Tehnoloogiainstituut

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    3D bounding box detection of moving objects for robot navigation in dynamic environments
    (Tartu Ülikool, 2021) Jõul, Jüri; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    3D object detection is widely used in the field of robotics to avoid collisions with dynamic objects, such as humans. Based on the trajectories of the detected objects and the noise of the detection pipeline, robots can use motion planning algorithms to safely navigate in crowded environments. This thesis proposes a hybrid approach to 3D object detection using depth data fused with a mature 2D object detector. Both simulated and real-world experiments were performed as a demonstration of the solution. An extensive noise analysis of the developed detection pipeline was also carried out for future use in robot navigation under uncertainty.
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    3D Face Reconstruction from a Single 2D Image
    (2021) Salimli, Mehin
    3D face reconstruction is the process of creating a 3D representation of a real human face. 3D face models have several applications like face recognition, 3D games, human-machine interaction, and plastic surgery simulations. Recently there has been a lot of research on deep learning methods for 3D face reconstruction from 2D face images. In this thesis, three deep learning-based methods for 3d reconstruction from a single image are reviewed. A new texturing method for 3D face models that uses the input photo as a UV texture image is proposed. Image warping is used to modify the input photo for this purpose. Warping is achieved using facial landmark detection and triangle meshes. A survey is conducted to assess the three face reconstruction methods and the proposed texturing method
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    3D reconstruction using Kinect v2 camera
    (Tartu Ülikool, 2016) Valgma, Lembit; Anbarjafari, Gholmareza; Daneshmand, Morteza; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Kinect is an easy to use and a ordable RGB-D acquisition device that provides both spatial and color information for captured pixels. That makes it an attractive alternative to regular 3D scanning devices that usually cost signi cantly more and do not provide color info. Second generation of Kinect (v2) provides even better quality depth and color images to user. This thesis describes and implements method for 3D reconstruction using Kinect v2. Method suitability for various objects is tested and analyzed. In most circumstances the method provided satisfactory reconstructions unless very high resolution is desired. However some limitation were observed. Reflective and transparent surfaces cause failure due to depth capturing technology in Kinect v2, symmetric objects cause problems for described frame registration algorithm. For better understanding, Kinect v2 depth measuring process is described.
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    5S rDNA copy number in WGS data
    (2022) Naghiyev, Farid
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    A preclinical trial of Bisdemethoxycurcumin in a mouse model of Alzheimer's disease
    (Tartu Ülikool, 2022) Mansouri, Seyedeh Elnaz Sadat; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
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    A Study of Anti-adenoviral activity of antimicrobial peptides
    (Tartu Ülikool, 2024) Nabeel, Muhammad; Rausalu, Kai, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Adenoviruses, non-enveloped DNA viruses, pose a significant health concern. This study explores the antiviral potential of four recombinant proteins with attached cationic antimicrobial peptides (H1mod1R, H2mod2R, HELP and HIn) against the human adenovirus (AdV-Gluc) in vitro. The proteins presented some antiviral activity, but this inhibitory effect was independent of the concentrations of the proteins within the tested range. The results are not aligned with the previous research on the cationic antimicrobial peptides with other viruses. Currently, these proteins are not ideal for use as therapeutic against adenovirus, but the good cytotoxicity profile suggests that further research is needed to optimize the efficacy and to explore their mechanism of action for beneficial future applications.
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    The Absence of GacA/S signal transduction system af-fects the frequency of base substitution and frameshift mutations in Pseudomonas putida KT2400
    (2020) Phan, Huynh Ngoc Chau; Kivisaar, Maia; Ilmjärv, Tanel
    GacA/GacS two-component system can be found in Gram-negative bacteria, including enteric bacteria and Pseudomonas. gacS gene encodes for a membrane-bound sensor kinase GacS, whereas a transcriptional response regulator GacA is encoded by gacA gene. The aim of this thesis was to investigate whether the inactivation of the GacA/GacS two-component system could affect mutation frequency in Pseudomonas putida. Two test systems were employed for measuring mutation frequency: chromosomal RifR assay and a plasmidial test system based on lactose degradation. RifR phenotype of bacteria is a result of mutations that decrease the affinity of rifampicin binding to the β subunit of RNA polymerase. This makes this enzyme insensitive to rifampicin. The second test system is based on the monitoring mutations in lacZ gene encoding for β-galactosidase, which turns the tester strains from Lac- to Lac+ phenotype. Usage of both test systems revealed that the inactivation of the gacA gene elevates mutation frequency in P. putida. In estonian: GacA/GacS kahekomponendiline süsteem on kirjeldatud erinevates Gram negatiivsetes bakteriliikides, kuhu kuuluvad ka enterobakterid ja erinevad Pseudomonase liigid. Geen gacS kodeerib membraan-seoselist sensorkinaasi GacS ning transkriptsiooni regulaator GacA, mis saab signaali GacS-lt, on kodeeritud geeni gacA poolt. Käesoleva bakalaureusetöö eesmärgiks oli välja selgitada, kas GacA/GacS süsteemi inaktiveerimine mõjutab bakteris Pseudomonas putida mutatsioonisagedust. Mutatsioonisageduse mõõtmiseks kasutati kahte testsüsteemi: kromosomaalset RifR süsteemi ja plasmiidset laktoosi lagundamisel põhinevat Lac+ süsteemi. RifR fenotüübiga bakterites on tekkinud mutatsioonid, mis vähendavad rifampitsiini seondumist RNA polümeraasi β-subühikuga, muutes sel viisil ensüümi rifampitsiini suhtes tundetuks. Teine testsüsteem põhineb β-galaktosidaasi kodeerivas geenis lacZ tekkivate mutatsioonide tuvastamisel, mis võimaldavad Lac- testertüvedel hakata lagundama laktoosi (Lac+ reversioon). Töö tulemustena selgus, et gacA geeni inaktiveerimine bakteris P. putida põhjustas mutatsioonisageduse suurenemist mõlemate testsüsteemide rakendamisel.
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    Activity of macrolides against uropathogenic Escherichia coli
    (Tartu Ülikool, 2023) Shahpazir, Ana; Kaldalu, Niilo, juhendaja
    Azithromycin is a macrolide antibiotic extensively used to treat several infections attributa- ble to Gram-positive bacteria. Exceptionally, azithromycin has proven to be effective in clin- ical treatment of widespread chronic infections caused by Gram-negative bacterium, Salmo- nella. While the underlying mechanisms of azithromycin’s activity against this Gram-nega- tive bacterium remain enigmatic, its efficacy brings up the question of whether this macro- lide can be used in treatment of other Gram-negative bacterial infections as well. The goal of this work was to investigate the possibility of utilizing azithromycin against uropatho- genic Escherichia coli. For this purpose, we determined the minimum inhibitory concentra- tion of azithromycin in conditions resembling intracellular infection sites. Additionally, we validated the use of four macrolide bioreporters that were based on the regulatory leader peptide coding sequence of the macrolide resistance gene, ermCL.
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    Acylation of N-Boc-N’-COCF3 protected hydrazine
    (Tartu Ülikool, 2024) Kurbanova, Karina; Mastitski,Anton, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Within the scope of the present thesis acylation of N-Boc-N’-COCF3 protected hydrazine was investigated. Acetic anhydride, benzoyl and butanoyl chlorides, activated esters and benzyl chloroformate were tested as acylating agents. The implementation of highly reactive acyl chlorides led to very good yields of hydrazines monoacylated at the Boc-protected nitrogen. Application of an excess of acyl chlorides promoted the formation of diacylated Boc-protected hydrazines and an unexpected loss of the trifluoroacetic group. Acylation by activated esters or benzyl chloroformate resulted solely in monoacylated products isolated in fair to poor yields. Reactions utilizing acetic anhydride gave no product irrespective of reaction conditions.
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    Aerosoolikasvati temperatuurikontroller
    (Tartu Ülikool, 2022) Kitsik, Kim; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Käesoleva bakalaureusetöö eesmärgiks on temperatuurikontrolleri arendamine aerosoolikasvatile, mille ülesandeks on hoida temperatuure süsteemi erinevates osades etteantud konstantsel nivool kasutades küttekehi või jahutuselemente. Valminud seade on jälgitav ja juhitav üle USB pordi. Aerosoolikasvati on oluline osa suuremast kalibratsiooniaerosoolide genereerimise süsteemist. Bakalaureusetöö sisaldab riistvaralise osa projekteerimist ja komplekteerimist ning samuti tarkvara loomist ja testimist. Töö on valminud koostöös eraettevõttega ning annab ülevaate firma esitatud nõuetest ja vastavatest autori poolt tehtud lahendustest. Laboriseade, millele nimetatud plaat on mõeldud, on valmistatud kommertsliku eesmärgiga ning on mõeldud väga spetsiifilistele valdkondadele.
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    AES algoritmi realiseerimine VHDL-is ning testimine FPGA riistvaral
    (Tartu Ülikool, 2015) Türk, Hendrik; Rosin, Margus, juhendaja; Tartu Ülikool. Loodus- ja tehnoloogiateaduskond; Tartu Ülikool. Tehnoloogiainstituut
    Lõputöö eesmärgiks oli teha ettevalmistusi krüptokiirendi loomiseks, mis oleks realiseeritud FPGA riistvaral. Selleks tuli kõigepealt mõista krüptoloogia olemust ning teostada ülevaade levinumatest krüpteerimisalgoritmidest ja neid kasutatavatest krüptokiirenditest. Kogutud informatsiooni põhjal valiti edasiseks uurimiseks ülemaailmselt populaarne AES algoritm. Algoritmi tööpõhimõtte väljaselgitamise järel alustati bakalaureusetöö praktilise osaga, mille eesmärkideks seati AES-i rakendamine VHDL-is ning simulatsiooni- ja riistvaratestide tegemine. Töö tulemuste põhjal järeldati, kas bakalaureusetöö käigus valitud meetodil on mõistlik jätkata krüptokiirendi arendamist, ning millised oleksid edasised tegevused selle loomiseks. Praktiline osa jagunes töö käigus loodud simulatsiooniprogrammi testimiseks ning AES-i krüpteerimisalgoritmi rakendamiseks Basys 3 arendusplaadil. Dekrüpteerimise algoritmiga riistvarateste ei tehtud, kuna krüpteerimisel ja dekrüpteerimisel kasutatavad funktsioonid on võrdse keerukusega ning dekrüpteerimise realiseerimine riistvaral oleks järgmine samm koos väliskeskkonnaga suhtluse realiseerimisega. Simulatsiooni- ja riistvaraprogrammid valmisid Vivado programmeerimis- ja simuleerimiskeskkonnas. Simulatsiooniprogrammi testiti erinevate NIST-i poolt väljastatud ning töö autori poolt defineeritud juhuslike testvektoritega. Riistvaratestide tegemiseks valiti juhuslik NIST-i poolt väljastatud testvektor ja töö autori poolt defineeritud testvektorid piirjuhtumite jaoks. Riistvara- ja simulatsioonitestide analüüsist järeldus, et töö käigus valitud meetodil on võimalik luua välise keskkonnaga suhtlev seade, mis võimaldab andmeid krüpteerida ning dekrüpteerida. Kuna see on ka olemasolevate krüptokiirendite põhiliseks funktsiooniks, on mõistlik defineerida tegevused töö käigus valminud ja esialgsed testid läbinud AES-i krüpteerimisalgoritmi rakendamise programmi edasiseks arendamiseks. Basys 3 arendusplaadil testitud AES krüpteerimisalgoritmile tuleks edasise arendamise eesmärgil kõigepealt lisada dekrüpteerimine. Järgmisena oleks vajalik kiirus- ning andmeturbetestide tegemine võrguliikluse krüpteerimisel ja dekrüpteerimisel, kasutades võrguga ühendamiseks näiteks Digilenti PmodNIC moodulit. Saadud tulemusi peaks edasiste järelduste tegemiseks võrdlema integreeritud krüpteerimismooduleid või eraldiseisvaid krüptokiirendeid kasutavate netiseadmete tulemustega.
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    AHHAA Teaduskeskuse poolhumanoidroboti Oskar kaasajastamine ja ühildamine ROS tarkvararaamistikuga
    (Tartu Ülikool, 2021) Hinn, Rando; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    AHHAA Teaduskeskusel on kaks kaugjuhitavat robotit Oskar, mis on mõlemad amortiseerunud. Töö eesmärgiks on Oskari arhitektuuri kaasajastamine uue versiooni loomiseks ja robotile ROS-i toe tagamine. Töö tulemuste saavutamiseks kavandati uus arhitektuur ja arendati sellele ROS-i draiver. Töö tulemusena loodi Oskar 3 arhitektuur ja implementeeriti ROS-i draiver koos MoveIt toega. Töö täitis oma eesmärgid ja selle baasilt on võimalik luua nõuetele vastav robot.
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    Aine ”Nutilahenduste praktikum” värskendamine
    (Tartu Ülikool, 2022) Rhede, Kaarel; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Käesoleva bakalureusetöö eesmärgiks on Tartu Ülikooli arvutitehnika bakalaureuse õppekava kohustusliku aine ”Nutilahenduste praktikum” uuendamine. Uuendatakse nii praktikumi riistvara kui ka praktiliste tööde juhendeid. Seni ühendati praktikumitöödes seadmed omavahel maketeerimislaua ja juhtmete abil. Kuna maketeerimislauad ei pea vastu sadadele seadmete paigaldamistele, mille tõttu ühendused katkevad ega ole stabiilsed, siis disainitakse bakalaureusetöö raames arendusplaat, millel on ESP32 mikrokontroller koos sisseehitatud WiFi ja Bluetoothiga, asendades Arduino Nano arendusplaati. Plaadil on ka spetsialiseeritud pesad põhiliste praktikumis kasutatavate välisseadmete ühendamiseks, samuti mitut tüüpi LED-id, potentsiomeeter ja kvadratuurkodeerija esmasteks lihtsamateks sisend-väljundseadmeteks.
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    Ainekavade ja materjalide koostamine gümnaasiumiastme valikainetele „Programmeerimine keeles Java I“ ja „Programmeerimine keeles Java II“
    (Tartu Ülikool, 2019) Õunapuu, Helen; Villems, Anne, supervisor; Hein, Merike, supervisor; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Bakalaureusetöö eesmärk on luua gümnaasiumiastmele sobivad ainekavad ning materjalid valikainetele „Programmeerimine keeles Java I“ ja „Programmeerimine keeles Java II“ ning viia loodud ainekavasid ning materjale kasutades läbi kaks valikkursust Tartu Jaan Poska gümnaasiumis. Valikkursused viidi bakalaureusetöö autori poolt läbi ajavahemikus 18. detsember 2018 kuni 12. aprill 2019. Hindamaks loodud materjalide ning ainekavade sobivust gümnaasiumiastmele, analüüsiti Tartu Jaan Poska gümnaasiumi õpilaste õpitulemusi ja viidi õpilaste seas läbi küsitlus, et selgitada välja nende rahulolu „Programmeerimine keeles Java I“ ja „Programmeerimine keeles Java II“ valikainega ning koguda ettepanekuid ainete parendamiseks. Töö lõpus esitab töö autor soovitusi teiste sarnaste valikkursuste korraldamiseks loodud õppematerjale ning ainekavasid kasutades.
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    An Open-Source Robotic Study Companion for University Students
    (Tartu Ülikool, 2023) Baksh, Farnaz; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    This thesis presents an evidence-based approach and develops an affordable and effective Robotic Study Companion (RSC) prototype for university students. It addresses the lack of social robots tailored to higher education and the scarcity of open-source educational platforms. Through a comprehensive literature review on Human-Robot Interaction (HRI), social and companion robots, and Natural Language Processing (NLP) technologies, this work identifies trends and best practices for educational social robots. The research systematically reviews select social robots, examining their applications, technical features, design, and human-centric interaction. It explores the human perspective of HRI, focusing on users in educational settings. Based on these insights, functional and non-functional requirements are established for the RSC, inspiring its design and development. The RSC prototype, built using off-the-shef components and leveraging OpenAI's large language models, demonstrates its potential to simplify complex concepts for students. The long-term goal is to enhance the RSC's design, durability, and commercial viability.
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    Analysis of Chikungunya Virus Capsid Interactome
    (Tartu Ülikool, 2024) Bratslavskaia, Elizaveta; Varjak, Margus, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    The ongoing global spread of alphaviruses presents a significant challenge, underscoring the urgent need for the development of novel antiviral treatments. Understanding the intricate host virus interactions that underlie virus infection is crucial for uncovering potential pro- or antiviral targets for such treatment strategies. In this study, we investigated the interactome of the Chikungunya virus (CHIKV) Capsid protein (CP), a key player in viral replication, assembly, and cell-virus interactions. Here, the quantitative label-free proteomics analysis was used to study CHIKV CP interactors in two different types of cells, in the human host and mosquito vector. A number of host and vector factors were identified, among them were many homologous proteins to be focused on in further downstream analysis. The effect of selected interactors on CHIKV pathogenesis was evaluated in mosquito and human cells. Notably, silencing of PGAM5, SRRT, and VIRMA proteins significantly reduced the level of viral replication, demonstrating a shared pro-viral effect in both, human and mosquito, cell types tested. These results underscore the conservation of CP function across different organisms and highlight the potential significance of these cellular factors in the context of CHIKV infection. Overall, this study provides valuable insights into the molecular mechanisms underlying CHIKV pathogenesis and identifies potential targets for the development of novel antiviral treatments.
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    Analysis of Clb6 degradation mechanisms
    (2022) Aghayari, Avishan
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    Analysis of different substrate docking pockets on Clb5- and Clb4-Cdk1
    (Tartu Ülikool, 2023) Kiselev, Viacheslav; Faustova, Ilona, juhendaja; Örd, Mihkel, juhendaja; Loog, Mart, juhendaja; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    Cell cycle is coordinated via temporally resolved protein phosphorylation by cyclin-dependent kinases (CDKs). CDKs form cell-cycle-stage-specific complexes with cyclins. Cyclins in turn recruit substrate proteins through specific binding motifs and direct the kinase to phosphorylate different proteins to trigger cell cycle events. While most of the cyclin-substrate interactions take place via a hydrophobic patch on the cyclin, recent studies have found novel pockets that could participate in substrate recognition. This work investigates the im- portance of two novel substrate binding pockets on Saccharomyces cerevisiae S and G2 phase cyclins Clb5 and Clb4. Structural and conservational analysis supported the presence of multiple substrate pockets on the cyclin surface. Kinase assays revealed that the phosphate-binding pocket and an NPFF motif pocket are critical in mediating phosphorylation of Kar9 by Clb4-Cdk1 complex. A comparison between Clb4-, Clb3-, and Clb5-Cdk1 revealed distinct substrate preferences for these complexes within a panel of 10 Cdk1 substrates of S/G2 phase. Further, assays using mutant cyclin-Cdk1 complexes suggested that the NPFF pocket is used by a small number of substrates. Overall, these findings highlight the im- portance of cyclins as substrate recruitment modules rather than just activators of CDKs.
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    Analysis of the docking interaction between Sld2 and Clb5 in budding yeast
    (Tartu Ülikool, 2021) Mikhailova, Valentina; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
    The cell cycle of Saccharomyces cerevisiae is governed by cyclin dependent kinases (Cdks), which are activated by periodically synthesized and degraded cyclins. The substrate target-ing by a cyclin-Cdk complex is mediated by the active site on the Cdk and the cyclin docking pocket. Docking interactions between short linear motifs (SLiMs) in target proteins and cy-clin-dependent kinases are shown to be critical regulators of different cell cycle events. SLiMs function in almost every pathway due to their role in regulatory function and signal transduction.