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).

A statistical shape model of the human second cervical vertebra.

PURPOSE: Statistical shape and appearance models play an important role in reducing the segmentation processing time of a vertebra and in improving results for 3D model development. Here, we describe the different steps in generating a statistical shape model (SSM) of the second cervical vertebra (C2) and provide the shape model for general use by the scientific community. The main difficulties in its construction are the morphological complexity of the C2 and its variability in the population. METHODS: The input dataset is composed of manually segmented anonymized patient computerized tomography (CT) scans. The alignment of the different datasets is done with the procrustes alignment on surface models, and then, the registration is cast as a model-fitting problem using a Gaussian process. A principal component analysis (PCA)-based model is generated which includes the variability of the C2. RESULTS: The SSM was generated using 92 CT scans. The resulting SSM was evaluated for specificity, compactness and generalization ability. The SSM of the C2 is freely available to the scientific community in Slicer (an open source software for image analysis and scientific visualization) with a module created to visualize the SSM using Statismo, a framework for statistical shape modeling. CONCLUSION: The SSM of the vertebra allows the shape variability of the C2 to be represented. Moreover, the SSM will enable semi-automatic segmentation and 3D model generation of the vertebra, which would greatly benefit surgery planning.

Vasicek interest rate model

Tässä tutkielmassa estimoidaan korkomallin parametrit Maximum likelihood metodilla sekä näytetään kuinka mallintaa lyhyen koron evoluutiota ja korkokäyrän rakennetta.

Modelagem de proteínas por homologia

Modeling methods to derive 3D-structure of proteins have been recently developed. Protein homology-modeling, also known as comparative protein modeling, is nowadays the most accurate protein modeling method. This technique can produce useful models for about an order of magnitude more protein sequences than there have been structures determined by experiment in the same amount of time. All current protein homology-modeling methods consist of four sequential steps: fold assignment and template selection, template-target alignment, model building, and model evaluation. In this paper we discuss in some detail the protein-homology paradigm, its predictive power and its limitations.

Modelling nitrogen and phosphorus loads in a Mediterranean river catchment (La Tordera, NE Spain)

Human activities have resulted in increased nutrient levels in many rivers all over Europe. Sustainable management of river basins demands an assessment of the causes and consequences of human alteration of nutrient flows, together with an evaluation of management options. In the context of an integrated and interdisciplinary environmental assessment (IEA) of nutrient flows, we present and discuss the application of the nutrient emission model MONERIS (MOdelling Nutrient Emissions into River Systems) to the Catalan river basin, La Tordera (north-east Spain), for the period 1996–2002. After a successful calibration and verification process (Nash-Sutcliffe efficiencies E=0.85 for phosphorus and E=0.86 for nitrogen), the application of the model MONERIS proved to be useful in estimating nutrient loads. Crucial for model calibration, in-stream retention was estimated to be about 50 % of nutrient emissions on an annual basis. Through this process, we identified the importance of point sources for phosphorus emissions (about 94% for 1996–2002), and diffuse sources, especially inputs via groundwater, for nitrogen emissions (about 31% for 1996–2002). Despite hurdles related to model structure, observed loads, and input data encountered during the modelling process, MONERIS provided a good representation of the major interannual and spatial patterns in nutrient emissions. An analysis of the model uncertainty and sensitivity to input data indicates that the model MONERIS, even in data-starved Mediterranean catchments, may be profitably used by water managers for evaluating quantitative nutrient emission scenarios for the purpose of managing river basins. As an example of scenario modelling, an analysis of the changes in nutrient emissions through two different future scenarios allowed the identification of a set of relevant measures to reduce nutrient loads.

Validation of an instrument to evaluate quality of life in the aging population: WHOQOL-AGE.

BACKGROUND: There is a need for short, specific instruments that assess quality of life (QOL) adequately in the older adult population. The aims of the present study were to obtain evidence on the validity of the inferences that could be drawn from an instrument to measure QOL in the aging population (people 50+ years old), and to test its psychometric properties. METHODS: The instrument, WHOQOL-AGE, comprised 13 positive items, assessed on a five-point rating scale, and was administered to nationally representative samples (n = 9987) from Finland, Poland, and Spain. Cronbach's alpha was employed to assess internal consistency reliability, whereas the validity of the questionnaire was assessed by means of factor analysis, graded response model, Pearson's correlation coefficient and unpaired t-test. Normative values were calculated across countries and for different age groups. RESULTS: The satisfactory goodness-of-fit indices confirmed that the factorial structure of WHOQOL-AGE comprises two first-order factors. Cronbach's alpha was 0.88 for factor 1, and 0.84 for factor 2. Evidence supporting a global score was found with a second-order factor model, according to the goodness-of-fit indices: CFI = 0.93, TLI = 0.91, RMSEA = 0.073. Convergent validity was estimated at r = 0.75 and adequate discriminant validity was also found. Significant differences were found between healthy individuals (74.19 ± 13.21) and individuals with at least one chronic condition (64.29 ± 16.29), supporting adequate known-groups validity. CONCLUSIONS: WHOQOL-AGE has shown good psychometric properties in Finland, Poland, and Spain. Therefore, considerable support is provided to using the WHOQOL-AGE to measure QOL in older adults in these countries, and to compare the QOL of older and younger adults.

Expression of Grapevine leafroll-associated virus 3 coat protein gene in Escherichia coli and production of polyclonal antibodies

Grapevine leafroll-associated virus 3 (GLRaV-3), the main viral species of the grapevine leafroll complex, causes yield and quality reduction in grapes (Vitis spp.). The coat protein gene was RT-PCR-amplified from total RNA extracted from infected grapevine leaves and the amplified fragment was cloned and completely sequenced. The fragment was subsequently subcloned into the pRSET-C expression vector. The recombinant plasmid was used to transform Escherichia coli BL21:DE3 and express the capsid protein. The coat protein, fused to a 6 His-tag, was purified by affinity chromatography using an Ni-NTA resin. The identity of the purified protein was confirmed by SDS-PAGE and Western blot. The in vitro-expressed protein was quantified and used for rabbit immunizations. The antiserum was shown to be sensitive and specific for the detection of GLRaV-3 in grapevine extracts in Western blot and DAS-ELISA assays, with no unspecific or heterologous reactions against other non-serologically related viruses being observed.

Development of a three-dimensional nonlinear viscoelastic constitutive model of solid propellant

A three dimensional nonlinear viscoelastic constitutive model for the solid propellant is developed. In their earlier work, the authors have developed an isotropic constitutive model and verified it for one dimensional case. In the present work, the validity of the model is extended to three-dimensional cases. Large deformation, dewetting and cyclic loading effects are treated as the main sources of nonlinear behavior of the solid propellant. Viscoelastic dewetting criteria is used and the softening of the solid propellant due to dewetting is treated by the modulus decrease. The nonlinearities during cyclic loading are accounted for by the functions of the octahedral shear strain measure. The constitutive equation is implemented into a finite element code for the analysis of propellant grains. A commercial finite element package ‘ABAQUS’ is used for the analysis and the model is introduced into the code through a user subroutine. The model is evaluated with different loading conditions and the predicted values are in good agreement with the measured ones. The resulting model applied to analyze a solid propellant grain for the thermal cycling load.

Modeling of the Fluid-Structure Interaction in Inelastic Piping Systems

In many engineering applications, compliant piping systems conveying liquids are subjected to inelastic deformations due to severe pressure surges such as plastic tubes in modern water supply transmission lines and metallic pipings in nuclear power plants. In these cases the design of such systems may require an adequate modeling of the interactions between the fluid dynamics and the inelastic structural pipe motions. The reliability of the prediction of fluid-pipe behavior depends mainly on the adequacy of the constitutive equations employed in the analysis. In this paper it is proposed a systematic and general approach to consistently incorporate different kinds of inelastic behaviors of the pipe material in a fluid-structure interaction analysis. The main feature of the constitutive equations considered in this work is that a very simple numerical technique can be used for solving the coupled equations describing the dynamics of the fluid and pipe wall. Numerical examples concerning the analysis of polyethylene and stainless steel pipe networks are presented to illustrate the versatility of the proposed approach.

Riskivastuullisuus turvallisuuskasvatuksen kulttuurissa. Oppilaiden vastuullisuus, turvallisuustaju ja tuottamistoiminnan riskiraja peruskoulun käsityön opetuksessa

Riskit ja riskittömyys uhkaavat yksilöitä, käsityötä ja yhteiskuntaa. Käsityökasvatukselleon haaste toimia kulttuurissa, joka tavoittelee täyttä riskittömyyttä. Käsityössä kasvatetaan kekseliäisyyteen ja varautumaan sen aiheuttaman riskin kohtaamiseen sekä ottamaan siitä vastuuta. Tämän tutkimuksen tehtävänä on riskivastuullisuuden mallin rakentamiseksi selvittää, kuinka oppilaiden vastuullisuus selittää riskirajaa käsityön turvallisuuskasvatuksen kulttuurissa. Välinearvojen saavuttamiseksi on siedettävä välineriskiä, joka ei ylitä turvallisuuskulttuurin riskirajaa. Välinearvot ovat välineiden laatua lisääviä ominaisuuksia, joilla pyritään peittämään välineriskejä. Siedettävän riskin rajan ratkaisemiseen tarvitaan tietoa käsityön tuottamisesta ja todellisuutta havainnoivien tiedonalojen tietoa. Viime kädessä ratkaisu tehdään rakentavalla ajattelulla, johon kuuluu välinearvojen tavoittelua ohjaava käsityötaju ja välineriskeihin varautumista ohjaava turvallisuustaju. Käsityössä onnistuminen kannustaa kohti uusia haasteita ja epäonnistumisen riski asettuu mittasuhteisiinsa. Kekseliäässä käsityön kulttuurissa kokeillaan omia ja ympäröivän todellisuuden mahdollisuuksia ottamalla oivaltaen riskejä, jotka saavat aikaan rakentavan kokemuksen riskistä. Käsityö on riskioivallusten oppiaine. Tutkimustehtävän toteuttamiseksi tässä tutkimuksessa rakennetaan uusi riskivastuullisuuden malli, jossa vastuullisuus selittää riskirajaa. Mallin vastaavuutta selvitetään valtakunnallisesti peruskoulun käsityön 6. ja 9. luokan käsityön opetuksessa (n = 393). Aineisto on analysoitu rakenneyhtälöanalyysein konfirmatorisella faktorianalyysilla ja polkumallinnuksella. Tutkimusaineisto ja riskivastuullisuuden malli vastaavat toisiaan. Vastuullisuuden selitysosuus turvallisuustajun ja käsityötajun ratkaisemasta riskirajasta on mallin mukaan 35 %. Oppilaat osoittivat tuntevansa oman tuottamisensa vaikutuksia ja vastuuta niistä. Vastuullisuus osoittautui tärkeäksi riskirajan selittäjäksi, joten käsityön turvallisuuskasvatuksen kulttuuri voi kohota uudelle tasolle riskivastuulliseksi. Käsityön turvallisuuskasvatus on kokonaisvaltaista turvallisuustajun kasvatusta. Riskivastuullisuus luo turvallisuuskulttuuriin yhteisen käsityksen siedettävän riskin rajasta. Oppilaiden mahdollisuuksia kekseliääseen tutkivaan tuottamiseen on vahvistettava eikä rajoitettava. Riskivastuullisessa käsityön turvallisuuskasvatuksen kulttuurissa opettajan tehtävänä ei ole estää mitään tapahtumasta vaan saada mahdollisimman paljon tapahtumaan, sillä vastuullisuus kasvaa vastuuta ottamalla. Se on kasvatuksen – käsityökasvatuksen – keino turvallisuustyössä.

Mathematical modeling and optimal control of malaria

Malaria continues to infect millions and kill hundreds of thousands of people worldwide each year, despite over a century of research and attempts to control and eliminate this infectious disease. Challenges such as the development and spread of drug resistant malaria parasites, insecticide resistance to mosquitoes, climate change, the presence of individuals with subpatent malaria infections which normally are asymptomatic and behavioral plasticity in the mosquito hinder the prospects of malaria control and elimination. In this thesis, mathematical models of malaria transmission and control that address the role of drug resistance, immunity, iron supplementation and anemia, immigration and visitation, and the presence of asymptomatic carriers in malaria transmission are developed. A within-host mathematical model of severe Plasmodium falciparum malaria is also developed. First, a deterministic mathematical model for transmission of antimalarial drug resistance parasites with superinfection is developed and analyzed. The possibility of increase in the risk of superinfection due to iron supplementation and fortification in malaria endemic areas is discussed. The model results calls upon stakeholders to weigh the pros and cons of iron supplementation to individuals living in malaria endemic regions. Second, a deterministic model of transmission of drug resistant malaria parasites, including the inflow of infective immigrants, is presented and analyzed. The optimal control theory is applied to this model to study the impact of various malaria and vector control strategies, such as screening of immigrants, treatment of drug-sensitive infections, treatment of drug-resistant infections, and the use of insecticide-treated bed nets and indoor spraying of mosquitoes. The results of the model emphasize the importance of using a combination of all four controls tools for effective malaria intervention. Next, a two-age-class mathematical model for malaria transmission with asymptomatic carriers is developed and analyzed. In development of this model, four possible control measures are analyzed: the use of long-lasting treated mosquito nets, indoor residual spraying, screening and treatment of symptomatic, and screening and treatment of asymptomatic individuals. The numerical results show that a disease-free equilibrium can be attained if all four control measures are used. A common pitfall for most epidemiological models is the absence of real data; model-based conclusions have to be drawn based on uncertain parameter values. In this thesis, an approach to study the robustness of optimal control solutions under such parameter uncertainty is presented. Numerical analysis of the optimal control problem in the presence of parameter uncertainty demonstrate the robustness of the optimal control approach that: when a comprehensive control strategy is used the main conclusions of the optimal control remain unchanged, even if inevitable variability remains in the control profiles. The results provide a promising framework for the design of cost-effective strategies for disease control with multiple interventions, even under considerable uncertainty of model parameters. Finally, a separate work modeling the within-host Plasmodium falciparum infection in humans is presented. The developed model allows re-infection of already-infected red blood cells. The model hypothesizes that in severe malaria due to parasite quest for survival and rapid multiplication, the Plasmodium falciparum can be absorbed in the already-infected red blood cells which accelerates the rupture rate and consequently cause anemia. Analysis of the model and parameter identifiability using Markov chain Monte Carlo methods is presented.

Accuracy improvement of a demand forecasting model

This research concerns different statistical methods that assist to increase the demand forecasting accuracy of company X’s forecasting model. Current forecasting process was analyzed in details. As a result, graphical scheme of logical algorithm was developed. Based on the analysis of the algorithm and forecasting errors, all the potential directions for model future improvements in context of its accuracy were gathered into the complete list. Three improvement directions were chosen for further practical research, on their basis, three test models were created and verified. Novelty of this work lies in the methodological approach of the original analysis of the model, which identified its critical points, as well as the uniqueness of the developed test models. Results of the study formed the basis of the grant of the Government of St. Petersburg.

Thermodynamic evaluation and modeling of proton and water exchange associated with benzamidine and berenil binding to ß-trypsin

Serine-proteases are involved in vital processes in virtually all species. They are important targets for researchers studying the relationships between protein structure and activity, for the rational design of new pharmaceuticals. Trypsin was used as a model to assess a possible differential contribution of hydration water to the binding of two synthetic inhibitors. Thermodynamic parameters for the association of bovine ß-trypsin (homogeneous material, observed 23,294.4 ± 0.2 Da, theoretical 23,292.5 Da) with the inhibitors benzamidine and berenil at pH 8.0, 25ºC and with 25 mM CaCl2, were determined using isothermal titration calorimetry and the osmotic stress method. The association constant for berenil was about 12 times higher compared to the one for benzamidine (binding constants are K = 596,599 ± 25,057 and 49,513 ± 2,732 M-1, respectively; the number of binding sites is the same for both ligands, N = 0.99 ± 0.05). Apparently the driving force responsible for this large difference of affinity is not due to hydrophobic interactions because the variation in heat capacity (DCp), a characteristic signature of these interactions, was similar in both systems tested (-464.7 ± 23.9 and -477.1 ± 86.8 J K-1 mol-1 for berenil and benzamidine, respectively). The results also indicated that the enzyme has a net gain of about 21 water molecules regardless of the inhibitor tested. It was shown that the difference in affinity could be due to a larger number of interactions between berenil and the enzyme based on computational modeling. The data support the view that pharmaceuticals derived from benzamidine that enable hydrogen bond formation outside the catalytic binding pocket of ß-trypsin may result in more effective inhibitors.

Reduced pancreatic ^6;-cell mass is associated with decreased FoxO1 and Erk1/2 protein phosphorylation in low-protein malnourished rats

A low-protein diet leads to functional and structural pancreatic islet alterations, including islet hypotrophy. Insulin-signaling pathways are involved in several adaptive responses by pancreatic islets. We determined the levels of some insulin-signaling proteins related to pancreatic islet function and growth in malnourished rats. Adult male Wistar rats (N = 20 per group) were fed a 17% protein (normal-protein diet; NP) or 6% protein (low-protein diet; LP), for 8 weeks. At the end of this period, blood glucose and serum insulin and albumin levels were measured. The morphometric parameters of the endocrine pancreas and the content of some proteins in islet lysates were determined. The ^6;-cell mass was significantly reduced (≅65%) in normoglycemic but hypoinsulinemic LP rats compared to NP rats. Associated with these alterations, a significant 30% reduction in insulin receptor substrate-1 and a 70% increase in insulin receptor substrate-2 protein content were observed in LP islets compared to NP islets. The phosphorylated serine-threonine protein kinase (pAkt)/Akt protein ratio was similar in LP and NP islets. The phosphorylated forkhead-O1 (pFoxO1)/FoxO1 protein ratio was decreased by 43% in LP islets compared to NP islets (P < 0.05). Finally, the ratio of phosphorylated-extracellular signal-related kinase 1/2 (pErk1/2) to total Erk1/2 protein levels was decreased by 71% in LP islets compared to NP islets (P < 0.05). Therefore, the reduced ^6;-cell mass observed in LP rats is associated with the reduction of phosphorylation in mitogenic-related signals, FoxO1 and Erk proteins. The cause/effect basis of this association remains to be determined.

Elevated levels of plasma osteoprotegerin are associated with all-cause mortality risk and atherosclerosis in patients with stages 3 to 5 chronic kidney disease

Osteoprotegerin (OPG) regulates bone mass by inhibiting osteoclast differentiation and activation, and plays a role in vascular calcification. We evaluated the relationship between osteoprotegerin levels and inflammatory markers, atherosclerosis, and mortality in patients with stages 3-5 chronic kidney disease. A total of 145 subjects (median age 61 years, 61% men; 36 patients on hemodialysis, 55 patients on peritoneal dialysis, and 54 patients with stages 3-5 chronic kidney disease) were studied. Clinical characteristics, markers of mineral metabolism (including fibroblast growth factor-23 [FGF-23]) and inflammation (high-sensitivity C-reactive protein [hsCRP] and interleukin-6 [IL-6]), and the intima-media thickness (IMT) in the common carotid arteries were measured at baseline. Cardiac function was assessed by color tissue Doppler echocardiography. After 36 months follow-up, the survival rate by Kaplan-Meier analysis was significantly different according to OPG levels ( 67;2=14.33; P=0.002). Increased OPG levels were positively associated with IL-6 (r=0.38, P<0.001), FGF-23 (r=0.26, P<0.001) and hsCRP (r=0.0.24, P=0.003). In addition, OPG was positively associated with troponin I (r=0.54, P<0.001) and IMT (r=0.39, P<0.0001). Finally, in Cox analysis, only OPG (HR=1.07, 95%CI=1.02-1.13) and hsCRP (HR=1.02, 95%CI=1.01-1.04) were independently associated with increased risk of death. These results suggested that elevated levels of serum OPG might be associated with atherosclerosis and all-cause mortality in patients with chronic kidney disease.