Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly.

Implementing NX Remote Desktop technology in the LTSP system

This project focuses on studying and testing the benefits of the NX Remote Desktop technology in administrative use for Finnish Meteorological Institutes existing Linux Terminal Service Project environment. This was done due to the criticality of the system caused by growing number of users as the Linux Terminal Service Project system expands. Although many of the supporting tasks can be done via Secure Shell connection, testing graphical programs or desktop behaviour in such a way is impossible. At first basic technologies behind the NX Remote Desktop were studied, and after that started the testing of two possible programs, FreeNX and NoMachine NX server. Testing the functionality and bandwidth demands were first done in a closed local area network, and results were studied. The better candidate was then installed in a virtual server simulating actual Linux Terminal Service Project server at Finnish Meteorological Institute and connection from Internet was tested to see was there any problems with firewalls and security policies. The results are reported in this study. Studying and testing the two different candidates of NX Remote Desktop showed, that NoMachine NX Server provides better customer support and documentation. Security aspects of the Finnish Meteorological Institute had also to be considered, and since updates along with the new developing tools are announced in next version of the program, this version was the choice. Studies also show that even NoMachine promises a swift connection over an average of 20Kbit/s bandwidth, at least double of that is needed. This project gives an overview of available remote desktop products along their benefits. NX Remote Desktop technology is studied, and installation instructions are included. Testing is done in both, closed and the actual environment and problems and suggestions are studied and analyzed. The installation to the actual LTSP server is not yet made, but a virtual server is put up in the same place in the view of network topology. This ensures, that if the administrators are satisfied with the system, installation and setting up the system will go as described in this report.

Should banking supervision and monetary policy tasks be given to different agencies?

This paper adds some new arguments to the thesis that the responsibility forbanking supervision should be assigned to an agency formally separated bythe Central bank. We also provide some additional evidence on the macroand microeconomic performance of OECD countries whose banking systems areclassified according to the regulatory regime in place. We find that theinflation rate is considerably higher and more volatile in countries wherethe Central bank acts as a monopolist in banking supervision. Besides,although banks seem to be more profitable when Central banks supervise them,they incur into higher costs and rely more on deposits with respect to moresophisticated liabilities as a funding source.The data are not definitively in favor of functional separation. However, we argue that the evolution of financial intermediaries, moral hazard problems and especially cost accountability seem to suggest that separation would be a better solution for industrialized countries.We also critically discuss the current arrangement of financial regulationand supervision in the EMU: our proposal is to establish an independentEuropean System of Financial Supervisors (ESFS) structured similarly to theESCB.

Method to assess and optimise dependability of complex macro-systems: application to a railway signalling system

Achieving a high degree of dependability in complex macro-systems is challenging. Because of the large number of components and numerous independent teams involved, an overview of the global system performance is usually lacking to support both design and operation adequately. A functional failure mode, effects and criticality analysis (FMECA) approach is proposed to address the dependability optimisation of large and complex systems. The basic inductive model FMECA has been enriched to include considerations such as operational procedures, alarm systems. environmental and human factors, as well as operation in degraded mode. Its implementation on a commercial software tool allows an active linking between the functional layers of the system and facilitates data processing and retrieval, which enables to contribute actively to the system optimisation. The proposed methodology has been applied to optimise dependability in a railway signalling system. Signalling systems are typical example of large complex systems made of multiple hierarchical layers. The proposed approach appears appropriate to assess the global risk- and availability-level of the system as well as to identify its vulnerabilities. This enriched-FMECA approach enables to overcome some of the limitations and pitfalls previously reported with classical FMECA approaches.

ProScan Automated Profilogram Reduction System, MLR-94-7, 1994

Kansas State University, with funding from the Kansas Department of Transportation (KDOT), has developed a computerized reduction system for profilograms produced by mechanical profilographs. The commercial version of the system (ProScan (trademark)) is marketed by Devore Systems, Inc. The system consists of an IBM Compatible PC 486SX33 computer or better, Epson LQ-570 printer, a Logitech Scanman 32 hand scanner system, a paper transport unit, and the ProScan software. The Scanner is not adaptable to IBM computers with the micro channel architecture. The Iowa DOT Transportation Centers could realize the following advantages by using ProScan: (1) Save about 5 to 8 staff hours of reduction and reporting time per Transportation Center per week for a Materials Technician 3 or 4 (the time savings would come during the busiest part of the season); (2) Reduce errors in reduction, transfer, and typing of profile values; (3) Increase the accuracy of the monitor results; and (4) Allow rapid evaluation of contractor traces when tolerance limits between monitor and certified results are exceeded.

Norms establishment of the Diagnosis and Recommendation Integrated System (DRIS) for nutritional diagnosis of sugarcane

The objectives of this study were to establish DRIS norms for sugarcane crop, to compare mean yield, foliar nutrient contents and variance of nutrient ratios of low- and high-yielding groups and to compare mean values of nutrient ratios selected as the DRIS norms of low- and high-yielding groups. Leaf samples (analyzed for N, P, K, Ca, Mg, S, Cu, Mn and Zn contents) and respective yields were collected in 126 commercial sugarcane fields in Rio de Janeiro State, Brazil and used to establish DRIS norms for sugarcane. Nearly all nutrient ratios selected as DRIS norms (77.8%) showed statistical differences between mean values of the low- and high-yielding groups. These different nutritional balances between the low- and high-yielding groups indicate that the DRIS norms developed in this paper are reliable. The DRIS norms for micronutrients with high S²l /S²h ratio and low coefficient of variation found can provide more security to evaluate the micronutrient status of sugarcane.

A Secure Mobile-based Authentication System

Financial information is extremely sensitive. Hence, electronic banking must provide a robust system to authenticate its customers and let them access their data remotely. On the other hand, such system must be usable, affordable, and portable.We propose a challengeresponse based one-time password (OTP) scheme that uses symmetriccryptography in combination with a hardware security module. The proposed protocol safeguards passwords from keyloggers and phishing attacks.Besides, this solution provides convenient mobility for users who want to bank online anytime and anywhere, not just from their owntrusted computers.

Short-term Hydropower Planning System

The Thesis gives a decision support framework that has significant impact on the economic performance and viability of a hydropower company. The studyaddresses the short-term hydropower planning problem in the Nordic deregulated electricity market. The basics of the Nordic electricity market, trading mechanisms, hydropower system characteristics and production planning are presented in the Thesis. The related modelling theory and optimization methods are covered aswell. The Thesis provides a mixed integer linear programming model applied in asuccessive linearization method for optimal bidding and scheduling decisions inthe hydropower system operation within short-term horizon. A scenario based deterministic approach is exploited for modelling uncertainty in market price and inflow. The Thesis proposes a calibration framework to examine the physical accuracy and economic optimality of the decisions suggested by the model. A calibration example is provided with data from a real hydropower system using a commercial modelling application with the mixed integer linear programming solver CPLEX.

Implementation of counter testing in Nokia Automation System

In this study the performance measurement, a part of the research and development of the RNC, was improved by implementing counter testing to the Nokia Automation System. The automation of counter testing is a feature the customer ordered, because performing counter testing manually is rather complex. The objective was to implement an automated counter testing system, which once configured correctly, would manage to run the testing and perform the analysis. The requirements for the counter testing were first studied. It was investigated if the auto-mation of the feature was feasible in the meetings with the customer. The basic functionality required for the automation was also drawn. The technologies used in the architecture of the Nokia Automation System were studied. Based on the results of the study, a new technology, wxWidgets, was introduced. The new technology was necessary to facilitate the implementing of the required feature. Finally the implementation of the counter testing was defined and implemented. The result of this study was the automation of the counter testing method developed as a new feature for the Nokia Automation System. The feature meets the specifications and requirements set by the customer. The performing of the counter testing feature is totally automated. Only configuration of the test cases is done by the user. The customer has presented new requests to further develop the feature and there are plans by the Nokia Automation System developers to implement those in the near future. The study describes the implementation of the counter testing feature introduced. The results of the study give guidelines for further developing the feature.

Sanitary quality of edible bivalve mollusks in Southeastern Brazil using an UV based depuration system

The increase in seafood production, especially in mariculture worldwide, has brought out the need of continued monitoring of shellfish production areas in order to ensure safety to human consumption. The purpose of this research was to evaluate pathogenic protozoa, viruses and bacteria contamination in oysters before and after UV depuration procedure, in brackish waters at all stages of cultivation and treatment steps and to enumerate microbiological indicators of fecal contamination from production site up to depuration site in an oyster cooperative located at the Southeastern estuarine area of Brazil. Oysters and brackish water were collected monthly from September 2009 to November 2010. Four sampling sites were selected for enteropathogens analysis: site 1- oyster growth, site 2- catchment water (before UV depuration procedure), site 3 - filtration stage of water treatment (only for protozoa analysis) and site 4- oyster's depuration tank. Three microbiological indicators ! were examined at sites 1, 2 and 4. The following pathogenic microorganisms were searched: Giardia cysts, Cryptosporidium oocysts, Human Adenovirus (HAdV), Hepatitis A virus (HAV), Human Norovirus (HnoV) (genogroups I and II), JC strain Polyomavirus (JCPyV) and Salmonella sp. Analysis consisted of molecular detection (qPCR) for viruses (oysters and water samples); immunomagnetic separation followed by direct immunofluorescence assay for Cryptosporidium oocysts and Giardia cysts and also molecular detection (PCR) for the latter (oysters and water samples); commercial kit (Reveal-Neogee (R)) for Salmonella analysis (oysters). Giardia was the most prevalent pathogen in all sites where it was detected: 36.3%, 18.1%, 36.3% and 27.2% of water from sites 1, 2, 3 and 4 respectively; 36.3% of oysters from site 1 and 54.5% of depurated oysters were harboring Giardia cysts. The huge majority of contaminated samples were classified as Giardia duodenalis. HAdv was detected in water and o! ysters from growth site and HnoV GI in two batches of oysters ! (site 1) in huge concentrations (2.11 x 10(13), 3.10 x 10(12) gc/g). In depuration tank site, Salmonella sp., HAV (4.84 x 10(3)) and HnoV GII (7.97 x 10(14)) were detected once in different batches of oysters. Cryptosporidium spp. oocysts were present in 9.0% of water samples from site four. These results reflect the contamination of oysters even when UV depuration procedures are employed in this shellfish treatment plant. Moreover, the molecular comprehension of the sources of contamination is necessary to develop an efficient management strategy allied to shellfish treatment improvement to prevent foodborne illnesses. (C) 2011 Elsevier Ltd. All rights reserved.

Building distributed high availability system

Today’s commercial web sites are under heavy user load and they are expected to be operational and available at all times. Distributed system architectures have been developed to provide a scalable and failure tolerant high availability platform for these web based services. The focus on this thesis was to specify and implement resilient and scalable locally distributed high availability system architecture for a web based service. Theory part concentrates on the fundamental characteristics of distributed systems and presents common scalable high availability server architectures that are used in web based services. In the practical part of the thesis the implemented new system architecture is explained. Practical part also includes two different test cases that were done to test the system's performance capacity.

Trigger and data link system for CMS Resistive Plate Chambers at the LHC accelerator

The purpose of the work was to realize a high-speed digital data transfer system for RPC muon chambers in the CMS experiment on CERN’s new LHC accelerator. This large scale system took many years and many stages of prototyping to develop, and required the participation of tens of people. The system interfaces to Frontend Boards (FEB) at the 200,000-channel detector and to the trigger and readout electronics in the control room of the experiment. The distance between these two is about 80 metres and the speed required for the optic links was pushing the limits of available technology when the project was started. Here, as in many other aspects of the design, it was assumed that the features of readily available commercial components would develop in the course of the design work, just as they did. By choosing a high speed it was possible to multiplex the data from some the chambers into the same fibres to reduce the number of links needed. Further reduction was achieved by employing zero suppression and data compression, and a total of only 660 optical links were needed. Another requirement, which conflicted somewhat with choosing the components a late as possible was that the design needed to be radiation tolerant to an ionizing dose of 100 Gy and to a have a moderate tolerance to Single Event Effects (SEEs). This required some radiation test campaigns, and eventually led to ASICs being chosen for some of the critical parts. The system was made to be as reconfigurable as possible. The reconfiguration needs to be done from a distance as the electronics is not accessible except for some short and rare service breaks once the accelerator starts running. Therefore reconfigurable logic is extensively used, and the firmware development for the FPGAs constituted a sizable part of the work. Some special techniques needed to be used there too, to achieve the required radiation tolerance. The system has been demonstrated to work in several laboratory and beam tests, and now we are waiting to see it in action when the LHC will start running in the autumn 2008.

On Transmission System Design for Wireless Broadcasting

This thesis considers aspects related to the design and standardisation of transmission systems for wireless broadcasting, comprising terrestrial and mobile reception. The purpose is to identify which factors influence the technical decisions and what issues could be better considered in the design process in order to assess different use cases, service scenarios and end-user quality. Further, the necessity of cross-layer optimisation for efficient data transmission is emphasised and means to take this into consideration are suggested. The work is mainly related terrestrial and mobile digital video broadcasting systems but many of the findings can be generalised also to other transmission systems and design processes. The work has led to three main conclusions. First, it is discovered that there are no sufficiently accurate error criteria for measuring the subjective perceived audiovisual quality that could be utilised in transmission system design. Means for designing new error criteria for mobile TV (television) services are suggested and similar work related to other services is recommended. Second, it is suggested that in addition to commercial requirements there should be technical requirements setting the frame work for the design process of a new transmission system. The technical requirements should include the assessed reception conditions, technical quality of service and service functionalities. Reception conditions comprise radio channel models, receiver types and antenna types. Technical quality of service consists of bandwidth, timeliness and reliability. Of these, the thesis focuses on radio channel models and errorcriteria (reliability) as two of the most important design challenges and provides means to optimise transmission parameters based on these. Third, the thesis argues that the most favourable development for wireless broadcasting would be a single system suitable for all scenarios of wireless broadcasting. It is claimed that there are no major technical obstacles to achieve this and that the recently published second generation digital terrestrial television broadcasting system provides a good basis. The challenges and opportunities of a universal wireless broadcasting system are discussed mainly from technical but briefly also from commercial and regulatory aspect

Supporting Solution Business with an Integrated Enterprise System

Some of the world’s leading companies now compete by providing integrated solutions to identify and solve each customer’s business problem by providing services to design, integrate, operate and finance a product or system during its life cycle. At the same time, because of the requirements of new global economy, companies are implementing new integrated ERP systems. The objective of this thesis was to define how solution offering can be implemented in the integrated ERP system so that it is possible to sell, deliver and maintain solution offering with the new enterprise applications. The research was conducted as a qualitative case study research consisting of literature review, theme-interviews and an analysis phase. For a start this study introduces new insight for combining solution business, offering modeling and modern ERP system theories. The results of this research illustrate the limitations of an integrated ERP system to support solution business and show the need to develop a commercial product model in order to improve the combination of solution offering and IT systems.

Earnings quality and performance in the banking industry: a profit frontier approach

The analysis of efficiency and productivity in banking has received a great deal of attention for almost three decades now. However, most of the literature to date has not explicitly accounted for risk when measuring efficiency. We propose an analysis of profit efficiency taking into account how the inclusion of a variety of bank risk measures might bias efficiency scores. Our measures of risk are partly inspired by the literature on earnings management and earnings quality, keeping in mind that loan loss provisions, as a generally accepted proxy for risk, can be adjusted to manage earnings and regulatory capital. We also consider some variants of traditional models of profit efficiency where different regimes are stipulated so that financial institutions can be evaluated in different dimensions—i.e., prices, quantities, or prices and quantities simultaneously. We perform this analysis on the Spanish banking industry, whose institutions have been deeply affected by the current international financial crisis, and where re-regulation is taking place. Our results can be explored in multiple dimensions but, in general, they indicate that the impact of earnings management on profit efficiency is of less magnitude than what might a priori be expected, and that on the whole, savings banks have performed less well than commercial banks. However, savings banks are adapting to the new regulatory scenario and rapidly catching up with commercial banks, especially in some dimensions of performance.