Development of principle culture medium formulations for Saccharomyces cerevisiae

Saccharomyces cerevisiae as well as other microorganisms are frequently used in industry with the purpose of obtain different kind of products that can be applied in several areas (research investigation, pharmaceutical compounds, etc.). In order to obtain high yields for the desired product, it is necessary to make an adequate medium supplementation during the growth of the microorganisms. The higher yields are typically reached by using complex media, however the exact formulation of these media is not known. Moreover, it is difficult to control the exact composition of complex media, leading to batch-to-batch variations. So, to overcome this problem, some industries choose to use defined media, with a defined and known chemical composition. However these kind of media, many times, do not reach the same high yields that are obtained by using complex media. In order to obtain similar yield with defined media the addition of many different compounds has to be tested experimentally. Therefore, the industries use a set of empirical methods with which it is tried to formulate defined media that can reach the same high yields as complex media. In this thesis, a defined medium for Saccharomyces cerevisiae was developed using a rational design approach. In this approach a given metabolic network of Saccharomyces cerevisiae is divided into a several unique and not further decomposable sub networks of metabolic reactions that work coherently in steady state, so called elementary flux modes. The EFMtool algorithm was used in order to calculate the EFM’s for two Saccharomyces cerevisiae metabolic networks (amino acids supplemented metabolic network; amino acids non-supplemented metabolic network). For the supplemented metabolic network 1352172 EFM’s were calculated and then divided into: 1306854 EFM’s producing biomass, and 18582 EFM’s exclusively producing CO2 (cellular respiration). For the non-supplemented network 635 EFM’s were calculated and then divided into: 215 EFM’s producing biomass; 420 EFM’s producing exclusively CO2. The EFM’s of each group were normalized by the respective glucose consumption value. After that, the EFMs’ of the supplemented network were grouped again into: 30 clusters for the 1306854 EFMs producing biomass and, 20 clusters for the 18582 EFM’s producing CO2. For the non-supplemented metabolic network the respective EFM’s of each metabolic function were grouped into 10 clusters. After the clustering step, the concentrations of the other medium compounds were calculated by considering a reasonable glucose amount and by accounting for the proportionality between the compounds concentrations and the glucose ratios. The approach adopted/developed in this thesis may allow a faster and more economical way for media development.

Spatial analysis of new cases of leprosy in the State of Espírito Santo, Brazil, between 2004 and 2009

INTRODUCTION: Leprosy in Brazil is a public health issue, and there are many regions in the State of Espírito Santo with high endemic incidence levels of leprosy, characterizing this state as a priority for leprosy programs. The aim of this study was to determine the spatial distribution of coefficients of new cases of leprosy in the State of Espírito Santo, Brazil. METHODS: We conducted a descriptive and ecologic study based on the spatial distribution of leprosy in the State of Espírito Santo between 2004 and 2009. Data were gathered from the available records of the Espírito Santo State Health Secretary. The global and local Bayesian empirical methods were used to produce an estimate of leprosy risk, smoothing the fluctuation effects of the detection coefficients. RESULTS: The study resulted in a coefficient adjustment of new cases in 10 towns that changed their classification, among which, 2 went from low to medium, 4 from medium to high, 3 from high to very high, and 1 from very high to hyper-endemic. An average variation of 1.02, fluctuating between 0 and 12.39 cases/100,000 inhabitants, was found in a comparative calculation between the Local Ebest value and the average coefficient of new leprosy cases in the State of Espírito Santo. CONCLUSIONS: The spatial analysis of leprosy favors the establishment of control strategies with a better cost-benefit relationship since it reveals specific and priority regions, thereby enabling the development of actions that can interfere in the transmission chain.

Antioxidant, cytotoxic and UVB-absorbing activity of Maytenus guyanensis Klotzch. (Celastraceae) bark extracts

Maytenus guyanensis Klotzch. is an Amazonian medicinal tree species known in Brazil by the common name chichuá and in Peru and Colombia by the name chuchuhuasi. It is used in traditional medicine as stimulant, tonic, and muscle relaxant, for the relief of arthritis, rheumatism, hemorrhoids, swollen kidney, skin eruptions, and skin cancer prevention, among others. Initially, different extraction solvents and methods were applied to dried, ground bark which made possible the preparation of extracts having both significant lethality to brine shrimp larvae (Artemia franciscana Leach) as well as antioxidant activity in vitro based on tests involving reactions with 2,2,-diphenyl-1-picrylhydrazyl (DPPH). Analysis of fractions from serial extractions with solvents of increasing polarity supports the notion that antioxidant activity is associated with compounds of intermediate polarity and cytotoxicity is associated with compounds of low to intermediate polarity. Variation of extraction time and conditions revealed that hot, continuous ethanol extraction provided good yields of bark extract in several hours. Hot extraction also provided ethanol extracts having greater lethality to brine shrimp and antioxidant activity (compared to the flavonoid rutin in semi-quantitative methods based on DPPH) than extracts obtained from maceration at room temperature. Freeze-dried ethanol extracts were prepared by: 1) maceration at room temperature and 2) hot extraction (eight hours) on several hundred gram scales and the latter extract was shown to have partial screening effects on UVB light. In this work, cytotoxic, antioxidant and potential sun-screening activity are shown for the first time in M. guyanensis.

Two different 3D biogeochemical models for the NW mediterranean sea: validation with Meris data and intercomparison

Report for the scientific sojourn carried out at the University of New South Wales from February to June the 2007. Two different biogeochemical models are coupled to a three dimensional configuration of the Princeton Ocean Model (POM) for the Northwestern Mediterranean Sea (Ahumada and Cruzado, 2007). The first biogeochemical model (BLANES) is the three-dimensional version of the model described by Bahamon and Cruzado (2003) and computes the nitrogen fluxes through six compartments using semi-empirical descriptions of biological processes. The second biogeochemical model (BIOMEC) is the biomechanical NPZD model described in Baird et al. (2004), which uses a combination of physiological and physical descriptions to quantify the rates of planktonic interactions. Physical descriptions include, for example, the diffusion of nutrients to phytoplankton cells and the encounter rate of predators and prey. The link between physical and biogeochemical processes in both models is expressed by the advection-diffusion of the non-conservative tracers. The similarities in the mathematical formulation of the biogeochemical processes in the two models are exploited to determine the parameter set for the biomechanical model that best fits the parameter set used in the first model. Three years of integration have been carried out for each model to reach the so called perpetual year run for biogeochemical conditions. Outputs from both models are averaged monthly and then compared to remote sensing images obtained from sensor MERIS for chlorophyll.

A Thematic Comparison of Eight Frameworks of Quality Criteria in Qualitative Health Research

Background: Despite the increasing incidences of the publication of assessment frameworks intending to establish the "standards" of the quality of qualitative research, the research conducted using such empirical methods are still facing difficulties in being published or recognised by funding agencies. Methods: We conducted a thematic content analysis of eight frameworks from psychology/psychiatry and general medicine. The frameworks and their criteria are then compared against each other. Findings: The results illustrated the difficulties in reaching consensus on the definition of quality criteria. This showed the differences between the frameworks from the point of views of the underlying epistemology and the criteria suggested. Discussion: The aforementioned differences reflect the diversity of paradigms implicitly referred to by the authors of the frameworks, although rarely explicitly mentioned in text. We conclude that the increase in qualitative research and publications has failed to overcome the difficulties in establishing shared criteria and the great heterogeneity of concepts raises methodological and epistemological problems.

iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach.

The n-octanol/water partition coefficient (log Po/w) is a key physicochemical parameter for drug discovery, design, and development. Here, we present a physics-based approach that shows a strong linear correlation between the computed solvation free energy in implicit solvents and the experimental log Po/w on a cleansed data set of more than 17,500 molecules. After internal validation by five-fold cross-validation and data randomization, the predictive power of the most interesting multiple linear model, based on two GB/SA parameters solely, was tested on two different external sets of molecules. On the Martel druglike test set, the predictive power of the best model (N = 706, r = 0.64, MAE = 1.18, and RMSE = 1.40) is similar to six well-established empirical methods. On the 17-drug test set, our model outperformed all compared empirical methodologies (N = 17, r = 0.94, MAE = 0.38, and RMSE = 0.52). The physical basis of our original GB/SA approach together with its predictive capacity, computational efficiency (1 to 2 s per molecule), and tridimensional molecular graphics capability lay the foundations for a promising predictor, the implicit log P method (iLOGP), to complement the portfolio of drug design tools developed and provided by the SIB Swiss Institute of Bioinformatics.

Patterns of pain-free response in 497 cases of classic trigeminal neuralgia treated with Gamma Knife surgery and followed up for least 1 year.

Object The goal of this study was to establish whether clear patterns of initial pain freedom could be identified when treating patients with classic trigeminal neuralgia (TN) by using Gamma Knife surgery (GKS). The authors compared hypesthesia and pain recurrence rates to see if statistically significant differences could be found. Methods Between July 1992 and November 2010, 737 patients presenting with TN underwent GKS and prospective evaluation at Timone University Hospital in Marseille, France. In this study the authors analyzed the cases of 497 of these patients, who participated in follow-up longer than 1 year, did not have megadolichobasilar artery- or multiple sclerosis-related TN, and underwent GKS only once; in other words, the focus was on cases of classic TN with a single radiosurgical treatment. Radiosurgery was performed with a Leksell Gamma Knife (model B, C, or Perfexion) using both MR and CT imaging targeting. A single 4-mm isocenter was positioned in the cisternal portion of the trigeminal nerve at a median distance of 7.8 mm (range 4.5-14 mm) anterior to the emergence of the nerve. A median maximum dose of 85 Gy (range 70-90 Gy) was delivered. Using empirical methods and assisted by a chart with clear cut-off periods of pain free distribution, the authors were able to divide patients who experienced freedom from pain into 3 separate groups: patients who became pain free within the first 48 hours post-GKS; those who became pain free between 48 hours and 30 days post-GKS; and those who became pain free more than 30 days after GKS. Results The median age in the 497 patients was 68.3 years (range 28.1-93.2 years). The median follow-up period was 43.75 months (range 12-174.41 months). Four hundred fifty-four patients (91.34%) were initially pain free within a median time of 10 days (range 1-459 days) after GKS. One hundred sixty-nine patients (37.2%) became pain free within the first 48 hours (Group PF(≤ 48 hours)), 194 patients (42.8%) between posttreatment Day 3 and Day 30 (Group PF((>48 hours, ≤ 30 days))), and 91 patients (20%) after 30 days post-GKS (Group PF(>30 days)). Differences in postoperative hypesthesia were found: in Group PF(≤ 48 hours) 18 patients (13.7%) developed postoperative hypesthesia, compared with 30 patients (19%) in Group PF((>48 hours, ≤ 30 days)) and 22 patients (30.6%) in Group PF(>30 days) (p = 0.014). One hundred fifty-seven patients (34.4%) who initially became free from pain experienced a recurrence of pain with a median delay of 24 months (range 0.62-150.06 months). There were no statistically significant differences between the patient groups with respect to pain recurrence: 66 patients (39%) in Group PF(≤ 48 hours) experienced pain recurrence, compared with 71 patients (36.6%) in Group PF((>48 hours, ≤ 30 days)) and 27 patients (29.7%) in Group PF(>30 days) (p = 0.515). Conclusions A substantial number of patients (169 cases, 37.2%) became pain free within the first 48 hours. The rate of hypesthesia was higher in patients who became pain free more than 30 days after GKS, with a statistically significant difference between patient groups (p = 0.014).

Numerical and ExperimentalModelling of Gas Flow and Heat Transfer in the Air Gap of An Electric Machine

This work deals with the cooling of high-speed electric machines, such as motors and generators, through an air gap. It consists of numerical and experimental modelling of gas flow and heat transfer in an annular channel. Velocity and temperature profiles are modelled in the air gap of a high-speed testmachine. Local and mean heat transfer coefficients and total friction coefficients are attained for a smooth rotor-stator combination at a large velocity range. The aim is to solve the heat transfer numerically and experimentally. The FINFLO software, developed at Helsinki University of Technology, has been used in the flow solution, and the commercial IGG and Field view programs for the grid generation and post processing. The annular channel is discretized as a sector mesh. Calculation is performed with constant mass flow rate on six rotational speeds. The effect of turbulence is calculated using three turbulence models. The friction coefficient and velocity factor are attained via total friction power. The first part of experimental section consists of finding the proper sensors and calibrating them in a straight pipe. After preliminary tests, a RdF-sensor is glued on the walls of stator and rotor surfaces. Telemetry is needed to be able to measure the heat transfer coefficients at the rotor. The mean heat transfer coefficients are measured in a test machine on four cooling air mass flow rates at a wide Couette Reynolds number range. The calculated values concerning the friction and heat transfer coefficients are compared with measured and semi-empirical data. Heat is transferred from the hotter stator and rotor surfaces to the coolerair flow in the air gap, not from the rotor to the stator via the air gap, althought the stator temperature is lower than the rotor temperature. The calculatedfriction coefficients fits well with the semi-empirical equations and precedingmeasurements. On constant mass flow rate the rotor heat transfer coefficient attains a saturation point at a higher rotational speed, while the heat transfer coefficient of the stator grows uniformly. The magnitudes of the heat transfer coefficients are almost constant with different turbulence models. The calibrationof sensors in a straight pipe is only an advisory step in the selection process. Telemetry is tested in the pipe conditions and compared to the same measurements with a plain sensor. The magnitudes of the measured data and the data from the semi-empirical equation are higher for the heat transfer coefficients than thenumerical data considered on the velocity range. Friction and heat transfer coefficients are presented in a large velocity range in the report. The goals are reached acceptably using numerical and experimental research. The next challenge is to achieve results for grooved stator-rotor combinations. The work contains also results for an air gap with a grooved stator with 36 slots. The velocity field by the numerical method does not match in every respect the estimated flow mode. The absence of secondary Taylor vortices is evident when using time averagednumerical simulation.

Rullaussylinterin ja painotelan mallinnus kiinnirullaimen simulointiin

Diplomityössä tutkitaan kaupallisen simulointiohjelmiston soveltuvuutta nykyaikaisen kiinnirullaimen dynamiikan tutkimiseen. Kiinnostuksen kohteena on erityisesti kahden telan välinen nippi, sekä siinä tapahtuvat värähtelyt. Työssä mallinnetaan rullaussylinterin ja telapainolaitteen simulointimallit. Rullaussylinterin simulointimalli yhdistetään Lappeenrannan teknillisessä korkeakoulussa mallinnettuun tampuuritelan simulointimalliin, jolloin nippikontaktin tutkiminen on mahdollista. Simuloituja tuloksia verrataan todellisella laitteella tehtyihin mittauksiin sekä elementtimenetelmällä laskettuihin tuloksiin. Diplomityön mekaniikka mallinnetaan ADAMS-ohjelmistossa monikappaledynamiikan keinoin. Toimilaitteiden sekä säätöjärjestelmien kuvaukseen käytetään MATLAB Simulink-ohjelmistoa. Telojen joustavuuden mallinnuksessa käytetään hyväksi keskittyneiden massojen periaatetta. Järjestelmän hydraulipiirit mallinnetaan keskittyneiden paineiden teorian mukaisesti ja toimilaitteiden mallinnuksessa käytetään puoliempiiristä mallinnustekniikkaa. Työssä havaitaan monikappaledynamiikan soveltuvan kiinnirullaimen dynamiikan tutkimiseen. Kahden diplomityön tuloksena laaditun nippimallin avulla voidaan kuvata rullaustapahtumassa vaikuttavat voimat oikein. Värähtelymittausten perusteella voidaan tehdä karkeita johtopäätöksiä, mallin toimivuuden arvioimiseksi värähtelyjen kuvaamisessa, joskin mallin havaitaan vaativan lisätutkimusta ja kehitystyötä.

Reaaliaikainen virtuaalihydrauliikka osana todellista konejärjestelmää

Diplomityössä tutkittiin hydrauliikan reaaliaikasimulointia ja sen mahdollisuuksia tuotekehityksen apuvälineenä. Työssä käytettiin dSPACE:n reaaliaikasimulointiin valmistamia laitteita ja ohjelmia. Työssä luotiin Matlab/Simulink –ympäristöön tyypillisimmistä hydrauliikkakomponenttien puoliempiirisistä malleista koostuva komponenttikirjasto, joista kootut hydrauliikkapiirien mallit voitiin kääntää reaaliaikaympäristöön. Työn tavoitteena oli kehittää menetelmä, jonka avulla voidaan nopeuttaa ja helpottaa hydraulismekaanisten konejärjestelmien suunnittelua ja tuotekehitystä. Kehitetyt menetelmät perustuvat todellisen konejärjestelmän osaksi kytketyn reaaliaikaisen virtuaalihydrauliikan avulla laskettuun uuteen ohjaussignaaliin, jonka avulla voidaan todellisella hydrauliikalla kuvata virtuaalisen hydrauliikan vaikutukset todelliseen järjestelmään. Näin ollen muutokset voidaan siis tehdä virtuaaliseen hydrauliikkaan ja niiden vaikutukset nähdä todellisen järjestelmän käyttäytymisessä.

Trimmerin kapasiteetin kasvattaminen dynamiikan mallinnuksen avulla

Työn tavoitteena oli kasvattaa sahan dimensiolaitoksella käytettävän trimmerin rakenteellista kapasiteettia. Tavoitteeseen pyrittiin modernisoimalla trimmerin teräyksikköä käyttävää toimilaite ja teräyksikön säätö dynamiikan mallinnuksen avulla. Trimmerin teräyksikön dynamiikka mallinnettiin MATLAB-matematiikkaohjelmistolla kaksiulotteisena kinematiikkamallina ja kolmeulotteisena kinetiikkamallina. Dynamiikkamallien tulosten perusteella valittin teräyksikköä käyttävä toimilaite komponentteineen. Kinetiikkamalliin mallinnettiin trimmeriä käyttävä hydraulipiiri valittuine komponentteineen keskittyneiden paineiden ja puoliempiirisen mallinnuksen periaatteita käyttäen. Teräyksikön työkiertoa säätämään mallinnettiin suljettu takaisinkytketty säätöpiiri. Tuloksien perusteella valittiin optimaalinen toimilaitteen asemointigeometria ja todettiin mallinnetun järjestelmän täyttävän asetetut vaatimukset. Järjestelmää testattiin muuttamalla jarjestelman parametreja ja tutkimalla muutosten vaikutuksia jarjestelman toimintaan. Lisaksi tutkittiin lyhyesti terayksikon rakenteen keventamisen vaikutuksia.

Standardized evaluation methodology and reference database for evaluating IVUS image segmentation

This paper describes an evaluation framework that allows a standardized and quantitative comparison of IVUS lumen and media segmentation algorithms. This framework has been introduced at the MICCAI 2011 Computing and Visualization for (Intra)Vascular Imaging (CVII) workshop, comparing the results of eight teams that participated. We describe the available data-base comprising of multi-center, multi-vendor and multi-frequency IVUS datasets, their acquisition, the creation of the reference standard and the evaluation measures. The approaches address segmentation of the lumen, the media, or both borders; semi- or fully-automatic operation; and 2-D vs. 3-D methodology. Three performance measures for quantitative analysis have been proposed. The results of the evaluation indicate that segmentation of the vessel lumen and media is possible with an accuracy that is comparable to manual annotation when semi-automatic methods are used, as well as encouraging results can be obtained also in case of fully-automatic segmentation. The analysis performed in this paper also highlights the challenges in IVUS segmentation that remains to be solved.

Estudo eletroquímico e químico-quântico da oxidação do antidepressivo tricíclico amitriptilina

This work presents the electrochemical and quantum chemical studies of the oxidation of the tricyclic antidepressant amitriptyline (AM) employing a carbon-polyurethane composite electrode (GPU) in a 0.1 mol L-1 BR buffer. The electrochemical results showed that the oxidation of AM occurs irreversibly at potentials close to 830 mV with the loss of one electron and one proton and is controlled by reagent and product adsorption. According to the PM3 results, the atom C16 is the region of highest probability for the oxidation of AM since it has the largest charge variation.

On the application of knoevenagel condensation for the synthesis of benzylidene benzothiazine compounds and structural study

The synthesis and physico-chemical properties of new 6-acetylamino or 6-benzoyl-amino 2-benzylidene-4-methyl-4H-benzo[1,4]thiazin-3-ones and 6-benzoylamino or 6-nitro 2-benzylidene-4H-benzo[1,4]thiazin-3-ones are described. These benzylidene benzothiazine compounds were prepared by the Knoevenagel condensation with benzaldehydes. The configurations and conformations of benzylidene benzothiazine derivatives were optimised using the semi-empirical method AM1.

Estudo teórico da interação existente entre a artemisinina e o heme

The purpose of this work is to study theoretically stereoelectronic aspects of the interaction between heme and artemisinin in the transitional heme-artemisinin complex. Through semi-empirical calculations using the PM3 method, the potential energy barrier of artemisinin rotation relative to heme in the heme-artemisinin complex was studied in vacuum and in the partially solvated state. The minimum heat of formation obtained for the complex with and without water molecules is -702.39 and -100.86 kcal mol-1, respectively, which corresponds to the dihedral angle C-Fe-O1-O2 of 43.93º and 51.90º around the iron-oxygen O1 bond, respectively. The water molecules bind to heme via 13 hydrogen bonds and O-H•••O and 6 C-H•••O interactions, which accounts for -67.23 kcal mol-1. It is observed that the inclusion of water molecules does not affect significantly the stability of the heme-artemisinin complex.