The development of Massively Parallel Sequencing (MPS) has enabled more accurate and less time-consuming DNA sequencing. Although MPS technologies are theoretically applicable to all samples and species, the majority of studies on microorganisms have been conducted on those able to be isolated and cultivated in laboratories. In the field of metagenomics, DNA from uncultivated environmental samples is analyzed. Whole genome sequencing of such complex samples poses difficult computational challenges due to the characteristics of metagenomic data, where one major challenge lies in determining the true origin of high similarity reads. In addition, the short-range information acquired from MPS reveals little about how reads from DNA sequencing fit together. Consequently, producing genome drafts from reads generated by MPS remains difficult. Here, the linked-read sequencing technology DB-Seq has been applied to bacterial samples in order to assess its potential in metagenomics. Specifically, its performance in retaining long-range information in de novo whole genome assembly has been tested. The results obtained in this initial study show great potential of DB-Seq in genome assembly, with significantly more contiguous results than conventional methods generate. / Utvecklingen av Massiv Parallel Sekvensering (MPS) har möjliggjort mer korrekt och mindre tidskrävande DNA sekvensering. Trots att MPS teoretiskt sett kan appliceras på alla provtyper och arter, har majoriteten av de studier som utförts på mikroorganismer varit fokuserade på de som kan isoleras och odlas i laboratorium. Inom ämnet metagenomik analyseras DNA från orörda miljöprover. Helgenomssekvensering av sådana prover ger upphov till komplicerade utmaningar för data-analys, där ett av de största problemen är att bestämma ursprunget av snarlika sekvenseringsresultat. Ytterligare komplikationer uppstår på grund av den data som erhålls från MPS, då denna ej ger information om hur sekvenseringsdata bör placeras i förhållande till varandra. Följdaktligen är det svårt att producera hopsatta genom utifrån MPS-data. I detta projekt har "linked-read"-sekvenseringsteknologin DB-Seq applicerats på bakterieprover för att undersöka metodens potential i metagenomik. Specifikt har metodens förmåga att bibehålla information om ursprungspositionen av sekvenseringsdata testats i de novo sammansättning av genom. De erhållna resultaten i denna förstagångsstudie tyder på stor potential för DB-Seq i genomsammansättning, med signifikant mer sammanhängande resultatsekvenser än vad konventionella metoder uppvisar.

Syftet med denna studie är att synliggöra på vilket sätt lärare arbetar för att väcka elevernas läslust i och utanför skolan.  För att uppnå studiens syfte har två frågeställningar skapats. Dessa lyder ”I vilken utsträckning och på vilket sätt arbetar lärare för att främja elevernas intresse för läsning?” och ”Vilka utmaningar och möjligheter ser lärarna för elevernas läsutveckling i relation till läslust?”    För att samla in data till denna studie användes en kvalitativ datainsamlingsmetod eftersom det skulle samlas in information som beskriver lärarnas upplevelser, tillvägagångssätt och föreställningar. Observationer av verkligheten har således inte genomförts, men lärarna har fått dela sina upplevelser och sin verklighet kring ämnet, vilket förhoppningsvis leder närmare en förklaring till elevernas dalande läslust.    Av resultaten framkom det att elever är mer motiverade att läsa när läsuppgifterna och aktiviteterna är relevanta för deras liv, när de har tillgång till ett brett utbud av läsmaterial, när de har stora möjligheter att engagera sig i varaktig läsning och när de har möjligheter att göra val om vad de läser och hur de engagerar sig i och slutför läskunnighetsuppgifter. Resultaten påvisade även att elever är mer motiverade att läsa när de har möjligheter att socialt interagera med andra om texten de läser, när de har möjligheter att lyckas med utmanande texter och när incitament i klassrummet återspeglar värdet och vikten av att läsa. För att besvara frågeställningarna tog jag hjälp av en didaktisk-metodisk handlingskompetens avseende hur lärare skapar motivation att läsa hos sina eleverna och Gambrells (2011) sju principer om hur lärare arbetar för att främja elevernas lust till att läsa. / The purpose of this study is to make visible in what way and why teachers work to arouse students' desire to read in and out of school. To achieve the purpose of the study, two issues have been created. These read "To what extent and in what way do teachers work to promote students' interest in reading?" and "What challenges and opportunities do teachers see for students' reading development about the desire to read?" To collect data for this study, a qualitative data collection method was used because it would collect information that describes the teachers' experiences, approaches, and ideas. Observations of reality have thus not been carried out, but the teachers have had to share their experiences and their reality on the subject, which hopefully leads to a closer explanation for the students' declining desire to read.  The results showed that students are more motivated to read when the reading tasks and activities are relevant to their lives, when they have access to a wide range of reading materials, when they have great opportunities to engage in lasting reading and when they have opportunities to do choices about what they read and how they engage in and complete literacy tasks. The results also showed that students are more motivated to read when they have the opportunity to socially interact with others about the text they read, when they have the opportunity to succeed with challenging texts, and when incentives in the classroom reflect the value and importance of reading. To answer the questions, I took the help of a didactic-methodological action competence regarding how teachers create motivation to read in their students and Gambrell's (2011) seven principles on how teachers work to promote students' desire to read.

Chromosomal structure variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismalphenotype. Some of these effects are caused by structural variations containing genes. Modern sequencing using short reads makes the detection of large structural variations (> 1kb) very difficult. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of Drosophila melanogaster (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Because the average read length used for these approaches are much longer than traditional short read sequencing, these maps facilitate the identification of chromosomal SVs of greater size and with more clarity. We found a wide diversity of structural variations in each of the five strains. These structural variations varied greatly in size and location, and significantly affected exonic regions of the genome. Structural variations accounted for a much larger difference in number of base pairs between strains than single nucleotide polymorphisms (SNPs).

京都大学 / 新制・課程博士 / 博士(工学) / 甲第24898号 / 工博第5178号 / 新制||工||1988(附属図書館) / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 伊藤 禎彦, 教授 松田 知成, 教授 越後 信哉 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

The purpose of this study is to contribute to an increased understanding of how preschool teachers work with reading aloud in preschool and what they think about reading aloud as a way of working for children's language development. To investigate this and to gather empirical evidence, we have used qualitative interviews where we interviewed ten working preschool teachers. The collected empirical evidence is processed through a thematic analysis. The investigation takes the socio-cultural theory as a point of departure, where we analyze the results based on theoretical concepts. The theoretical concepts have given us an increased understanding of the results that we have obtained. The results of this study show that reading aloud is used frequently, both spontaneously and planned in the preschool’s activities. The preschool teachers repeatedly mention in our interviews that reading aloud is a central part of the activities. The reading aloud is further described as something that can be used as a starting point for several different follow-up works. Furthermore, reading aloud is described as developing on several levels, not at least as language development. The conclusion made in this study is that reading aloud is a central part of the preschool’s activities. The reading aloud takes place both spontaneously and planned, and in this study we have been able to see how the preschool teachers continue to work with the reading aloud. / Syftet med undersökningen är att den ska bidra till en ökad förståelse för hurförskollärare arbetar med högläsning i förskolan och vad de anser omhögläsningen som ett arbetssätt för barns språkutveckling. För att undersökadetta och samla in empiri har vi använt oss av kvalitativa intervjuer där viintervjuade tio verksamma förskollärare. Den insamlade empirin bearbetasgenom en tematisk analys. Undersökningen tar utgångspunkt i densociokulturella teorin där vi utifrån teoretiska begrepp analyserar resultaten.De teoretiska begreppen har gett oss en ökad förståelse för de resultat som vifått. Resultatet av undersökningen visar att högläsning används frekvent, bådespontant och planerat i förskolans verksamhet. Förskollärarna nämneråterkommande i våra intervjuer att högläsningen är en central del iverksamheten. Högläsningen beskrivs vidare som något som kan användassom en utgångspunkt till flera olika uppföljningsarbeten. Högläsningenbeskrivs ytterligare som utvecklande på flera plan, inte minst somspråkutvecklande.Slutsatsen som görs i denna undersökning är att högläsning är en central del iförskolans verksamhet. Högläsningen sker både spontant och planerat och vihar i denna undersökning fått ta del av hur förskollärarna arbetar vidare medhögläsningen.

The purpose of the study was to examine preschool teacher's perceptions in their speech when talking about stereotypes and norm critical literature in read alouds. The theory used in this study was discourse analysis, which here also uses some concepts from the discourse theory by Laclau and Mouffe. Some of these concepts were contextualization, sign and equivalence chain. The speech was later catagorized and analyzed. This study used interviews to gather information, where six preschool teachers from three different preschools were interviewed. The information resulted in a pattern where four categories were presented. These categories were called the corrective, the articulating, the debating and the representing preschool teacher. The analysis resulted in an understanding of a discourse, which used a speech that correlates to preschool teachers understanding of preschool policy documents, the norm critical perspective and their profession. / Studien syftar till att synliggöra förskollärares föreställningar kring högläsningav normkritisk litteratur och normbekräftande litteratur. Undersökningen haren diskursanalytisk ansats, vilket här uppfattas som ett synliggörande av det talsom kan kopplas till situation och sammanhang. Som stöd i analysen användsbegrepp som kontextualisering, subjektspositioner, tecken ochekvivalenskedja. Begreppen används som ett tillvägagångssätt för attundersöka talet och hur det används utifrån kontexten.Studien använder intervjuer som metod, där sex förskollärare från tre olikaförskolor intervjuades. Det resulterade i ett belysande av enförskollärardiskurs, vilket i denna text kategoriseras som: den korrigerande-,en artikulerande-, den diskuterande- och den representerande förskolläraren.Analysen resulterade i ett synliggörande av olika diskurser som förhåller signära till förskolans styrdokument och förskollärarens uppfattning av ettnormkritiskt förhållningsätt

Students at risk for reading difficulties often display skills deficits in basic reading skills (e.g., phonological awareness or PA, fluency, and comprehension). Phonological awareness instruction (PAI) and scaffolded instruction have been effective in improving reading skills for all students (National Reading Council, 1998). In relation, Reading to Read (RTR), a remedial reading program based on the methods of applied behavior analysis, direct instruction, and curriculum-based assessment, has been found to improve oral reading fluency and comprehension (e.g., Edwards, Tingstrom, & Cottingham, 1993; Tingstrom, Edwards, & Olmi, 1995). Despite the effectiveness of PAI and RTR in isolation, little research has been conducted to determine effectiveness of PAI and scaffolding combined with the RTR intervention. The purpose of this study was to investigate effectiveness of using PAI in combination with RTR as another instructional method for increasing reading fluency and comprehension. Participants included 5 elementary-aged students who have a special education diagnosis and are from rural southeastern region of the U.S. Data were collected using a single-subject research methodology and included correct words per minute (CWPM), errors per minute (EPM), and percent correct comprehension in all phases for all intervention conditions: (a) PAI, (b) RTR, and (c) PAI + RTR. Data were analyzed using visual inspection or graphical representation assessed by level, trend, and variability around level and trend between the different interventions as it relates to CWPM, EPM, and percent correct comprehension. When examining reading fluency, 1 of the 5 students who received the PAI + RTR interventions improved in reading fluency from baseline to intervention. When examining reading comprehension, all students demonstrated little to no change in percent correct comprehension questions across all conditions and phases. Implications, limitations, and future research relating to the results of this study are also discussed.

The participants in this study were referred by the teacher or the teacher support team for a functional behavioral assessment (FBA) and development of a positive behavior support plan to address disruptive behavior and academic skills deficits. Therefore, the purpose of Experiment I was to examine the ability of FBA procedures to identify students with reading difficulty who demonstrated problem behavior potentially maintained by escape from academic demands. Each environmental variable introduced during the brief functional analysis was manipulated via a multiple element design (Cooper, Wacker, Sasso, Reimers, & Donn, 1990; Derby et al., 1992; Northup et al., 1991). Experiment II sought to empirically evaluate the effectiveness of the Reading to Read (RTR) intervention package in addressing the oral reading fluency and comprehension deficits of referred elementary students. Experiment II also examined the generalized effects of the reading intervention on reducing the identified escapemaintained problem behaviors (i.e., off-task) during the reading class. For Experiment II, a multiple baseline (MBL) across participants design was used to evaluate the impact of the RTR intervention on addressing both academic and problem behaviors (e.g., identified on the FAIR-T). Results from descriptive and functional analysis procedures in Experiment I revealed that all of the participants were performing at least one grade level below expectations in regarding to reading fluency. In addition, all of the participants exhibited more off-task behavior during the difficult task demand versus the easy task demand conditions of the brief functional analysis. The participants also obtained lower scores on comprehension questions during the difficult task demand versus the easy task demand conditions. This pattern of responding suggested the off-task behavior was potentially maintained by escape from academic demands in reading. Results from Experiment II revealed that all participants increased their oral reading fluency levels on intervention probes in comparison to the baseline levels. In addition to the increase in oral reading fluency, there was an increase in their percentage of correct responses in reading comprehension when compared to baseline data. In regards to generalization reading probes, all of the participants evidenced overall increases in their reading skills in comparison to baseline data. In fact, all of the participants increased from frustrational to near mastery levels. Finally, results from Experiment II revealed that all participants’ experienced reduction in their off-task behavior while partaking in the RTR intervention in comparison to baseline levels. This notable decrease extended throughout the study for all participants. Overall, the present results revealed that the RTR intervention was effective in addressing the reading fluency and comprehension deficits of identified students. In addition, remediation of reading skills appeared to have assisted in the reduction of social problem behavior performed during reading instruction in the general education classroom. Important implications for practice and inclusion of the procedures used in this study within applied settings are discussed. In addition, important limitations and considerations for future research are outlined.

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