GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Power quality improving with virtual flux-based voltage source line converter

Line converters have become an attractive AC/DC power conversion solution in industrial applications. Line converters are based on controllable semiconductor switches, typically insulated gate bipolar transistors. Compared to the traditional diode bridge-based power converters line converters have many advantageous characteristics, including bidirectional power flow, controllable de-link voltage and power factor and sinusoidal line current. This thesis considers the control of the lineconverter and its application to power quality improving. The line converter control system studied is based on the virtual flux linkage orientation and the direct torque control (DTC) principle. A new DTC-based current control scheme is introduced and analyzed. The overmodulation characteristics of the DTC converter are considered and an analytical equation for the maximum modulation index is derived. The integration of the active filtering features to the line converter isconsidered. Three different active filtering methods are implemented. A frequency-domain method, which is based on selective harmonic sequence elimination, anda time-domain method, which is effective in a wider frequency band, are used inharmonic current compensation. Also, a voltage feedback active filtering method, which mitigates harmonic sequences of the grid voltage, is implemented. The frequency-domain and the voltage feedback active filtering control systems are analyzed and controllers are designed. The designs are verified with practical measurements. The performance and the characteristics of the implemented active filtering methods are compared and the effect of the L- and the LCL-type line filteris discussed. The importance of the correct grid impedance estimate in the voltage feedback active filter control system is discussed and a new measurement-based method to obtain it is proposed. Also, a power conditioning system (PCS) application of the line converter is considered. A new method for correcting the voltage unbalance of the PCS-fed island network is proposed and experimentally validated.

Clinical relevance of L-carnitine-supplemented total parenteral nutrition in postoperative trauma. Metabolic effects of continuous or acute carnitine administration with special reference to fat oxidation and nitrogen utilization.

Carnitine-free total parenteral nutrition (TPN) is claimed to result in a carnitine deficiency with subsequent impairment of fat oxidation. The present study was designed to evaluate the possible benefit of carnitine supplementation on postoperative fat and nitrogen utilization. Sixteen patients undergoing total esophagectomy were evenly randomized and received TPN without or with L-carnitine supplementation (74 mumol.kg-1.d-1) during 11 postoperative days. On day 11, a 4-h infusion of L-carnitine (125 mumol/kg) was performed in both groups. The effect of supplementation was evaluated by indirect calorimetry, N balance, and repeated measurements of plasma lipids and ketone bodies. Irrespective of continuous or acute supplementation, respiratory quotient and fat oxidation were similarly maintained throughout the study in both groups whereas N balance appeared to be more favorable without carnitine. We conclude that carnitine-supplemented TPN does not improve fat oxidation or promote N utilization in the postoperative phase.

Characteristics of a good customer reference for a process equipment supplier

Työn tavoitteena oli tutkia hyvän asiakasreferenssin ominaisuuksia suodatinvalmistaja Laroxin myynnin ja huollon sekä yrityksen asiakkaiden näkökulmasta. Larox voi käyttää saatua tietoa referenssien tehokkaampaan valintaan ja hyödyntämiseen. Kaksi internet-kyselyä toteutettiin, välineenä Webropol. Alustava kysely sunnattiin Laroxin myynnille ja huollolle. Kysely koostui viidestä kategoriasta asiakasreferenssejä, joiden tärkeyttä arvioitiin, sekä vapaista vastauksista. Tunnistettuja hyvän asiakasreferenssin ominaisuuksia ovat hyvä suhde referenssiasiakkaaseen, positiiviset jarehelliset suosittelut asiakkaalta, referenssilaitteen hyvä toimintakyky ja asiakas joka ymmärtää huollon tärkeyden. Pääkysely suunnattiin Laroxin asiakkaille. Tilastollisilla analyyseilla tutkittiin koetun riskin mallinmuuttujien välisiä yhteyksiä. Analyysit eivät paljastaneet merkittäviä riippuvuuksia asiakasreferenssin ominaisuuksien tärkeydessä eritaustaisten vastaajien tai tilannetekijöiden välillä, mutta asiakasreferenssin ominaisuuksien faktorit tukevat mallia. Referenssilaitteiden toimintakyky vaikuttaa tärkeimmältä ja huollon tärkeys on myös merkittävä.

Clinical chemistry variables in normal elderly and healthy ambulatory populations: comparison with reference values.

Laboratory values of the most commonly assayed clinical chemistry variables were determined in selected elderly and healthy ambulatory populations. The upper and lower limits (2.5 and 97.5 fractiles) were compared with the adult reference values in use in university hospitals of Switzerland. The results suggest that conventional adult reference values can be used for most variables in the elderly and that these values are also useful in an ambulatory population.

The maximum voltage drop in an on-chip power distribution network: analysis of square, triangular and hexagonal power pad arrangements

A mathematical model of the voltage drop which arises in on-chip power distribution networks is used to compare the maximum voltage drop in the case of different geometric arrangements of the pads supplying power to the chip. These include the square or Manhattan power pad arrangement, which currently predominates, as well as equilateral triangular and hexagonal arrangements. In agreement with the findings in the literature and with physical and SPICE models, the equilateral triangular power pad arrangement is found to minimize the maximum voltage drop. This headline finding is a consequence of relatively simple formulas for the voltage drop, with explicit error bounds, which are established using complex analysis techniques, and elliptic functions in particular.

β1- and β3- voltage-gated sodium channel subunits modulate cell surface expression and glycosylation of Nav1.7 in HEK293 cells.

Voltage-gated sodium channels (Navs) are glycoproteins composed of a pore-forming α-subunit and associated β-subunits that regulate Nav α-subunit plasma membrane density and biophysical properties. Glycosylation of the Nav α-subunit also directly affects Navs gating. β-subunits and glycosylation thus comodulate Nav α-subunit gating. We hypothesized that β-subunits could directly influence α-subunit glycosylation. Whole-cell patch clamp of HEK293 cells revealed that both β1- and β3-subunits coexpression shifted V ½ of steady-state activation and inactivation and increased Nav1.7-mediated I Na density. Biotinylation of cell surface proteins, combined with the use of deglycosydases, confirmed that Nav1.7 α-subunits exist in multiple glycosylated states. The α-subunit intracellular fraction was found in a core-glycosylated state, migrating at ~250 kDa. At the plasma membrane, in addition to the core-glycosylated form, a fully glycosylated form of Nav1.7 (~280 kDa) was observed. This higher band shifted to an intermediate band (~260 kDa) when β1-subunits were coexpressed, suggesting that the β1-subunit promotes an alternative glycosylated form of Nav1.7. Furthermore, the β1-subunit increased the expression of this alternative glycosylated form and the β3-subunit increased the expression of the core-glycosylated form of Nav1.7. This study describes a novel role for β1- and β3-subunits in the modulation of Nav1.7 α-subunit glycosylation and cell surface expression.

Regulation of the expression of Nav1.5, the cardiac voltage-gated sodium channel

Abstract The cardiac sodium channel Nav1.5 plays a key role in cardiac excitability and conduction. Its importance for normal cardiac function has been highlighted by descriptions of numerous mutations of SCN5A (the gene encoding Nav1.5), causing cardiac arrhythmias which can lead to sudden cardiac death. The general aim of my PhD research project has been to investigate the regulation of Nav1.5 along two main axes: (1) We obtained experimental evidence revealing an interaction between Nav1.5 and a multiprotein complex comprising dystrophin. The first part of this study reports the characterization of this interaction. (2) The second part of the study is dedicated to the regulation of the cardiac sodium channel by the mineralocorticoid hormone named aldosterone. (1) Early in this study, we showed that Nav1.5 C-terminus was associated with dystrophin and that this interaction was mediated by syntrophin proteins. We used dystrophin-deficient mdx5cv mice to study the role of this interaction. We reported that dystrophin deficiency led to a reduction of both Nav1.5 protein level and the sodium current (INa). We also found that mdx5cv mice displayed atrial and ventricular conduction defects. Our results also indicated that proteasome inhibitor MG132 treatment of mdx5cv mice rescued Nav1.5 protein level and INa in cardiac tissue. (2) We showed that aldosterone treatment of mice cardiomyocytes led to an increase of the sodium current with no modification of Nav1.5 transcript and protein level. Altogether, these results suggest that the sodium current can be increased by distribution of intracellular pools of protein to the plasma membrane (e.g. upon aldosterone stimulation) and that interaction with dystrophin multiprotein complex is required for the stabilization of the channel at the plasma membrane. Finally, we obtained preliminary results suggesting that the proteasome could regulate Nav1.5 in mdx5cv mice. This study defines regulatory mechanisms of Nav1.5 which could play an important role in cardiac arrhythmia and bring new insight in cardiac conduction alterations observed in patients with dystrophinopathies. Moreover, this work suggests that Brugada syndrome, and some of the cardiac alterations seen in Duchenne patients may be caused by overlapping molecular mechanisms leading to a reduction of the cardiac sodium current.

Converter-flux-based current control of voltage source PWM rectifiers - analysis and implementation

Pulsewidth-modulated (PWM) rectifier technology is increasingly used in industrial applications like variable-speed motor drives, since it offers several desired features such as sinusoidal input currents, controllable power factor, bidirectional power flow and high quality DC output voltage. To achieve these features,however, an effective control system with fast and accurate current and DC voltage responses is required. From various control strategies proposed to meet these control objectives, in most cases the commonly known principle of the synchronous-frame current vector control along with some space-vector PWM scheme have been applied. Recently, however, new control approaches analogous to the well-established direct torque control (DTC) method for electrical machines have also emerged to implement a high-performance PWM rectifier. In this thesis the concepts of classical synchronous-frame current control and DTC-based PWM rectifier control are combined and a new converter-flux-based current control (CFCC) scheme is introduced. To achieve sufficient dynamic performance and to ensure a stable operation, the proposed control system is thoroughly analysed and simple rules for the controller design are suggested. Special attention is paid to the estimationof the converter flux, which is the key element of converter-flux-based control. Discrete-time implementation is also discussed. Line-voltage-sensorless reactive reactive power control methods for the L- and LCL-type line filters are presented. For the L-filter an open-loop control law for the d-axis current referenceis proposed. In the case of the LCL-filter the combined open-loop control and feedback control is proposed. The influence of the erroneous filter parameter estimates on the accuracy of the developed control schemes is also discussed. A newzero vector selection rule for suppressing the zero-sequence current in parallel-connected PWM rectifiers is proposed. With this method a truly standalone and independent control of the converter units is allowed and traditional transformer isolation and synchronised-control-based solutions are avoided. The implementation requires only one additional current sensor. The proposed schemes are evaluated by the simulations and laboratory experiments. A satisfactory performance and good agreement between the theory and practice are demonstrated.

Analysis of the voltage source inverter with small DC-link capacitor

IIn electric drives, frequency converters are used to generatefor the electric motor the AC voltage with variable frequency and amplitude. When considering the annual sale of drives in values of money and units sold, the use of low-performance drives appears to be in predominant. These drives have tobe very cost effective to manufacture and use, while they are also expected to fulfill the harmonic distortion standards. One of the objectives has also been to extend the lifetime of the frequency converter. In a traditional frequency converter, a relatively large electrolytic DC-link capacitor is used. Electrolytic capacitors are large, heavy and rather expensive components. In many cases, the lifetime of the electrolytic capacitor is the main factor limiting the lifetime of the frequency converter. To overcome the problem, the electrolytic capacitor is replaced with a metallized polypropylene film capacitor (MPPF). The MPPF has improved properties when compared to the electrolytic capacitor. By replacing the electrolytic capacitor with a film capacitor the energy storage of the DC-linkwill be decreased. Thus, the instantaneous power supplied to the motor correlates with the instantaneous power taken from the network. This yields a continuousDC-link current fed by the diode rectifier bridge. As a consequence, the line current harmonics clearly decrease. Because of the decreased energy storage, the DC-link voltage fluctuates. This sets additional conditions to the controllers of the frequency converter to compensate the fluctuation from the supplied motor phase voltages. In this work three-phase and single-phase frequency converters with small DC-link capacitor are analyzed. The evaluation is obtained with simulations and laboratory measurements.

Direct torque control of permanent magnet synchronous machines - analysis and implementation

Thedirect torque control (DTC) has become an accepted vector control method besidethe current vector control. The DTC was first applied to asynchronous machines,and has later been applied also to synchronous machines. This thesis analyses the application of the DTC to permanent magnet synchronous machines (PMSM). In order to take the full advantage of the DTC, the PMSM has to be properly dimensioned. Therefore the effect of the motor parameters is analysed taking the control principle into account. Based on the analysis, a parameter selection procedure is presented. The analysis and the selection procedure utilize nonlinear optimization methods. The key element of a direct torque controlled drive is the estimation of the stator flux linkage. Different estimation methods - a combination of current and voltage models and improved integration methods - are analysed. The effect of an incorrect measured rotor angle in the current model is analysed andan error detection and compensation method is presented. The dynamic performance of an earlier presented sensorless flux estimation method is made better by improving the dynamic performance of the low-pass filter used and by adapting the correction of the flux linkage to torque changes. A method for the estimation ofthe initial angle of the rotor is presented. The method is based on measuring the inductance of the machine in several directions and fitting the measurements into a model. The model is nonlinear with respect to the rotor angle and therefore a nonlinear least squares optimization method is needed in the procedure. A commonly used current vector control scheme is the minimum current control. In the DTC the stator flux linkage reference is usually kept constant. Achieving the minimum current requires the control of the reference. An on-line method to perform the minimization of the current by controlling the stator flux linkage reference is presented. Also, the control of the reference above the base speed is considered. A new estimation flux linkage is introduced for the estimation of the parameters of the machine model. In order to utilize the flux linkage estimates in off-line parameter estimation, the integration methods are improved. An adaptive correction is used in the same way as in the estimation of the controller stator flux linkage. The presented parameter estimation methods are then used in aself-commissioning scheme. The proposed methods are tested with a laboratory drive, which consists of a commercial inverter hardware with a modified software and several prototype PMSMs.

Effect of water velocity on the uptake of polychlorinatedd biphenyls (PCBs) by silicone rubber (SR) and low-density polyethylene (LDPE) passive samplers: an assessment of the efficiency of performance reference compounds (PRCs) in river-like flow conditions

One aim of this study is to determine the impact of water velocity on the uptake of indicator polychlorinated biphenyls (iPCBs) by silicone rubber (SR) and low-density polyethylene (LDPE) passive samplers. A second aim is to assess the efficiency of performance reference compounds (PRCs) to correct for the impact of water velocity. SR and LDPE samplers were spiked with 11 or 12 PRCs and exposed for 6 weeks to four different velocities (in the range of 1.6 to 37.7 cm s−1) in river-like flow conditions using a channel system supplied with river water. A relationship between velocity and the uptakewas found for each iPCB and enables to determine expected changes in the uptake due to velocity variations. For both samplers, velocity increases from 2 to 10 cm s−1, 30 cm s−1 (interpolated data) and 100 cm s−1 (extrapolated data) lead to increases of the uptake which do not exceed a factor of 2, 3 and 4.5, respectively. Results also showed that the influence of velocity decreased with increasing the octanol-water coefficient partition (log Kow) of iPCBs when SR is used whereas the opposite effect was observed for LDPE. Time-weighted average (TWA) concentrations of iPCBs in water were calculated from iPCB uptake and PRC release. These calculations were performed using either a single PRC or all the PRCs. The efficiency of PRCs to correct the impact of velocity was assessed by comparing the TWA concentrations obtained at the four tested velocities. For SR, a good agreement was found among the four TWA concentrations with both methods (average RSD b 10%). Also for LDPE, PRCs offered a good correction of the impact of water velocity (average RSD of about 10 to 20%). These results contribute to the process of acceptance of passive sampling in routine regulatory monitoring programs.

Global Diversity Lines-A Five-Continent Reference Panel of Sequenced Drosophila melanogaster Strains.

Reference collections of multiple Drosophila lines with accumulating collections of "omics" data have proven especially valuable for the study of population genetics and complex trait genetics. Here we present a description of a resource collection of 84 strains of Drosophila melanogaster whose genome sequences were obtained after 12 generations of full-sib inbreeding. The initial rationale for this resource was to foster development of a systems biology platform for modeling metabolic regulation by the use of natural polymorphisms as perturbations. As reference lines, they are amenable to repeated phenotypic measurements, and already a large collection of metabolic traits have been assayed. Another key feature of these strains is their widespread geographic origin, coming from Beijing, Ithaca, Netherlands, Tasmania, and Zimbabwe. After obtaining 12.5× coverage of paired-end Illumina sequence reads, SNP and indel calls were made with the GATK platform. Thorough quality control was enabled by deep sequencing one line to >100×, and single-nucleotide polymorphisms and indels were validated using ddRAD-sequencing as an orthogonal platform. In addition, a series of preliminary population genetic tests were performed with these single-nucleotide polymorphism data for assessment of data quality. We found 83 segregating inversions among the lines, and as expected these were especially abundant in the African sample. We anticipate that this will make a useful addition to the set of reference D. melanogaster strains, thanks to its geographic structuring and unusually high level of genetic diversity.

Delivery of European Cross-Border Health Care and the Relevance and Effects of EU Regulations and Judicial Processes with Reference to Delivery of Drugs and Blood Donor Information Material.

Valtion rajat ylittävät terveyspalvelut Euroopan unionissa sekä Euroopan unionin säädösten merkitys ja vaikutus erityisesti lääkejakeluun ja verenluovuttajille jaettavaan tiedotusaineistoon Valtion rajat ylittävä terveydenhuolto on suuren kiinnostuksen kohteena Euroopan unionissa. Resurssien hyödyntäminen parhaalla mahdollisella tavalla ja tiedon keskittäminen ovat tarpeen terveydenhuollon kustannusten alati noustessa. Terveydenhuoltopalvelut kuuluvat Euroopan sisämarkkinoiden vapaan liikkuvuuden piiriin. Euroopan unionilla ei ole kuitenkaan toimivaltaa säädellä terveydenhuoltojärjestelmiä, vaan sen mahdollisuudet ovat enimmäkseen kansanterveyden edistämisessä ja suojelussa, myös muilla toimialueilla kuin terveydenhuollossa. Tutkimuksen tavoitteena oli tutkia Euroopan unionin säädösten vaikutusta terveydenhuoltosektoriin, erityisesti valtion rajat ylittäviin terveydenhuoltopalveluihin. Erityiskohteena olivat lääkemääräyksen toimittaminen toisen Euroopan unionin jäsenmaan apteekista, resepti-lääkkeiden maahantuonti omaan henkilökohtaiseen käyttöön, sähköisen lääkemääräyksen käyttö kansallisesti ja mahdollisuudet sen käyttöön eri jäsenmaiden välillä, online-apteekkien soveltuvuus Euroopan unionin sisämarkkinoille sekä verenluovuttajille jaettavan tiedotusaineiston yhtenäistämistarve Euroopan unionin alueella. Tutkimuksen osa-alueiden aineisto koottiin vuosina 1999–2003, jolloin Euroopan unioniin kuului 15 jäsenmaata. Apteekit toimittivat useimmiten myös ei-kansalliset, toisessa Euroopan unionin jäsenmaassa annetut lääkemääräykset. Kaikki jäsenmaat rajoittivat lääkemääräyksen vaativien lääkkeiden maahantuontia. Rajoituksia oli maahantuontimäärissä ja -tavoissa. Lisäksi sairasvakuutuskorvausten saaminen ulkomailla lunastetuista reseptilääkkeistä oli hankalaa. Sähköiset lääkemääräykset olivat käytössä vain kahdessa maassa, mutta useissa maissa suunniteltiin niiden kokeilua. Standardit ja käyttöjärjestelmät olivat erilaisia eri maissa. Euroopan unionin alueelle on perustettu online-apteekkeja, joiden toiminta on kuitenkin vaatimatonta. Verenluovuttajille annettava tiedotusaineisto ei missään maassa täyttänyt veridirektiivin vaatimuksia. Tutkimuksen tulokset osoittivat kansallisten käytäntöjen eroavaisuuksien rajoittavan valtion rajat ylittäviä terveydenhuoltopalveluita. Vaikka Euroopan unionin tavoitteena ei ole yhtenäistää terveydenhuoltojärjestelmiä, on tarpeen arvioida uudelleen unionin ja jäsenmaiden välistä työnjakoa. Kansalliset terveydenhuoltojärjestelmät eivät ole erillään Euroopan sisämarkkinoista, jotka merkittävästi vaikuttavat terveydenhuoltoon.