presented model and the parameters estimated from the data of the unsupported oxides. The metal uptake capacities of the prepared materials were quite small. For example, the final copper loading was 0.14 mmol/gMnO2. According to the results the special MnO2 materials are potential for a specific environmental application to uptake harmful metal ions.

Temporal variability of soil CO2 emission after conventional and reduced tillage described by an exponential decay in time model

To study Assessing the impact of tillage practices on soil carbon losses dependents it is necessary to describe the temporal variability of soil CO2 emission after tillage. It has been argued that large amounts of CO2 emitted after tillage may serve as an indicator for longer-term changes in soil carbon stocks. Here we present a two-step function model based on soil temperature and soil moisture including an exponential decay in time component that is efficient in fitting intermediate-term emission after disk plow followed by a leveling harrow (conventional), and chisel plow coupled with a roller for clod breaking (reduced) tillage. Emission after reduced tillage was described using a non-linear estimator with determination coefficient (R²) as high as 0.98. Results indicate that when emission after tillage is addressed it is important to consider an exponential decay in time in order to predict the impact of tillage in short-term emissions.

Performance of UASB reactors in two stages under different HRT and OLR treating residual waters of swine farming

In this study it was evaluated the effects of hydraulic retention time (HRT) and Organic Loading Rate (OLR) on the performance of UASB (Upflow Anaerobic Sludge Blanket) reactors in two stages treating residual waters of swine farming. The system consisted of two UASB reactors in pilot scale, installed in series, with volumes of 908 and 188 L, for the first and second stages (R1 and R2), respectively. The HRT applied in the system of anaerobic treatment in two stages (R1 + R2) was of 19.3, 29.0 and 57.9 h. The OLR applied in the R1 ranged from 5.5 to 40.1 kg CODtotal (m³ d)-1. The average removal efficiencies of chemical oxygen demand (COD) and total suspended solids (TSS) ranged, respectively, from 66.3 to 88.2% and 62.5 to 89.3% in the R1, and from 85.5 to 95.5% and 76.4 to 96.1% in the system (R1 + R2). The volumetric production of methane in the system (R1 + R2) ranged from 0.295 to 0.721 m³CH4 (m³ reactor d)-1. It was found that the OLR applied were not limiting to obtain high efficiencies of CODtotal and TSS removal and methane production. The inclusion of the UASB reactor in the second stage contributed to increase the efficiencies of CODtotal and TSS removal, especially, when the treatment system was submitted to the lowest HRT and the highest OLR.

COD, TSS, nutrients and coliforms removals in UASB reactors in two stages treating swine wastewater

The performance of two upflow anaerobic sludge blanket (UASB) reactors was evaluated in pilot scale (908 and 188 L), installed in series (R1 and R2), fed with swine wastewater with TSS around 5 and 13 g L-1. The UASB reactors were submitted to HDT of 36 and 18 h with VOL of 5.5 to 34.4 g COD (L d)-1 in the R1 and HDT of 7.5 e 3.7 h with VOL from 5.1 to 45.2 g COD (L d)-1 in the R2. The average removal efficiencies of COD ranged from 55 to 85% in the R1 and from 43 to 57% in the R2, resulting in values from 82 to 93% in the UASB reactors in two stage. Methane concentrations in the biogas were 69 to 74% with specific production from 0.05 to 0.27 L CH4 (g removedCOD)-1 in the R1 and of 0.10 to 0.12 L CH4 (g removedCOD)-1 in the R2. The average removal efficiencies were 61 to 75% for totalP, 39 to 69% for KN, 82 to 93% for orgN and 20 to 94% for Fe, Zn, Cu and Mn. The amN concentration were not reduced indicating the need to post-treatment for effluent disposal into water bodies. There were reductions of total coliforms from 99.8123 to 99.9989% and of thermotolerant coliforms from 99.9725 to 99.9999%. The conditions imposed to the UASB reactors in two stage provided high conversions of removedCOD into methane (up to 77%) and reductions of organic an inorganic pollution loads from swine wastewater.

Tuotekustannuslaskentamallin kehittäminen elintarvikealan yritykseen

Työn tavoitteena oli kehittää tuotekustannuslaskentamalli elintarvikealan yritykseen. Laskentamallin avulla halutaan saada tarkempaa tietoa tuotteiden kustannuksista ja kannattavuuksista. Työ muodostuu teoreettisesta kirjallisuusselvityksestä sekä empiirisestä case-tutkimuksesta. Aineiston perusteella kohdeyritykselle saatiin kehitettyä tuotekustannuslaskentamalli. Työn tutkimusote on konstruktiivinen. Laskentamallin kehittäminen edellytti välillisten kustannusten kohdistamisperiaatteiden määrittämistä. Välilliset kustannukset kohdistetaan perinteisellä kaksivaiheisella menetelmällä. Kustannukset kohdistetaan ensin niille kuuluville kustannuspaikoille. Kustannuspaikoilta kustannukset kohdistetaan edelleen tuoteryhmille ja tuotteille. Kohdeyrityksen tuotekustannuslaskenta on aikaisemmin perustunut ainoastaan standardikustannuslaskentaan. Kehitetyn kustannuslaskentamallin avulla tuotteiden kustannuksista ja kannattavuudesta saadaan tarkempaa tietoa, koska välillisten kustannusten kohdistamiseen luotiin selkeät menetelmät. Parantunutta kus-tannustietoa voidaan hyödyntää tuotteita koskevissa päätöksentekotilanteissa.

Tuotelanseerausprosessin kehittäminen

Työn lähtökohtana on vuonna 2009 case-yksikölle luotu stage-gate-malli, jonka ymmärtäminen ja käyttö ei ole ollut toivotulla tasolla. Asenteet ja perehdytys tämän mallin käyttöön ovat aiheuttaneet sen, että osa yksikön henkilöstöstä ei tunnista mallin käyttöä omassa työssään, vaikka sitä käytetään jokaisessa tuotekehitysprojektissa. Työn tavoitteena on kuvata case-yksikön stage-gate-mallin etenemistä selkeämmin, jotta se saataisiin tehokkaammin käyttöön koko henkilöstölle, sekä tutkia ovatko eri toimintojen roolitukset mallin mukaan optimaaliset. Tavoitteena on myös tutkia kuinka tiedon tulisi kulkea toimintojen välillä, jotta se olisi mahdollisimman tehokasta. Työtä varten on kerätty kirjallisuusmateriaalia teorian pohjustamiseksi ja haastateltu 14 yksikön toimihenkilöä nykyisten ongelmakohtien kartoittamiseksi. Lisäksi työhön liittyen tehtiin benchmark-haastattelu mahdollisimman lähellä case-yksikön liiketoimintaa olevasta saman yrityksen yksiköstä. Yksikölle luodun stage-gate-mallin tuntemus oli haastattelujen perusteella suhteellisen heikolla tasolla. Vain noin puolet tunnisti sen jokapäiväisessä työskentelyssään. Ongelmakohtia mallin käyttämiseen liittyen ilmeni paljon ja niistä iso osa kohdistui myyntiin, markkinointiin sekä projektipäällikön toimintaan. Havaittujen ongelmien perusteella yksikön roolituksista tehtiin selventävä kaavio, jotta jokaisen on helpompi hahmottaa prosessia. Lisäksi henkilöstön osallistamiseen ja tiedonjakamiseen annettiin kehitysehdotuksia. Näin ollen koko henkilöstö saadaan ymmärtämään mallin vaiheet ja tärkeimpänä, ymmärtämään oman roolinsa kussakin stage-gate-mallin vaiheessa.

Bayesian analysis of SEIR epidemic models

This thesis concerns the analysis of epidemic models. We adopt the Bayesian paradigm and develop suitable Markov Chain Monte Carlo (MCMC) algorithms. This is done by considering an Ebola outbreak in the Democratic Republic of Congo, former Zaïre, 1995 as a case of SEIR epidemic models. We model the Ebola epidemic deterministically using ODEs and stochastically through SDEs to take into account a possible bias in each compartment. Since the model has unknown parameters, we use different methods to estimate them such as least squares, maximum likelihood and MCMC. The motivation behind choosing MCMC over other existing methods in this thesis is that it has the ability to tackle complicated nonlinear problems with large number of parameters. First, in a deterministic Ebola model, we compute the likelihood function by sum of square of residuals method and estimate parameters using the LSQ and MCMC methods. We sample parameters and then use them to calculate the basic reproduction number and to study the disease-free equilibrium. From the sampled chain from the posterior, we test the convergence diagnostic and confirm the viability of the model. The results show that the Ebola model fits the observed onset data with high precision, and all the unknown model parameters are well identified. Second, we convert the ODE model into a SDE Ebola model. We compute the likelihood function using extended Kalman filter (EKF) and estimate parameters again. The motivation of using the SDE formulation here is to consider the impact of modelling errors. Moreover, the EKF approach allows us to formulate a filtered likelihood for the parameters of such a stochastic model. We use the MCMC procedure to attain the posterior distributions of the parameters of the SDE Ebola model drift and diffusion parts. In this thesis, we analyse two cases: (1) the model error covariance matrix of the dynamic noise is close to zero , i.e. only small stochasticity added into the model. The results are then similar to the ones got from deterministic Ebola model, even if methods of computing the likelihood function are different (2) the model error covariance matrix is different from zero, i.e. a considerable stochasticity is introduced into the Ebola model. This accounts for the situation where we would know that the model is not exact. As a results, we obtain parameter posteriors with larger variances. Consequently, the model predictions then show larger uncertainties, in accordance with the assumption of an incomplete model.

Stochastic particle models: mean reversion and burgers dynamics. An application to commodity markets

The aim of this study is to propose a stochastic model for commodity markets linked with the Burgers equation from fluid dynamics. We construct a stochastic particles method for commodity markets, in which particles represent market participants. A discontinuity in the model is included through an interacting kernel equal to the Heaviside function and its link with the Burgers equation is given. The Burgers equation and the connection of this model with stochastic differential equations are also studied. Further, based on the law of large numbers, we prove the convergence, for large N, of a system of stochastic differential equations describing the evolution of the prices of N traders to a deterministic partial differential equation of Burgers type. Numerical experiments highlight the success of the new proposal in modeling some commodity markets, and this is confirmed by the ability of the model to reproduce price spikes when their effects occur in a sufficiently long period of time.