Pathways of selection in avian reproduction: a functional framework and its application in the population study of the great tit (parus major)

http://www.ester.ee/record=b1053245~S1*es

Tartu linna rattasõidu sobivus

Master’s thesis Curriculum in Landscape ArchitectureToday, many cities around the world want to increase the share of sustainable transport, especially cycling. Increasing the use of bikes in the city makes people healthier, improves the environment, and creates new healthy habits. To create bike-friendly cities you need a well-thought-out and safe cityscape. The aim of this research was to look at the use of bicycles in the city of Tartu, the main routes used, numbers over time, and the views and perceptions of the users old and new. In order to achieve the goal, several observations were carried out at different times and locations in Tartu, interviews with various experts were conducted and an online questionnaire asking about people's cycling habits was also done. The obtained results can be useful in improving the cityscape of Tartu, so that in the future the development of bicycle traffic would become one of the important points in the construction and design of roads. This would make the infrastructure of the city of Tartu safer and more efficient for all road users.Paljud maailma linnad tänapäeval soovivad suurendada säästva transpordi osakaalu, eriti just jalgrattaga liikumise osas. Jalgrattaga liikumine soodustab inimestel head tervist, muudab keskkonna paremaks ning loob uusi tervislike harjumusi. Et muuta linn jalgratta sõbralikuks on vaja hästi läbimõeldud ja turvalist linnapilti. Antud uurimistöö eesmärgiks oli uurida jalgrataste kasutamist Tartu linnas, peamisi kasutatavaid marsruute, palju inimesi üldse rattaga ringi liigub ning inimeste vaateid ja arusaamu rattakultuurist Tartus üldiselt. Eesmärgi saavutamiseks viidi läbi erinevatel aegadel ja erinevates kohtades mitu vaatlust, tehti intervjuud erinevate ekspertidega ning lisaks viidi läbi ka veebiküsimustik, milles uuriti inimeste enda rattakasutuse kohta. Saadud tulemused võivad olla kasuks Tartu linnapildi parandamisel, et tulevikus oleks teede ehitamisel ja projekteerimisel üheks oluliseks punktiks ka jalgrattaliikluse arendamine. Läbi selle muutuks Tartu linna infrastruktuur ohutumaks ja tõhusamaks kõigile liiklejatele

Privaatsust säilitava raalnägemise meetodi arendamine kehalise aktiivsuse automaatseks jälgimiseks koolis

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKuidas vaadelda inimesi ilma neid nägemata? Öeldakse, et ei ole viisakas jõllitada. Õigus privaatsusele on lausa inimõigus. Siiski on inimkäitumises palju sellist, mida teadlased tahaksid uurida inimesi vaadeldes. Näiteks tahame teada, kas lapsed hakkavad vahetunnis rohkem liikuma, kui koolis keelatakse nutitelefonid? Selle välja selgitamiseks peaks teadlane küsima lapsevanematelt nõusolekut võsukeste vaatlemiseks. Eeldusel, et lapsevanemad annavad loa, oleks klassikaliseks vaatluseks vaja tohutult palju tööjõudu – mitu vaatlejat koolimajas iga päev piisavalt pikal perioodil enne ja pärast nutitelefoni keelu kehtestamist. Doktoritööga püüdsin lahendada korraga privaatsuse probleemi ja tööjõu probleemi, asendades inimvaatleja tehisaruga. Kaasaegsed masinõppe meetodid võimaldavad luua mudeleid, mis tuvastavad automaatselt pildil või videos kujutatud objekte ja nende omadusi. Kui tahame tehisaru, mis tunneb pildil ära inimese, tuleb moodustada masinõppe andmestik, kus on pilte inimestest ja pilte ilma inimesteta. Kui tahame tehisaru, mis eristaks videos madalat ja kõrget kehalist aktiivsust, on vaja vastavat videoandmestikku. Doktoritöös kogusingi andmestiku, kus video laste liikumisest on sünkroniseeritud puusal kantavate aktseleromeetritega, et treenida mudel, mis eristaks videopikslites madalamat ja kõrgemat liikumise intensiivsust. Koostöös Tehonoloogiainstituudi iCV laboriga arendasime välja videoanalüüsi sensori prototüübi, mis suudab reaalaja kiirusel hinnata kaamera vaateväljas olevate inimeste kehalise aktiivsuse taset. Just see, et tehisaru suudab tuletada videost kehalise aktiivsuse informatsiooni ilma neid videokaadreid salvestamata ega inimestele üldsegi näitamata, võimaldab vaadelda inimesi ilma neid nägemata. Väljatöötatud meetod on mõeldud kehalise aktiivsuse mõõtmiseks koolipõhistes teadusuuringutes ning seetõttu on arenduses rõhutatud privaatsuse kaitsmist ja teaduseetikat. Laiemalt vaadates illustreerib doktoritöö aga raalnägemistehnoloogiate potentsiaali töötlemaks visuaalset infot linnaruumis ja töökohtadel ning mitte ainult kehalise aktiivsuse mõõtmiseks kõrgete teaduseetika kriteerimitega. Siin ongi koht avalikuks aruteluks – millistel tingimustel või kas üldse on OK, kui sind jõllitab robot?  How to observe people without seeing them? They say it's not polite to stare. The right to privacy is considered a human right. However, there is much in human behavior that scientists would like to study via observation. For example, we want to know whether children will start moving more during recess if smartphones are banned at school? To figure this out, scientists would have to ask parental consent to carry out the observation. Assuming parents grant permission, a huge amount of labour would be needed for classical observation - several observers in the schoolhouse every day for a sufficiently long period before and after the smartphone ban. With my doctoral thesis, I tried to solve both the problem of privacy and of labor by replacing the human observer with artificial intelligence (AI). Modern machine learning methods allow training models that automatically detect objects and their properties in images or video. If we want an AI that recognizes people in images, we need to form a machine learning dataset with pictures of people and pictures without people. If we want an AI that differentiates between low and high physical activity in video, we need a corresponding video dataset. In my doctoral thesis, I collected a dataset where video of children's movement is synchronized with hip-worn accelerometers to train a model that could differentiate between lower and higher levels of physical activity in video. In collaboration with the ICV lab at the Institute of Technology, we developed a prototype video analysis sensor that can estimate the level of physical activity of people in the camera's field of view at real-time speed. The fact that AI can derive information about physical activity from the video without recording the footage or showing it to anyone at all, makes it possible to observe without seeing. The method is designed for measuring physical activity in school-based research and therefore highly prioritizes privacy protection and research ethics. But more broadly, the thesis illustrates the potential of computer vision technologies for processing visual information in urban spaces and workplaces, and not only for measuring physical activity or adhering to high ethical standards. This warrants wider public discussion – under what conditions or whether at all is it OK to have a robot staring at you?https://www.ester.ee/record=b555972

Regulation of transposition of transposon Tn4652 in Pseudomonas putida

http://www.ester.ee/record=b4338450~S1*es

Orgaanilise keemia praktikumi üldjuhend

https://www.ester.ee/record=b1189879*es

City to Nature

Bakalaureusetöö keskkonnaplaneerimise ja maastikukujunduse erialalTöö eesmärgiks oli muuta Turu tänav ja selle ümbrus jätkusuutlikumaks. Üheks katsumuseks oli just Emajõe ja Karlova linnaosa ühendamine, et muuta ala inimestele meeldivamaks. Tänavat analüüsides tuleb välja, et Turu tänav on barjääriks Emajõe ja Karlova linnaosa vahel ning liiklus tänaval on väga tihe. Inimesed eelistavad pigem liikuda kesklinna poolel kui Sõpruse silla lähed.Väljapakutud projekteerimise eesmärgiks oli omavahel paremini siduda Karlova linnaosa ja Emajõgi eri tüüpi haljasaladega ning tagada jalakäijate juurdepääs jõeäärsele alale. Samuti muudab haljastus liikluse Turu tänaval rahulikumaks ja loob kauni sissekäigu kesklinna.The aim of the design project was to change Turu street into sustainable urban space. Challenges of this street are the non-existent connections between Karlova district and river Emajõgi. The analysis of the spaces around the Turu street lead to fact that connection between river Emajõgi and Karlova district is bad and there is really heavy traffic. People also use space more near the city centre then near the Sõpruse bridge. The purpose of the proposed design project was to make better connection between city and river with different types of green areas and to ensure access for pedestrians to the riverside. Also to make traffic in Turu street more calm and create this welcoming entrance to the city centre

Humanistlikud riskitajud ja usk teaduse võimekusse üldises postmoderniseerumise protsessis üheksa Euroopa riigi näitel

Käesolevas magistritöös uuriti, kas postmoderniseerumine toob endaga kaasa tõusvad humanistlikud riskitajud ja väheneva usu teaduse võimekusse. Selleks võrreldi üheksat Euroopa riiki ja kolme vanusegruppi neis riikides faktoranalüüsidega moodustatud laiemate keskkonnaga seotud riskitajude ja teadusorientatsioonide poolest lähtuvalt Ronald Ingleharti (1997; Inglehart ja Baker, 2000; Inglehart ja Welzel, 2005) moderniseerumise teooriast. Tuleb välja, et uuritud Skandinaavia maades ning jõukates Lääne-Euroopa riikides on tõepoolest teistest maadest tunduvalt madalam usk teaduse võimekusse, samas on need riigid ökoloogilise katastroofi riski tajude poolest väga erinevad ning puudub ka arvestatav seos eneseväljenduslike väärtuste ja riskitajude vahel indiviidi tasemel. Analüüsi tulemused tõid esile ka idee, mille kohaselt võib dogmaatiline usk teaduse võimekusse olla riigi tasemel seotud katoliikliku ajalooga. Kõrgem teadlaste usaldamine nooremates vanusegruppides enamikes uuritud riikides ja seose puudumine postmodernsuse ja teadlaste usaldamise vahel pani kahtluse alla Becki (1986/2005) refleksiivse teaduslikustumise idee, mille kohaselt peaks uues modernsuses – riskiühiskonnas kerkima esile just kriitilisem suhtumine teadusesse ja teadlastesse. Töös jõuti seisukohale, et Euroopa väärtuste uuringus mõõdetud riskitajude indikaatorid on väga laialt, abstraktselt ja radikaalselt sõnastatud (väljendid nagu „katastroof“ ja „hukatuslikud tagajärjed“) ning võib-olla just selle tõttu ei lähe tulemused kokku Ingleharti ja Becki eeldustega kõrgematest riskitajudest hilismodernsuses.http://www.ester.ee/record=b4498764*es

Identification of ColR binding consensus and prediction of regulon of ColRS two-component system

<p>Abstract</p> <p>Background</p> <p>Conserved two-component system ColRS of <it>Pseudomonas </it>genus has been implicated in several unrelated phenotypes. For instance, deficiency of <it>P. putida </it>ColRS system results in lowered phenol tolerance, hindrance of transposition of Tn<it>4652 </it>and lysis of a subpopulation of glucose-grown bacteria. In order to discover molecular mechanisms behind these phenotypes, we focused here on identification of downstream components of ColRS signal transduction pathway.</p> <p>Results</p> <p>First, highly similar ColR binding sites were mapped upstream of outer membrane protein-encoding <it>oprQ </it>and a putative methyltransferase-encoding PP0903. These two ColR binding sequences were used as an input in computational genome-wide screening for new potential ColR recognition boxes upstream of different genes in <it>P. putida</it>. Biological relevance of a set of <it>in silico </it>predicted ColR-binding sites was analysed <it>in vivo </it>by studying the effect of ColR on transcription from promoters carrying these sites. This analysis disclosed seven novel genes of which six were positively and one negatively regulated by ColR. Interestingly, all promoters tested responded more significantly to the over-expression than to the absence of ColR suggesting that either ColR is limiting or ColS-activating signal is low under the conditions applied. The binding sites of ColR in the promoters analysed were validated by gel mobility shift and/or DNase I footprinting assays. ColR binding consensus was defined according to seven ColR binding motifs mapped by DNase I protection assay and this consensus was used to predict minimal regulon of ColRS system.</p> <p>Conclusion</p> <p>Combined usage of experimental and computational approach enabled us to define the binding consensus for response regulator ColR and to discover several new ColR-regulated genes. For instance, genes of outer membrane lipid A 3-O-deacylase PagL and cytoplasmic membrane diacylglycerol kinase DgkA are the members of ColR regulon. Furthermore, over 40 genes were predicted to be putatively controlled by ColRS two-component system in <it>P. putida</it>. It is notable that many of ColR-regulated genes encode membrane-related products thus confirming the previously proposed role of ColRS system in regulation of membrane functionality.</p

The impact of ColRS two-component system and TtgABC efflux pump on phenol tolerance of Pseudomonas putida becomes evident only in growing bacteria

<p>Abstract</p> <p>Background</p> <p>We have recently found that <it>Pseudomonas putida </it>deficient in ColRS two-component system is sensitive to phenol and displays a serious defect on solid glucose medium where subpopulation of bacteria lyses. The latter phenotype is significantly enhanced by the presence of phenol in growth medium. Here, we focused on identification of factors affecting phenol tolerance of the <it>colR</it>-deficient <it>P. putida</it>.</p> <p>Results</p> <p>By using transposon mutagenesis approach we identified a set of phenol-tolerant derivatives of <it>colR</it>-deficient strain. Surprisingly, half of independent phenol tolerant clones possessed miniTn5 insertion in the <it>ttgABC </it>operon. However, though inactivation of TtgABC efflux pump significantly enhanced phenol tolerance, it did not affect phenol-enhanced autolysis of the <it>colR </it>mutant on glucose medium indicating that phenol- and glucose-caused stresses experienced by the <it>colR</it>-deficient <it>P. putida </it>are not coupled. Inactivation of TtgABC pump significantly increased the phenol tolerance of the wild-type <it>P. putida </it>as well. Comparison of phenol tolerance of growing <it>versus </it>starving bacteria revealed that both ColRS and TtgABC systems affect phenol tolerance only under growth conditions and not under starvation. Flow cytometry analysis showed that phenol strongly inhibited cell division and to some extent also caused cell membrane permeabilization to propidium iodide. Single cell analysis of populations of the <it>ttgC- </it>and <it>colRttgC-</it>deficient strains revealed that their membrane permeabilization by phenol resembles that of the wild-type and the <it>colR </it>mutant, respectively. However, cell division of <it>P. putida </it>with inactivated TtgABC pump seemed to be less sensitive to phenol than that of the parental strain. At the same time, cell division appeared to be more inhibited in the <it>colR</it>-mutant strain than in the wild-type <it>P. putida</it>.</p> <p>Conclusions</p> <p>ColRS signal system and TtgABC efflux pump are involved in the phenol tolerance of <it>P. putida</it>. However, as they affect phenol tolerance of growing bacteria only, this indicates that they participate in the regulation of processes which are active during the growth and/or cell division. Single cell analysis data indicated that the cell division step of cell cycle is particularly sensitive to the toxic effect of phenol and its inhibition can be considered as an adaptive response under conditions of phenol stress.</p