"Soap-Bubble" visualization and quantitative analysis of 3D coronary magnetic resonance angiograms.

In order to compare coronary magnetic resonance angiography (MRA) data obtained with different scanning methodologies, adequate visualization and presentation of the coronary MRA data need to be ensured. Furthermore, an objective quantitative comparison between images acquired with different scanning methods is desirable. To address this need, a software tool ("Soap-Bubble") that facilitates visualization and quantitative comparison of 3D volume targeted coronary MRA data was developed. In the present implementation, the user interactively specifies a curved subvolume (enclosed in the 3D coronary MRA data set) that closely encompasses the coronary arterial segments. With a 3D Delaunay triangulation and a parallel projection, this enables the simultaneous display of multiple coronary segments in one 2D representation. For objective quantitative analysis, frequently explored quantitative parameters such as signal-to-noise ratio (SNR); contrast-to-noise ratio (CNR); and vessel length, sharpness, and diameter can be assessed. The present tool supports visualization and objective, quantitative comparisons of coronary MRA data obtained with different scanning methods. The first results obtained in healthy adults and in patients with coronary artery disease are presented.

Coscheduling techniques and monitoring tools for non-dedicated cluster computing

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel performance against the local interactive response. Explicit and implicit coscheduling techniques in a PVM-Linux NOW (or cluster) have been implemented. Furthermore, dynamic coscheduling remains an open question when parallel jobs are executed in a non-dedicated Cluster. A basis model for dynamic coscheduling in Cluster systems is presented in this paper. Also, one dynamic coscheduling algorithm for this model is proposed. The applicability of this algorithm has been proved and its performance analyzed by simulation. Finally, a new tool (named Monito) for monitoring the different queues of messages in such an environments is presented. The main aim of implementing this facility is to provide a mean of capturing the bottlenecks and overheads of the communication system in a PVM-Linux cluster.

Level Set Methods in Image Processing

This thesis gives an overview of the use of the level set methods in the field of image science. The similar fast marching method is discussed for comparison, also the narrow band and the particle level set methods are introduced. The level set method is a numerical scheme for representing, deforming and recovering structures in an arbitrary dimensions. It approximates and tracks the moving interfaces, dynamic curves and surfaces. The level set method does not define how and why some boundary is advancing the way it is but simply represents and tracks the boundary. The principal idea of the level set method is to represent the N dimensional boundary in the N+l dimensions. This gives the generality to represent even the complex boundaries. The level set methods can be powerful tools to represent dynamic boundaries, but they can require lot of computing power. Specially the basic level set method have considerable computational burden. This burden can be alleviated with more sophisticated versions of the level set algorithm like the narrow band level set method or with the programmable hardware implementation. Also the parallel approach can be used in suitable applications. It is concluded that these methods can be used in a quite broad range of image applications, like computer vision and graphics, scientific visualization and also to solve problems in computational physics. Level set methods and methods derived and inspired by it will be in the front line of image processing also in the future.

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies

Background: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLS http://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease"s rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). Results: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. Conclusions: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.

Laajakaistaverkon topologian visualisointi

Viimeisten vuosien aikana laajakaistaoperaattoreiden laajakaistaverkot ovat nopeiden ja kiinteähintaisten laajakaistaliittymien johdosta kasvaneet suuriksi kokonaisuuksiksi. Kokonaisuuksia hallitaan erilaisilla verkonhallintatyökaluilla. Verkonhallintatyökalut sisältävät suuren määrän eri tasoista tietoa laitteista ja laitteiden välisistä suhteista. Kokonaisuuksien hahmottaminen ilman tiedoista rakennettua kuvaa on vaikeaa ja hidasta. Laajakaistaverkon topologian visualisoinnissa muodostetaan kuva laitteista ja niiden välisistä suhteista. Visualisoitua kuvaa voidaan käyttää osana verkonhallintatyökalua, jolloin käyttäjälle muodostuu nopeasti näkymä verkon laitteista ja rakenteesta eli topologiasta. Visualisoinnissa kuvan piirto-ongelma täytyy muuttaa graafin piirto-ongelmaksi. Graafin piirto-ongelmassa verkon rakennetta käsitellään graafina, joka mahdollistaa kuvan muodostamisen automaattisia piirtomenetelmiä hyväksikäyttäen. Halutunlainen ulkoasu kuvalle muodostetaan automaattisilla piirtomenetelmillä, joilla laitteiden ja laitteiden välisten suhteiden esitystapoja voidaan muuttaa. Esitystavoilla voidaan muuttaa esimerkiksi laitteiden muotoa, väriä ja kokoa. Esitystapojen lisäksi piirtomenetelmien tärkein tehtävä on laskea laitteiden sijaintien koordinaattien arvot, jotka loppujen lopuksi määräävät koko kuvan rakenteen. Koordinaattien arvot lasketaan piirtoalgoritmeilla, joista voimiin perustuvat algoritmit sopivat parhaiten laajakaistaverkkojen laitteiden sijaintien laskemiseen. Tämän diplomityön käytännön työssä toteutettiin laajakaistaverkon topologian visualisointityökalu.

Novel Genome-Editing Tools to Model and Correct Primary Immunodeficiencies.

Severe combined immunodeficiency (SCID) and other severe non-SCID primary immunodeficiencies (non-SCID PID) can be treated by allogeneic hematopoietic stem cell (HSC) transplantation, but when histocompatibility leukocyte antigen-matched donors are lacking, this can be a high-risk procedure. Correcting the patient's own HSCs with gene therapy offers an attractive alternative. Gene therapies currently being used in clinical settings insert a functional copy of the entire gene by means of a viral vector. With this treatment, severe complications may result due to integration within oncogenes. A promising alternative is the use of endonucleases such as ZFNs, TALENs, and CRISPR/Cas9 to introduce a double-stranded break in the DNA and thus induce homology-directed repair. With these genome-editing tools a correct copy can be inserted in a precisely targeted "safe harbor." They can also be used to correct pathogenic mutations in situ and to develop cellular or animal models needed to study the pathogenic effects of specific genetic defects found in immunodeficient patients. This review discusses the advantages and disadvantages of these endonucleases in gene correction and modeling with an emphasis on CRISPR/Cas9, which offers the most promise due to its efficacy and versatility.

Development of the Simulation Environment for the Mobile Phone User Interfaces

Diplomityössä käsitellään Nokia Mobile Phonesin matkapuhelimien käyttöliittymäohjelmistojen suunnittelu-ja testausympäristön kehitystä. Ympäristöön lisättiin kaksi ohjelmistomodulia avustamaan simulointia ja versionhallintaa. Visualisointityökalulla matkapuhelimen toiminta voidaan jäljittää suunnittelu- kaavioihin tilasiirtyminä, kun taas vertailusovelluksella kaavioiden väliset erot nähdään graafisesti. Kehitetyt sovellukset parantavat käyttöliittymien suunnitteluprosessia tehostaen virheiden etsintää, optimointia ja versionhallintaa. Visualisointityökalun edut ovat merkittävät, koska käyttöliittymäsovellusten toiminta on havaittavissa suunnittelu- kaavioista reaaliaikaisen simuloinnin yhteydessä. Näin virheet ovat välittömästi paikannettavissa. Lisäksi työkalua voidaan hyödyntää kaavioita optimoitaessa, jolloin sovellusten kokoja muistintarve pienenee. Graafinen vertailutyökalu tuo edun rinnakkaiseen ohjelmistosuunnitteluun. Eri versioisten suunnittelukaavioiden erot ovat nähtävissä suoraan kaaviosta manuaalisen vertailun sijaan. Molemmat työkalut otettiin onnistuneesti käyttöön NMP:llä vuoden 2001 alussa.

Development of e-Service tools for customer services and processes, Case: KONE Oyj Finland

Tutkimuksen tavoitteena oli selvittää miten kehittää yrityksen nykyistä e-palvelujärjestelmää, Internet -teknologiaan perustuvaa sähköisiä kommunikaatio- ja tiedonjakojärjestelmää, yrityksen business-to-business asiakkuuksien johtamisessa. Tavoitteena oli myös luoda ehdotukset uusista e-palvelusopimusmalleista. Tutkimuksen teoriaosuudessa pyrittiin kehittämään aikaisempiin tutkimuksiin, tietokirjallisuuteen ja asiantuntijoihin perustuva viitekehysmalli. Empiirisessä osassa tutkimuksen tavoitteisiin pyrittiin haastattelemalla yrityksen asiakkaita ja henkilöstöä, sekä tarkastelemalla asiakaskontaktien nykyistä tilaa ja kehittymistä. Näiden tietojen perusteella selvitettiin e-palvelun käyttäjien tarpeita, profiilia ja valmiuksia palvelun käyttöön sekä palvelun nykyistä houkuttelevuutta. Tutkimuksen teoriaosan lähdeaineistona käytettiin kirjallisuutta, artikkeleita ja tilastoja asiakashallinnasta sekä e-palveluiden, erityisesti Internet ja verkkopalveluiden markkinoinnista, nykytilasta sekä palveluiden kehittämisestä. Lisäksi tutkittiin kirjallisuutta arvoverkostoanalyysistä, asiakkaan arvosta, informaatioteknologiasta, palvelun laadusta ja asiakastyytyväisyydestä. Tutkimuksen empiirinen osa perustuu yrityksen henkilöstöltä sekä asiakkailta haastatteluissa kerättyihin tietoihin, yrityksen ennalta keräämiin materiaaleihin sekä Taloustutkimuksen keräämiin tietoihin. Tutkimuksessa käytettiin case -menetelmää, joka oli yhdistelmä sekä kvalitatiivista että kvantitatiivista tutkimusta. Casen tarkoituksena oli testata mallin paikkansapitävyyttä ja käyttökelpoisuutta, sekä selvittää onko olemassa vielä muita tekijöitä, jotka vaikuttavat asiakkaan saamaan arvoon. Kvalitatiivinen aineisto perustuu teemahaastattelumenetelmää soveltaen haastateltuihin asiakkaisiin ja yrityksen työntekijöihin. Kvantitatiivinen tutkimus perustuu Taloustutkimuksen tutkimukseen ja yrityksen asiakaskontakteista kerättyyn tietoon. Haastatteluiden perusteella e-palvelut nähtiin hyödyllisinä ja tulevaisuudessa erittäin tärkeinä. E-palvelut nähdään yhtenä tärkeänä kanavana, perinteisten kanavien rinnalla, tehostaa business-to-business -asiakkuuksien johtamista. Tutkimuksen antamien tulosten mukaan asiakkaiden palveluun liittyvän tieto-, taito-, tarpeellisuus- ja kiinnostavuustasojen vaihtelevaisuus osoittaa selvän tarpeen eritasoisille e-palvelupaketti ratkaisuille. Tuloksista muodostettu ratkaisuehdotus käsittää neljän eri e-palvelupaketin rakentamisen asiakkaiden eri tarpeita mukaillen.

Intra-organizational use of communication tools in value nets - Cases from the ICT industry

Tutkimuksen tavoitteena oli selvittää sisäisen kommunikoinnin tilannetta case-yrityksissä. Yritykset kuuluvat kahteen case-arvoverkostoon, jotka toimivat informaatio- ja kommunikaatioteknologian alalla. Sisäinen kommunikointi valittiin tutkimusalueeksi, koska se muodostaa perustan ulkoiselle, yritysten väliselle kommunikoinnille. Tutkimuksen painopiste oli web-pohjaisessa kommunikoinnissa ja webin ominaisuuksissa arvoverkoston näkökulmasta. Tutkimusprosessissa käytettiin sekä kvalitatiivisia että kvantitatiivisia menetelmiä. Tutkimuksen kvantitatiivinen osa toteutettiin web-kyselynä, jonka tulokset osoittivat, että case-yritysten sisäinen kommunikointi perustuu pääasiassa perinteisten kommunikointivälineiden käyttöön. Toisin sanoen, webin hyödyntäminen on vähäistä, mihin vaikuttavat monet eri tekijät. Webissä on kuitenkin useita ominaisuuksia, jotka parantavat kommunikointia arvoverkostossa ja siksi nämä web-pohjaiset välineet tulisi huomioida, kun suunnitellaan yleistä kommunikointijärjestelmää. Tutkimuksen teoreettisessa osassa määriteltiin vuorovaikutteisuus-ominaisuuteen perustuva kommunikointivälineiden luokittelu. Tämän lisäksi määriteltiin myös arvoverkoston käsite. Empiirinen osa koostui web-kyselyn toteutuksen ja tulosten raportoinnista, jonka jälkeen yhteenvetokappale koosti merkittävimmät havainnot sekä mahdolliset jatkotutkimusaiheet.

Calculation analysis of energy saving tools for fan and pump applications

This thesis analyses the calculation of FanSave and PumpSave energy saving tools calculation. With these programs energy consumption of variable speed drive control for fans and pumps can be compared to other control methods. With FanSave centrifugal and axial fans can be examined and PumpSave deals with centrifugal pumps. By means of these programs also suitable frequency converter can be chosen from the ABB collection. Programs need as initial values information about the appliances like amount of flow and efficiencies. Operation time is important factor when calculating the annual energy consumption and information about it are the length and profile. Basic theory related to fans and pumps is introduced without more precise instructions for dimensioning. FanSave and PumpSave contain various methods for flow control. These control methods are introduced in the thesis based on their operational principles and suitability. Also squirrel cage motor and frequency converter are introduced because of their close involvement to fans and pumps. Second part of the thesis contains comparison between results of FanSave’s and PumpSave’s calculation and performance curve based calculation. Also laboratory tests were made with centrifugal and axial fan and also with centrifugal pump. With the results from this thesis the calculation of these programs can be adjusted to be more accurate and also some new features can be added.

Fluoroscopic-Guided Radial Endobronchial Ultrasound Without Guide Sheath For Peripheral Pulmonary Lesions: A Safe And Efficient Combination.

BACKGROUND: Several guidelines recommend computed tomography scans for populations with high-risk for lung cancer. The number of individuals evaluated for peripheral pulmonary lesions (PPL) will probably increase, and with it non-surgical biopsies. Associating a guidance method with a target confirmation technique has been shown to achieve the highest diagnostic yield, but the utility of bronchoscopy with radial probe endobronchial ultrasound using fluoroscopy as guidance without a guide sheath has not been reported. METHODS: We conducted a retrospective analysis of bronchoscopy with radial probe endobronchial ultrasound using fluoroscopy procedures for the investigation of PPL performed by experienced bronchoscopists with no specific previous training in this particular technique. Operator learning curves and radiological predictors were assessed for all consecutive patients examined during the first year of application of the technique. RESULTS: Fifty-one PPL were investigated. Diagnostic yield and visualization yield were 72.5 and 82.3% respectively. The diagnostic yield was 64.0% for PPL ≤20mm, and 80.8% for PPL>20mm. No false-positive results were recorded. The learning curve of all diagnostic tools showed a DY of 72.7% for the first sub-group of patients, 81.8% for the second, 72.7% for the third, and 81.8% for the last. CONCLUSION: Bronchoscopy with radial probe endobronchial ultrasound using fluoroscopy as guidance is safe and simple to perform, even without specific prior training, and diagnostic yield is high for PPL>and ≤20mm. Based on these findings, this method could be introduced as a first-line procedure for the investigation of PPL, particularly in centers with limited resources.

Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.

An important aspect of immune monitoring for vaccine development, clinical trials, and research is the detection, measurement, and comparison of antigen-specific T-cells from subject samples under different conditions. Antigen-specific T-cells compose a very small fraction of total T-cells. Developments in cytometry technology over the past five years have enabled the measurement of single-cells in a multivariate and high-throughput manner. This growth in both dimensionality and quantity of data continues to pose a challenge for effective identification and visualization of rare cell subsets, such as antigen-specific T-cells. Dimension reduction and feature extraction play pivotal role in both identifying and visualizing cell populations of interest in large, multi-dimensional cytometry datasets. However, the automated identification and visualization of rare, high-dimensional cell subsets remains challenging. Here we demonstrate how a systematic and integrated approach combining targeted feature extraction with dimension reduction can be used to identify and visualize biological differences in rare, antigen-specific cell populations. By using OpenCyto to perform semi-automated gating and features extraction of flow cytometry data, followed by dimensionality reduction with t-SNE we are able to identify polyfunctional subpopulations of antigen-specific T-cells and visualize treatment-specific differences between them.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper webcite.

Impact of quality improvement tools on the performance of firms using different quality management systems

This study compares the impact of quality management tools on the performance of organisations utilising the ISO 9001:2000 standard as a basis for a quality-management system band those utilising the EFQM model for this purpose. A survey is conducted among 107 experienced and independent quality-management assessors. The study finds that organisations with qualitymanagement systems based on the ISO 9001:2000 standard tend to use general-purpose qualitative tools, and that these do have a relatively positive impact on their general performance. In contrast, organisations adopting the EFQM model tend to use more specialised quantitative tools, which produce significant improvements in specific aspects of their performance. The findings of the study will enable organisations to choose the most effective quality-improvement tools for their particular quality strategy