Integration of Ligand- and Target-Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand-Based Virtual Screening (LBVS) and Target-Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled-rank-by-number, rank-by-rank and rank-by-vote, with the most thriving the scaled-rank-by-number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand-based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.

Simple telemedicine for developing regions: Camera phones and paper-based microfluidic devices for real-time, off-site diagnosis

This article describes a prototype system for quantifying bioassays and for exchanging the results of the assays digitally with physicians located off-site. The system uses paper-based microfluidic devices for running multiple assays simultaneously, camera phones or portable scanners for digitizing the intensity of color associated with each colorimetric assay, and established communications infrastructure for transferring the digital information from the assay site to an off-site laboratory for analysis by a trained medical professional; the diagnosis then can be returned directly to the healthcare provider in the field. The microfluidic devices were fabricated in paper using photolithography and were functionalized with reagents for colorimetric assays. The results of the assays were quantified by comparing the intensities of the color developed in each assay with those of calibration curves. An example of this system quantified clinically relevant concentrations of glucose and protein in artificial urine. The combination of patterned paper, a portable method for obtaining digital images, and a method for exchanging results of the assays with off-site diagnosticians offers new opportunities for inexpensive monitoring of health, especially in situations that require physicians to travel to patients (e.g., in the developing world, in emergency management, and during field operations by the military) to obtain diagnostic information that might be obtained more effectively by less valuable personnel.

Alternative Identities and Foreign Language Learning

My D-essay has the working title “Alternative Identities and Foreign Language Learning”. I have chosen this area because I have noticed a certain reluctance among Swedish students to use the foreign language English in English classes. They often seem embarrassed to express themselves in a language which is not their mother tongue, but they seem less embarrassed when they are allowed to act somebody else. These two observations converge into a focus of discussion on the matter, which will be supported by a minor study of my own, by extracts from other people’s essays on the matter, and by an overview of current litterature on language, identity and drama.The aim of my essay is to compare Swedish students’ willingness to use the foreign language English when acting minor plays in school, as themselves and as a chosen character, and to investigate the possibility of improving students’ willingness to use a foreign language, when given the opportunity to do so through acting somebody else.

Integration av webbaserat analysprogram och kartprogram : Integration of web based analysis-software andmap-software

I takt med att GIS (Grafiska InformationsSystem) blir allt vanligare och mer användarvänligt har WM-data sett att kunder skulle ha intresse i att kunna koppla information från sin verksamhet till en kartbild. Detta för att lättare kunna ta till sig informationen om hur den geografiskt finns utspridd över ett område för att t.ex. ordna effektivare tranporter. WM-data, som det här arbetet är utfört åt, avser att ta fram en prototyp som sedan kan visas upp för att påvisa för kunder och andra intressenter att detta är möjligt att genomföra genom att skapa en integration mellan redan befintliga system. I det här arbetet har prototypen tagits fram med skogsindustrin och dess lager som inriktning. Befintliga program som integrationen ska skapas mellan är båda webbaserade och körs i en webbläsare. Analysprogrammet som ska användas heter Insikt och är utvecklat av företaget Trimma, kartprogrammet heter GIMS som är WM-datas egna program. Det ska vara möjligt att i Insikt analysera data och skapa en rapport. Den ska sedan skickas till GIMS där informationen skrivs ut på kartan på den plats som respektive information hör till. Det ska även gå att välja ut ett eller flera områden i kartan och skicka till Insikt för att analysera information från enbart de utvalda områdena. En prototyp med önskad funktionalitet har under arbetets gång tagits fram, men för att ha en säljbar produkt är en del arbeta kvar. Prototypen har visats för ett antal intresserade som tyckte det var intressant och tror att det är något som skulle kunna användas flitigt inom många områden.

Optical Characterization and Optimization of Display Components : Some Applications to Liquid-Crystal-Based and Electrochromics-Based Devices

This dissertation is focused on theoretical and experimental studies of optical properties of materials and multilayer structures composing liquid crystal displays (LCDs) and electrochromic (EC) devices. By applying spectroscopic ellipsometry, we have determined the optical constants of thin films of electrochromic tungsten oxide (WOx) and nickel oxide (NiOy), the films’ thickness and roughness. These films, which were obtained at spattering conditions possess high transmittance that is important for achieving good visibility and high contrast in an EC device. Another application of the general spectroscopic ellipsometry relates to the study of a photo-alignment layer of a mixture of azo-dyes SD-1 and SDA-2. We have found the optical constants of this mixture before and after illuminating it by polarized UV light. The results obtained confirm the diffusion model to explain the formation of the photo-induced order in azo-dye films. We have developed new techniques for fast characterization of twisted nematic LC cells in transmissive and reflective modes. Our techniques are based on the characteristics functions that we have introduced for determination of parameters of non-uniform birefringent media. These characteristic functions are found by simple procedures and can be utilised for simultaneous determination of retardation, its wavelength dispersion, and twist angle, as well as for solving associated optimization problems. Cholesteric LCD that possesses some unique properties, such as bistability and good selective scattering, however, has a disadvantage – relatively high driving voltage (tens of volts). The way we propose to reduce the driving voltage consists of applying a stack of thin (~1µm) LC layers. We have studied the ability of a layer of a surface stabilized ferroelectric liquid crystal coupled with several retardation plates for birefringent color generation. We have demonstrated that in order to accomplish good color characteristics and high brightness of the display, one or two retardation plates are sufficient.

Predictive models for chronic renal disease using decision trees, naïve bayes and case-based methods

Data mining can be used in healthcare industry to “mine” clinical data to discover hidden information for intelligent and affective decision making. Discovery of hidden patterns and relationships often goes intact, yet advanced data mining techniques can be helpful as remedy to this scenario. This thesis mainly deals with Intelligent Prediction of Chronic Renal Disease (IPCRD). Data covers blood, urine test, and external symptoms applied to predict chronic renal disease. Data from the database is initially transformed to Weka (3.6) and Chi-Square method is used for features section. After normalizing data, three classifiers were applied and efficiency of output is evaluated. Mainly, three classifiers are analyzed: Decision Tree, Naïve Bayes, K-Nearest Neighbour algorithm. Results show that each technique has its unique strength in realizing the objectives of the defined mining goals. Efficiency of Decision Tree and KNN was almost same but Naïve Bayes proved a comparative edge over others. Further sensitivity and specificity tests are used as statistical measures to examine the performance of a binary classification. Sensitivity (also called recall rate in some fields) measures the proportion of actual positives which are correctly identified while Specificity measures the proportion of negatives which are correctly identified. CRISP-DM methodology is applied to build the mining models. It consists of six major phases: business understanding, data understanding, data preparation, modeling, evaluation, and deployment.

The Role of Motivational Strategies in the Upper Elementary Classroom : A systematic literature review about teacher strategies that promote self-confidence, motivation and a conducive learning environment

The aim of this literature review is to investigate which strategies teachers use to motivate pupils to communicate orally in English. The literature review also investigates how these teacher strategies affect pupils. The methodology used for this investigation is a systematic literature review. Various databases have been used when searching for literature. Scientific articles and theses have been searched for. They have also been read and analyzed before they have become a part of this review. The results indicate that some teachers feel insecure when speaking English. Therefore Swedish is spoken in many language classrooms. Teachers speaking in front of the class is the traditional way of teaching, and it does not seem to be a strategy who influences pupils positively. If teachers speak the target language among pupils they often get more motivated and focused pupils who feel comfortable speaking English. Young pupils are fast learners. By exposing them to the English language in early ages they receive great opportunities to learn a foreign language and strengthen their self-confidence. Drama, songs and rhymes are preferable strategies to use when teaching young learners. What position teachers decide to take in the classroom is also a significant element when teaching foreign languages.

Informations- och kommunikationsteknologi som stöd för patienter med astma och kronisk obstruktiv lungsjukdom avseende egenvård. En litteraturstudie.

Bakgrund: Astma och KOL är två vanlig kroniska sjukdomar som är kopplade till stort sjukdomslidande och lägre livskvalité. Många personer som idag lever med sjukdomarna lever isolerat från andra. Idag har vi en ständig utveckling av sociala nätverk som öppnar en ny möjlighet för egenvård. Egenvård kan göra att patienter får en bättre vardag samt att det lättare kan få ett socialt umgänge. Syfte: Syftet är sammanställa befintlig litteratur och där undersöka hur informations- och kommunikationsteknologi underlättar egenvården för patienter med astma och KOL. Metod: Litteraturstudie där artiklarna söktes i databaser för omvårdnadsvetenskap så som Web Of Science, pubmed och Cinahl. Litteraturstudien baseras på 16 vetenskapliga artiklar som både är kvalitativa och kvantitativa. Artiklarna som valdes är inte äldre än 10 år gamla, skrivna på engelska och publicerade i en vetenskaplig tidning. Resultat: Resultatet som artiklarna påvisade är grundade på IKT i form av datorer, mobiltelefoner, surfplattor och web-baserad program. Artiklarna visar att egenvården kan förbättras genom ökad livskvalité, bättre kommunikation och bättre sjukdomsinsikt när man använder IKT. Slutsats: IKT är en viktig roll i våran hälso- och sjukvård idag. Det finns dock liten forskning på hur egenvården kring astma och KOL påverkas av IKT. Den forskning som finns pekar åt är att den förbättrar för patienter. Det behövs även mer forskning kring IKT som en resurs för egenvård kring ett omvårdnadsperspektiv.