Prokaryote growth temperature prediction with machine learning

Archaea and bacteria can be divided into four groups based on their growth temperature adaptation: mesophiles, thermophiles, hyperthermophiles, and psychrophiles. The thermostability of proteins is a sum of multiple different physical forces such as van der Waals interactions, chemical polarity, and ionic interactions. Genes causing the adaptation have not been identified and this thesis aims to identify temperature adaptation linked genes and predict temperature adaptation based on the absence or presence of genes. A dataset of 4361 genes from 711 prokaryotes was analyzed with four different machine learning algorithms: neural network, random forest, gradient boosting machine, and logistic regression. Logistic regression was chosen to be an explanatory and predictive model based on micro averaged AUC and Occam’s razor principle. Logistic regression was able to predict temperature adaptation with good performance. Machine learning is a powerful predictor for temperature adaptation and less than 200 genes were needed for the prediction of each adaptation. This technique can be used to predict the adaptation of uncultivated prokaryotes. However, the statistical importance of genes connected to temperature adaptation was not verified and this thesis did not provide much additional support for previously proposed temperature adaptation linked genes

Bacterial community structure and petroleum hydrocarbon degradation in the Baltic Sea

The Baltic Sea is unique by its biological, geochemical and physical features. The number of species of larger organisms is small and the species composition is distinctive. On the contrary microbial communities are diverse. Because of the low salinity levels, bacterial communities differ from the ones in the oceans. Knowing the structure of these communities better and how they response to different environmental conditions helps us to estimate how different factors affect the balance and function of the Baltic Sea ecosystem. Bacteria are the key players when it comes to natural biogeochemical processes and human-induced phenomena like eutrophication, oil spills or disposal of other harmful substances to the sea ecosystem. In this thesis, bacterial community structure in the sea surface microlayer and subsurface water of the Archipelago Sea were compared. In addition, the effect of diatom derived polyunsaturated aldehydes on bacterial community structure was studied by a mesocosm experiment. Diesel, crude oil and polycyclic aromatic hydrocarbon degradation capacity of the Baltic Sea bacteria was studied in smaller scale microcosm experiments. In diesel oil experiments bacteria from water phase of the Archipelago Sea was studied. Sediment and iron manganese concretions collected from the Gulf of Finland were used in the crude oil and polycyclic aromatic hydrocarbon experiments. The amount of polycyclic aromatic hydrocarbon degradation genes was measured in all of the oil degradation experiments. The results show how differences in bacterial community structure can be seen in the sea surface when compared to the subsurface waters. The mesocosm experiment demonstrated how diatom-bacteria interactions depend on other factors than diatom derived polyunsaturated aldehydes, which do not seem to have an effect on the bacterial community structure as has been suggested in earlier studies. The dominant bacterial groups in the diesel microcosms differed in samples taken from a pristine site when compared to a site with previous oil exposure in the Archipelago Sea area. Results of the study with sediment and iron-manganese concretions indicate that there are diverse bacterial communities, typical to each bottom type, inhabiting the bottoms of the Gulf of Finland capable to degrade oil and polycyclic aromatic hydrocarbon compounds.  Itämeri on ainutlaatuinen biologisilta, geokemiallisilta ja fysikaalisilta ominaisuuksiltaan. Suurempien eliöiden suhteen lajisto on Itämerelle tunnusomainen ja harvalukuinen, mutta mikrobilajisto on monimuotoinen. Alhaisemman suolapitoisuuden vuoksi bakteeriyhteisöt poikkeavat valtamerten yhteisöistä. Tutkimustieto Itämeren bakteeriyhteisöistä ja niiden vasteista erilaisille ympäristötekijöille auttaa arvioimaan myös laajemmin erilaisten tekijöiden vaikutusta Itämeren ekosysteemin tasapainoon ja toimintaan. Bakteerit ovat keskeisessä roolissa luonnon biogeokemiallisissa prosesseissa ja ihmisen aiheuttamissa ilmiöissä kuten rehevöityminen, öljyonnettomuudet tai haitallisten aineiden päätyminen mereen. Tässä väitöskirjatyössä verrattiin Saaristomeren pinnan mikrokerroksen bakteeriyhteisöjä niiden alapuolisen veden bakteeriyhteisöihin. Lisäksi tutkittiin piilevien tuottamien monityydyttymättömien aldehydiyhdisteiden vaikutusta Itämeren veden bakteeriyhteisöihin mesokosmoskokeen avulla. Diesel- ja raakaöljyn sekä polysyklisten aromaattisten hiilivetyjen hajottamispotentiaalia seurattiin pienempien mikrokosmoskokeiden avulla. Dieselöljykokeissa tutkittiin Saaristomeren vesifaasin bakteerien kykyä hajottaa dieselöljyä. Suomenlahden sedimentin ja rautamangaanisaostumien bakteerien kykyä hajottaa raakaöljyä ja polysyklisiä aromaattisia hiilivetyjä tutkittiin niitä sisältävissä kokeissa. Polysyklisten aromaattisten hiilivetyjen hajoamisprosessiin liittyvien geenien määrää mitattiin kaikissa öljykokeissa. Tulokset osoittavat kuinka Saaristomeren pinnan mikrokerroksen bakteeriyhteisöt poikkeavat alusveden bakteeriyhteisöistä. Mesokosmoskokeiden perusteella selvisi, että piilevien tuottamat monityydyttymättömät aldehydiyhdisteet eivät ole piileväbakteeri- vuorovaikutukseen vaikuttava tekijä, toisin kuin aiemmissa laboratoriotutkimuksissa on esitetty. Dieselöljykokeissa hallitsevat bakteeriryhmät riippuivat aiemmasta öljyaltistuksesta; bakteeriryhmät poikkesivat aiemmin öljylle altistuneessa vesinäytteessä puhtaan alueen näytteen yhteisöistä. Raakaöljyn- ja polysyklisten aromaattisten hiilivetyjen hajotusta tutkittaessa kokeiden tulokset osoittivat, että Suomenlahden sedimentissä ja rauta-mangaanisaostumissa on niille tyypilliset monimuotoiset bakteeriyhteisöt, joilla on kyky hajottaa näitä yhdisteitä.Siirretty Doriast

Pedagogical documentation and its relation to everyday activities in early years

Documentation in early childhood education and care (ECEC) institutions has been developed for decades in various contexts. Today, documentation is preferred as an inclusive method of evaluating, planning, and developing ECEC in the curricula of many countries. Qualitative research on documentation has increased in past years, but quantitative research on the connections between documentation and ECEC practice has remained behind. We will present a study in which a total of 2889 children, 194 kindergartens and preschools, and 179 teams of ECEC educators in 13 municipalities in Finland participated. On the basis of our quantitative analysis, we argue that documentation is inherently connected with child-centred and carefully planned ECEC practices and the children's participation, well-being, and ability to learn. One of our main findings is that documentation is not yet fully exploited in the Finnish ECEC. As a result, we encourage ECEC officers and educators to develop documentation further.Peer reviewe

Children's Peer Relations and Children's Physical Activity

AbstractPeers have an impact on children's physical activity (PA) in day care. To obtain the whole picture of children's physical activities we need to study the PA design of children and their peers. The activities of 838 children, including the PA level, were observed using systematic sampling. Children's skills were evaluated. The level of the children's PA tended to be lower if they had weaker social contacts with their peers. The children that were physically active sought each other's company. In company with a more independent and self-directive peer, the children tended to be less physically active

Is physical activity a pathway to culturally and linguistically diverse children’s participation in early childhood education and care?

The Finnish early childhood education’s main principle is to guarantee all children’s and families' rights, prevent segregation, and enhance equality, inclusion, diversity, participation, and communality. Physical activities are one significant way to support all children’s well-being and participation. According to previous studies physical activities were also connected to participation among culturally and linguistically diverse children (Arvola, 2021; Arvola et al., 2020). The study aims to find out if physical activity is a pathway to culturally and linguistically diverse children’s participation. This study is a part of the large Progressive Feedback research results gathered in Finland (see https://blogs.helsinki.fi/orientate/). The main method of the study is systematic observation. According to these results, culturally and linguistically diverse children move enough during their day care day, but they were more often interrupted, less involved, and less participative in their activities. Physical activity was related to continuous involvement. The most increasing physical activity was in sustaining intense involvement: a third of all movement happened in high involvement. The observation results indicate that physical activity is related to increased involvement and building social processes among culturally and linguistically diverse children.

You do not like the activity arranged by the teacher: What do you do?

Peer reviewe

Children’s negative experiences as a part of quality evaluation in early childhood education and care

Quality factors are the subject of increasing interest in the research and practice of early childhood education and care (ECEC). The purpose of the article is to emphasize the importance of the children's voice in relation to the quality of ECEC. This article focuses on children's negative experiences of ECEC as they can be used to improve services and increase children's wellbeing. The data was collected by means of a questionnaire from 2500 children aged 2-6 years (girls 50.4%) in Finland. The data was analysed using qualitative and quantitative content analysis. According to the results, children mentioned both structural and process factors. Peer interaction among children was mentioned the most when referring to negative experiences in ECEC. We conclude that children's negative experiences provide an opportunity for ECEC professionals to support children's resilience and a sense of belonging, which are important elements in the process quality of ECEC.Peer reviewe

The Amount of Physical Activity in Finnish Day Care

Peer reviewe

Physical Activity and Learning Environment Qualities in Finnish Day Care

AbstractWhen evaluating children's physical activity in day care, both the direct education and the children's activities in their personal contexts must be studied. In this study children's physical activity level was systematically observed in 2010 in 47 day care centre groups. Other children increased children‘s physical activity (p < .05). If the educators had spent more time planning activities or concentrated more on children's social relations, children were more physically active (p < .05). The planning of educational activities and interaction planned between children in the group may activate them more effectively than traditional planning for the group

Children’s creative thinking abilities and social orientations in Finnish early childhood education and care

The study presented in this article is part of a larger study called Progressive Feedback (blogs.helsinki.fi/orientate), which is an early childhood education and care (ECEC) research and development project. The aim of this article is to find out (a) how childrens tested creative thinking abilities, fluency, originality and imagination correlated with childrens social orientations in kindergarten and (b) how childrens participative orientations occur in relation with the teacher and peers. The data consist of Reunamo's child interview tool and the Thinking Creatively in Action and Movement (TCAM) test. The data (280 children from 23 kindergartens and pre-primary schools) were gathered from two municipalities in southern Finland. The results show that the participative orientation was strongly connected with creative thinking abilities, but it was rare in social situations concerning adults. In participative orientation, children concern the situation and intend to change it.Peer reviewe