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1

Cheema, Tabinda Shahid, of Western Sydney Nepean University, and Faculty of Education. "Laboratory based instruction in Pakistan: comparative evaluation of three laboratory instruction methods in biological science at higher secondary school level." THESIS_FE_XXX_Cheema_T.xml, 1994. http://handle.uws.edu.au:8081/1959.7/271.

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This study of laboratory based instruction at higher secondary school level was an attempt to gain some insight into the effectiveness of three laboratory instruction methods: cooperative group instruction method, individualised instruction method and lecture demonstration method on biology achievement and retention. A Randomised subjects, Pre-test Post-test Comparative Methods Design was applied. Three groups of students from a year 11 class in Pakistan conducted experiments using the different laboratory instruction methods. Pre-tests, achievement tests after the experiments and retention tests one month later were administered. Results showed no significant difference between the groups on total achievement and retention, nor was there any significant difference on knowledge and comprehension test scores or skills performance. Future research investigating a similar problem is suggested
Master of Education (Hons)
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2

Perry, Janet Elise. "Envirothon teaching methods: how do they impact learning in the traditional biology classroom?" Montana State University, 2011. http://etd.lib.montana.edu/etd/2011/perry/PerryJ0811.pdf.

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My Action Research Project connects the Envirothon contest with a traditional biology classroom. In the Envirothon, a national environmental contest, teams of high school students work together outdoors, solving site-based natural resource questions and problems in aquatics, forestry, soils, wildlife, and a current environmental issue. During this competition, teams rotate from Station to Station, working on a variety of "hands on" tasks specific to each environmental area; the students are also tested on sets of questions that cover a very wide range of information for each topic. "Envirothon Teaching Methods" typically used to successfully prepare teams for this competition involve bringing in knowledgeable professionals to help students learn about each of these environmental areas. The lessons, presented by local natural resource people with expertise and experience, usually focus on providing students with "real world" information. Students typically learn in an outdoor setting and/or use local materials and resources. "Hands on" authentic activities are emphasized as an important way to increase student comprehension of environmental subject matter. In this Action Research Project, I incorporated the same teaching methods commonly used to train students for Envirothon contests into my high school College Biology course. When used by an entire class of students within a traditional school day setting, Envirothon teaching methods had positive impacts on students' comprehension of environmental topics.
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Kvarnström, Josefin. "Consistency and heritability of personality in red junglefowl (Gallus gallus) : Applying scientific research methods when teaching biology." Thesis, Linköpings universitet, Biologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-94246.

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Observations of consistency in behavioural responses in animals suggest that animals have personality, a term previously mainly used when describing humans. The expression of differences in personality, similar to expression of variation in behaviour, is in principle dependent on genetic background, environmental factors and experiences. Therefore, by estimating heritability one can determine to which extent the genes affect the phenotypic expression of behaviour. This has rarely been done for variation in animal personality. The aim of the present study was therefore to estimate the consistency and heritability of personality traits in red junglefowl chicks (Gallus gallus). Consistency of behaviours within individuals (n=100) was determined from their responses to repeated novel arena tests, novel object tests and tonic immobility tests. A comparison between the offspring and the parent generation, both with known personalities, through a linear regression enabled me to estimate heritability of behavioural responses in these birds. The results showed a consistency in exploratory, boldness, risk-taking behaviour, and fearfulness in red junglefowl. Additionally, heritability estimates for exploratory, risk-taking and foraging behaviours were found. Taken together, this shows that in the red junglefowl, similar to in other species, personality have both a heritable and an environmental component. An important aim in biology education is the scientific approach, where hypothesis, experimentation, processing results and discussing the results are in focus. Learning and gaining knowledge through the process is a key factor, and will hopefully increase the interest in science among Swedish pupils.
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Paterson, Craig Chalmers. "An experimental study of self-regulated learning in biology with special reference to instructional control, locus of control, and academic performance." Master's thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/15996.

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Bibliography: pages 189-198.
Applying theoretical conceptualisations of current theories of self-regulated learning, a biology instructional programme facilitating learner perceptions of control by offering choices in task engagement was undertaken with two intact samples of Caucasian standard ten higher grade biology pupils in Cape Town, with the student groups matched for IQ and ability. A counter-balanced, quasi-experimental research design was implemented for two five-day cycles. Learner locus of control and self-regulatory behaviour were established using, respectively, the Intellectual Achievement Responsibility Questionnaire (Crandall, et al, 1965), and the Motivated Strategies for Learning Questionnaire (Pintrich and De Groot, 1990). The primary aim was to test the prediction that, in contrast to teacher-regulated instruction, academic performance after learner self-regulation would be appreciably greater. Differences between the experimental and control group mean achievement scores at the end of the programme were highly significant.
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Martinez, Mabell Jeannette. "Moving traditional teaching methods of advanced placement biology toward improving opportunity for students to develop understanding of scientific principles." CSUSB ScholarWorks, 2006. https://scholarworks.lib.csusb.edu/etd-project/2972.

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This project investigated the role of the advanced placement program in the classroom. The research suggested that implementation of inquiry-based methods in science classrooms, including advanced placement biology courses, would improve student understanding.
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Agboola, Oluwaseun O. "Inclusive Teaching Strategies: An Evaluation of Course Structure and Summative Assessment in Introductory Biology." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etd/3221.

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Several active learning strategies have been used when increasing the structure of a course as increasing course structure has been known to improve student learning in introductory STEM courses. Much has been studied on the value of frequent formative assessment; however, few studies have evaluated the effective modes of delivering summative assessment. This study examines the use of summative assessment as an inclusive teaching practice to improve first generation college student success in introductory biology and also uses faculty surveys to find out how instructors structure their introductory biology course and why they are structured that way. Final exams were evaluated by Bloom’s Taxonomy of Learning. Survey results showed that many instructors used online activities most of the time to supplement face-to-face courses. However, student and faculty viewpoints on assessments offer many interesting insights into how instructors may modify teaching strategies to increase the success of diverse student populations.
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7

Karlsson, Ann-Christin. "Hur man fångar elevers intresse för ämnet biologi." Thesis, Karlstad University, Faculty of Social and Life Sciences, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-854.

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From interviews with biology teachers and pupils, some important factors are presented that motivates and interests pupils in biology. Some of these are varied education, commitment of the teacher, narrative skill and individually reachable goals. Other important factors are practical application and connection to daily life, as well as actuality of the subject and pupils experience of the use of learning.

Circumstance around teacher and pupils will influence which factors that has the most impact. It´s up to each teacher to make a decision which factors to be used based on his or her own qualities and depending on the group they will teach.

Teachers and pupils agreed about factors that will cause an interesting lesson. The pupils emphasize that variation is the most important factor. Their experience is that many teachers have theoretical introductions that are too long.


Utifrån intervjuer med biologilärare och elever presenteras ett antal punkter som viktiga, eller som grundförutsättningar, för att motivera och intressera elever för ämnet biologi. Några av dessa är varierad undervisning, lärarens engagemang och berättarförmåga samt individuella greppbara mål. Praktisk tillämpning och verklighetsanknytning, ämnets mediala aktualitet samt att eleverna upplever nytta av sitt lärande är andra exempel på viktiga faktorer.

Omständigheter runt lärare och elever påverkar vilka faktorer som spelar mest in. Detta måste varje pedagog känna av, beroende på egna egenskaper och elevmålgrupp.

Lärare och elever är eniga om vilka faktorer som är viktiga för att göra lektionen intressant. Eleverna betonar dock vikten av variation och menar att flertalet lärare har alltför långa teoretiska genomgångar.

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Robison, Diane F. "Active learning in a large enrollment introductory biology class : problem solving, formative feedback, and teaching as learning /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1338.pdf.

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Sterve, Hanna. "The Influence of the View of Nature on Biology Education in Zimbabwe, a Minor Field Study." Thesis, Linköping University, Department of Educational Science (IUV), 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-1546.

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The purpose of this thesis is to look into the teaching methods and content in Zimbabwean biology education, and the possible influences that the teachers’ view of nature have on this education. The study was performed in and around Mutare in eastern Zimbabwe with eleven observations and six interviews in primary and secondary schools, corresponding to years four to nine in the Swedish compulsory school.

My study shows that the teachers’ view of nature is in many parts similar to the Swedish view of nature, but differ in a closer connection to religiosity and in a more every-day-life relation to nature. This is reflected in several of the concepts that view of nature consist of. The view of nature is influencing the content in biology partly. Since science hold universal concepts which are the same all around the world, the view of nature does not influence the scientific parts of biology, but have influence on where the emphases in the education is put. The results show no direct influence of the view of nature on teaching methods, but indirectly influenced by the choice of content.

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Li, Feng. "Evaluating High School Biology Modeling Instruction in South Florida: A Comparative Case Study." FIU Digital Commons, 2017. https://digitalcommons.fiu.edu/etd/3522.

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The dissertation, with a collected papers approach, focused on evaluating the implementation of MI curriculum in high school Biology I classes in south Florida. The dissertation included the development and validation of the Biology Identity and Persistence Survey (BIPS), the connection of instructors’ teaching practices with students’ biology identities, evolution identities, and career aspirations, and the connection of instructors’ teaching practice with students’ conceptual understanding in evolution. In the first part of the dissertation study, the BIPS was validated through expert review and student cognitive interviews for its face and content validity. Confirmatory factor analysis addressed the construct validity of the final version of the BIPS, after removing four problematic items. The Cronbach’s alpha and test-retest reliability analysis indicated that the BIPS was a reliable instrument in terms of its internal reliability and stability. In the second part of the dissertation study, the comparison between the MI and non-MI classes indicated that there was no detectable significant difference between the MI classes and non-MI classes in students’ development of biology identities and evolution identities, and shifts in career aspirations. Using the analysis of the MI and non-MI instructors’ teaching practices, it was suggested that the use of intentional lack of inquiry closure, seeding, small-group collaboration, whole-class discussion, and Socratic questioning might contribute to students’ biology/evolution identity development. In the third part of the dissertation study, the Evolution Concept Inventory was demonstrated as an invalid and unreliable research instrument. Qualitative analysis of instructors’ teaching practices suggested that interactions between MI instructional materials and MI pedagogical techniques, including student-centered teaching, small-group collaboration, student-student interaction, whole-class discussion, and Socratic questioning, might contribute to students’ gain of conceptual understanding in evolution. On the basis of the research findings, this dissertation provided suggestions for high school biology MI instructors and high school biology MI workshops.
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Hurst, March Robin. "A comparison of students' achievement and attitude as a function of lecture/lab sequencing in a non-science majors introductory biology course /." free to MU campus, to others for purchase, 1997. http://wwwlib.umi.com/cr/mo/fullcit?p9842590.

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Dyer, Brian Jay. "How Does Student Understanding of a Concept Change Throughout a Unit of Instruction? Support Toward the Theory of Learning Progressions." PDXScholar, 2013. https://pdxscholar.library.pdx.edu/open_access_etds/1528.

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This study documented the changes in understanding a class of eighth grade high school-level biology students experienced through a biology unit introducing genetics. Learning profiles for 55 students were created using concept maps and interviews as qualitative and quantitative instruments. The study provides additional support to the theory of learning progressions called for by experts in the field. The students' learning profiles were assessed to determine the alignment with a researcher-developed learning profile. The researcher-developed learning profile incorporated the learning progressions published in the Next Generation Science Standards, as well as current research in learning progressions for 5-10th grade students studying genetics. Students were found to obtain understanding of the content in a manner that was nonlinear, even circuitous. This opposes the prevailing interpretation of learning progressions, that knowledge is ascertained in escalating levels of complexity. Learning progressions have implications in teaching sequence, assessment, education research, and policy. Tracking student understanding of other populations of students would augment the body of research and enhance generalizability.
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Jacobsson, Catharina. "”Let´s talk about sex” - But how? : Lärares beskrivningar kring val av arbetssätt inom sex- och samlevnadsundervisning kopplat till hur känsligt ämnet är." Thesis, Högskolan Dalarna, Institutionen för lärarutbildning, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:du-38108.

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Skolinspektionen menar att alla elever har rätt till att få sex- och samlevnadsundervisning. Den syftar till att stärka självkänslan hos eleverna och bidra till att de kan ta ansvarsfulla och medvetna beslut rörande sexualitet, relationer och hälsa. För att lärare ska känna sig bekväma och trygga i sin undervisande roll krävs kompetens i form av faktakunskaper och insikter om vilka arbetsmetoder som lämpar sig för ett visst moment. Skolinspektionen för fram vikten av att verktyg och stöd görs tillgängliga för lärare.Syftet med denna studie är att utifrån lärares beskrivningar få en fördjupad kunskap inom känsliga ämnen i sex- och samlevnadsundervisningen i gymnasiekurserna Biologi 2 och Naturkunskap 1a1. I denna studie genererade tre kvalitativa intervjuer, en parintervju samt två enskilda intervjuer resultat som användes som underlag för diskussion och slutsatser.Tidigare forskning på området har varit knapp och svår att hitta. Detta arbete söker öka kunskapsbidraget inom val av arbetssätt och hur undervisningen av känsliga ämnen inom sex- och samlevnadsundervisningen kan bedrivas.Som teoretisk utgångspunkt används den didaktiska triangeln som visar på en grundläggande beskrivning av hur lärare, elev och innehåll förhåller sig till varandra. Den utökade didaktiska triangeln ligger närmre som förklaringsmodell till detta arbete och fokus ligger på hur lärarens olika kompetenser utgör grunden för valet av vilka arbetssätt som används vid undervisning av känsliga ämnen.Lärarna har en hög medvetenhet om vilka faktorer som kan påverka sex- och samlevnadundervisningen. Informanterna uttrycker att det är av stor vikt att elevernas egna frågor får ta plats och att det är viktigt som lärare att skapa strukturer, arbetssätt, i undervisningen som avpersonifierar framförallt elever men även lärare och istället fokusera på sakfrågan.Även om elevernas önskemål till viss del bör ligga till grund för den undervisning som bedrivs är det läraren utifrån sin profession som ska styra den. Resultatet i denna studie visar att utifrån det informanterna berättat bör alla parametrar i den didaktiska triangeln (didaktisk kompetens, ämneskompetens samt social kompetens) tas i beaktning men att den sociala kompetensen i sex- och samlevnadsundervisningen verkar ha en mer avgörande roll än de övriga två.
The Swedish Schools Inspectorate believes that all students have the right to receive sex and cohabitation education. It aims to strengthen students' self-esteem and help them make responsible and conscious decisions regarding sexuality, relationships and health. In order for teachers to feel comfortable and secure in their teaching role, competence is required in the form of factual knowledge and insights into which working methods are suitable for a particular part. The Swedish Schools Inspectorate emphasizes the importance of tools and support being made available to teachers.The purpose of this study is to, based on teachers' descriptions, gain an in-depth knowledge of sensitive subjects in sex and cohabitation teaching in the upper secondary school courses Biology 2 and Natural Science 1a1. In this study, three qualitative interviews, a couple interview and two individual interviews generated results that were used as a basis for discussion and conclusions.Previous research in the field has been scarce and difficult to find. This work seeks to increase the knowledge contribution within the choice of working methods and how the teaching of sensitive subjects in sex and cohabitation education can be conducted.As a theoretical starting point, the didactic triangle is used, which shows a basic description of how teachers, students and content relate to each other. The extended didactic triangle is closer as an explanatory model for this work and the focus is on how the teacher's different competencies form the basis for the choice of which working methods are used in teaching sensitive subjects.Teachers have a high level of awareness of the factors that can affect sex and cohabitation education. The informants express that it is of great importance that the students' own questions take place and that it is important as a teacher to create structures, working methods, in teaching that depersonalize primarily students but also teachers and instead focus on the issue.Although the students' wishes should to some extent form the basis for the teaching that is conducted, it is the teacher based on his profession who should guide it. The results of this study show that based on what the informants said, all parameters in the didactic triangle (didactic competence, subject competence and social competence) should be taken into account, but that social competence in sex and cohabitation education seems to play a more decisive role than the other two.
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Correia, Sónia de Jesus Elias. "O ensino da evolução biológica em contexto de sala de aula. Uma abordagem com alunos do 11º ano de escolaridade na disciplina de biologia e geologia." Master's thesis, Universidade de Évora, 2011. http://hdl.handle.net/10174/11900.

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A teoria da evolução Darwin tem sido o eixo integrador do desenvolvimento do pensamento biológico. Neste sentido, esta investigação teve como problema o ensino da evolução biológica e as aprendizagens realizadas, procurando dar resposta às questões de investigação: (i) Como é tratado pelos professores o tema evolução biológica na sala de aula? e (ii) Que aprendizagens são efectuadas pelos alunos sobre o tema evolução biológica? O estudo incidiu sobre duas turmas do 11.º ano e respectivos professores, na disciplina de Biologia e Geologia, seguindo uma abordagem qualitativa e interpretativa, na forma de um estudo de caso. No sentido de obter dados e dar resposta às questões formuladas, foram utilizados inquéritos por questionário e testes de aprendizagens, realizadas entrevistas semi-estruturadas aos alunos e aos professores das turmas e foi feita observação de aulas. Utilizaram-se, assim, vários instrumentos de recolha de dados, de forma a aprofundar a análise e a triangular a informação obtida. Após analisados os dados, foram cruzadas as informações obtidas e aferidos os principais resultados e conclusões. Os resultados mostram que embora o ensino praticado seja muito centrado no professor, existe uma manifesta preocupação em envolver os alunos no processo de ensino e de aprendizagem. Por sua vez, os estudantes revelaram dificuldade em estabelecer relações entre conceitos e em alcançar aprendizagens mais profundas. O que nos leva a concluir que as aprendizagens realizadas foram pouco rigorosas do ponto de vista científico; ### Abstract: Darwin’s evolution theory has been the integrating axis of the development of biological thinking. In this sense, this investigation had has the aim to finding out about the teaching of Biological Evolution and the learning that takes place, searching for the answers for the investigation questions: (i) How is the teaching of Biological Evolution handled by the teachers in the classroom? ; and: (ii) How is the learning of Biological Evolution by the students rigorous enough from a scientific point of view?. The study focused on two classes from the 11th grade and their teachers, in the class of Biology and Geology, following a qualitative and interpretive approach, being this case study qualitative and analytical. The information was collected through direct class observation, interviews, questionnaires, learning test and document analysis. The results shown that the teaching was priority expositive. There is a clear concern to engage students in the teaching and learning process. The students shown difficulties in establishing relationships between concepts and to took more profound approaches, which leads us to conclude that the learning performed is not very accurate.
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Tempa, Tshering. "Teaching wildlife biology in Bhutan development of wildlife biology curriculum and teaching modules /." CONNECT TO THIS TITLE ONLINE, 2008. http://etd.lib.umt.edu/theses/available/etd-10212008-220358/.

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Delahoyde, Theresa Hawkins Peggy L. Morin Patricia J. Hutchinson Christine. "Generational differences of baccalaureate nursing students' preferred teaching methods and faculty use of teaching methods." Click here for access, 2009. http://www.csm.edu/Academics/Library/Institutional_Repository.

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Thesis (Ed. D)--College of Saint Mary -- Omaha, 2009.
A dissertation submitted by Theresa Delahoyde, MSN, RN to College of Saint Mary in partial fulfillment of the requirement for the degree of Doctor in Education with an emphasis on health professions education. This dissertation has been accepted for the faculty of College of Saint Mary by: Peggy Hawkins, PhD, RN, BC, CNE - chair ; Patricia Morin, PhD, RN - committee member ; Christine Hutchinson, JD - committee member. Includes bibliographical references.
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Paley, Christopher John. "Network methods in evolutionary biology." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611209.

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Nalbandian, Christopher John. "Catalytic Methods for Chemical Biology." Thesis, University of California, San Diego, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10812166.

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Inspired by atropisomerism and examples of differential biology displayed by enantiomeric compounds, I set out to develop a late stage regioselective functionalization of known kinase inhibitors that exhibit atropisomerism. The regioselective functionalization of these target atropisomeric scaffolds is pivotal in order to increase their barrier to rotation, rendering them isolable enantiomers. Chapter 1 explores the chemical methods developed in order to achieve this transformation. The mild late stage regioselective chlorination, and more broadly, halogenation of several diverse aromatics along with the target atropisomeric kinase inhibitor was achieved by employing phosphine sulfide Lewis base catalysts. Encouraged by this mild catalytic approach to functionalizing electron rich aromatics and heterocycles, I was intrigued to see if similar conditions could be extended to aromatic sulfenylation. Chapter 2 explores aromatic sulfenylation and the development of several bifunctional Lewis base-Bronsted acid catalysts to affect a mild sulfenylation of electron rich aza-heterocycles. The sulfenylation reagents employed in this project were diverse and the notable azido group was incorporated into one of the reagents. This advancement was applied to bioactives and peptides. When functionalizing di-substituted and tetra-substituted peptides our sulfenylation conditions were shown to be amenable in the presence of other electron rich side chains included amino acids, histidine and tyrosine. Though this methodology is selective, the limitation of this methodology is the scope of the reaction, limited to electron rich aza-heterocycles. This limitation was overcome by employing more electron rich selenoether Lewis base catalysts along with catalytic acid described in chapter 3. The findings in chapter 3 provide an improvement to mild sulfenylation methodologies by increasing the scope of reaction along with uncovering key mechanistic findings. The SCF3 group was applied to 3 FDA-approved drugs and shown to have significant increases in reactivity when catalytic selenoether Lewis base, along with catalytic acid are present. A comparison of electron rich and electron poor sulfenylation reagents corroborate the kinetic findings in this project.

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Zeldin, Robert Oliver. "Methods development for structural biology." Thesis, University of Oxford, 2013. https://ora.ox.ac.uk/objects/uuid:6f86c710-c507-405c-b58f-cd2eb6264eca.

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Two research questions are investigated here: the first, major, section addresses the problem of uneven distributions of dose (absorbed energy per unit mass) in crystals used for macromolecular crystallography (MX), and the second presents the develop- ment of a high-throughput metalloprotein characterisation technique, HT microPIXE. In MX, the advent of X-ray microbeam data collection has led to uneven distributions of dose within the crystal volume becoming increasingly common. In these cases, the rotation method creates a highly damaged central region of crystal that stays within the beam throughout exposure, and less damaged outer regions, which are introduced during rotation. This thesis presents a new software program, raddose-3d, which performs a full 3D simulation of the profile of absorbed energy (the dose state) within a crystal during X-ray exposure. In order to utilise this time resolved, 3D picture of the dose state of the crystal, a new metric – Diffraction Weighted Dose – is proposed. This metric is then experimentally validated, and is found to summarise the dose state into a single dose value, which reflects the damage state of the crystal. Simulations are performed using raddose-3d and Diffraction Weighted Dose to compare possible dose spreading strategies, and generalised recommendations for MX experimentalists are offered. Uniquely identifying the species and stoichiometry of bound metals in protein sam- ples is a significant challenge for biophysical characterisation. Low throughput mi- crobeam Proton Induced X-ray Emission (microPIXE) provides an unambiguous anal- ysis of these properties, but has a limited throughput of ∼10 samples per day. As a consequence, its applicability has been restricted to niche cases. This thesis presents significant progress, including proof of principle experiments, on developing sample preparation methods, data acquisition systems, and data analysis protocols to increase this throughput by an order of magnitude, opening up major new applications for the technique.
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Nivens, Ryan Andrew. "Teaching Mathematics Methods During Residency 1." Digital Commons @ East Tennessee State University, 2015. https://dc.etsu.edu/etsu-works/220.

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Tajzai, Vagma. "Preschool teachers' perceptions of biology teaching : Biology teaching in an outdoor environment from the child's perspective." Thesis, Karlstads universitet, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-85829.

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Abstract This study is about preschool teachers' perceptions of biology teaching in preschool. The study examines three questions based on the purpose of the study that focus on preschool teachers 'perceptions of biology teaching in preschool, the child's perspective as a starting point in biology teaching and preschool teachers' reasoning about the importance of the outdoor environment as a learning environment for biology teaching. The study is based on previous research results that highlight preschool teachers' lack of subject knowledge and uncertainty in science teaching at preschool. In addition, both the preschool curriculum and research studies emphasize the child's perspective in teaching. Learning environment in the form of both indoor and outdoor environment in accordance with previous research studies is a contributing factor in children's learning and development. In this study, the learning environment is highlighted as an outdoor environment in the form of the forest, nature walks and the preschool yard. The study results are based on empirical data collected based on semi-structured interviews with six preschool teachers in two different municipalities in western Sweden. Interviews are then analyzed based on a phenomenographic methodological approach. The results show that preschool teachers' perceptions of the subject of biology and its teaching in preschool are mostly linked to nature, animals, plants, and the human body. The results also show in different ways where the preschool teachers take care of children's questions and perspectives and set it as a starting point in the planning of biology teaching. This is done by planning the teaching with the children where the children get a chance to talk about what they want to learn and do in preschool. Finally, the preschool teachers explained that the learning and teaching environment as an outdoor environment in the form of the forest, walks and the preschool yard has an important role in children's learning in biology.
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Miller, David J. Ghosh Avijit. "New methods in computational systems biology /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2810.

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Li, Limin, and 李丽敏. "Machine learning methods for computational biology." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44546749.

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Selega, Alina. "Computational methods for RNA integrative biology." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/29630.

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Ribonucleic acid (RNA) is an essential molecule, which carries out a wide variety of functions within the cell, from its crucial involvement in protein synthesis to catalysing biochemical reactions and regulating gene expression. Such diverse functional repertoire is indebted to complex structures that RNA can adopt and its flexibility as an interacting molecule. It has become possible to experimentally measure these two crucial aspects of RNA regulatory role with such technological advancements as next-generation sequencing (NGS). NGS methods can rapidly obtain the nucleotide sequence of many molecules in parallel. Designing experiments, where only the desired parts of the molecule (or specific parts of the transcriptome) are sequenced, allows to study various aspects of RNA biology. Analysis of NGS data is insurmountable without computational methods. One such experimental method is RNA structure probing, which aims to infer RNA structure from sequencing chemically altered transcripts. RNA structure probing data is inherently noisy, affected both by technological biases and the stochasticity of the underlying process. Most existing methods do not adequately address the issue of noise, resorting to heuristics and limiting the informativeness of their output. In this thesis, a statistical pipeline was developed for modelling RNA structure probing data, which explicitly captures biological variability, provides automated bias-correcting strategies, and generates a probabilistic output based on experimental measurements. The output of our method agrees with known RNA structures, can be used to constrain structure prediction algorithms, and remains robust to reduced sequence coverage, thereby increasing sensitivity of the technology. Another recent experimental innovation maps RNA-protein interactions at very high temporal resolution, making it possible to study rapid binding events happening on a minute time scale. In this thesis, a non-parametric algorithm was developed for identifying significant changes in RNA-protein binding time-series between different conditions. The method was applied to novel yeast RNA-protein binding time-course data to study the role of RNA degradation in stress response. It revealed pervasive changes in the binding to the transcriptome of the yeast transcription termination factor Nab3 and the cytoplasmic exoribonuclease Xrn1 under nutrient stress. This challenged the common assumption of viewing transcriptional changes as the major driver of changes in RNA expression during stress and highlighted the importance of degradation. These findings inspired a dynamical model for RNA expression, where transcription and degradation rates are modelled using RNA-protein binding time-series data.
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25

Jung, Min Kyung. "Statistical methods for biological applications." [Bloomington, Ind.] : Indiana University, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3278454.

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Thesis (Ph.D.)--Indiana University, Dept. of Mathematics, 2007.
Source: Dissertation Abstracts International, Volume: 68-10, Section: B, page: 6740. Adviser: Elizabeth A. Housworth. Title from dissertation home page (viewed May 20, 2008).
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26

Rabb-Liu, Amy Felice 1968. "Teaching methods and student understanding in calculus." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/288725.

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This study is a comparative case study of what three college calculus teachers did in their classrooms and what their students understood about the concept of derivatives. The teachers were solicited on the basis of peer, supervisor and student recommendations as being good teachers; several volunteer student subjects were selected from each class. Using a naturalistic participant-observer paradigm, the data were collected primarily via extensive classroom observations and in-depth interviews with the teachers and students. Examination of written work, such as student exams, was employed for additional confirmation of hypotheses generated in the field. This study contributes to the bodies of knowledge on pedagogy, effective teaching, classroom dynamics, student understanding and teacher beliefs. The results should be of interest to teachers, teacher educators, mathematics text authors and people interested in how students learn and think about mathematics at the collegiate level. The study of these three classrooms reveals that there is a variety of effective teaching models for undergraduate calculus classrooms. There were, however, important commonalties among these models, the examination of which leads to some characterization of effective teaching practices. These teachers kept the focus on what their students were learning, rather than on covering material. In three different ways, these teachers each gave their students the opportunity to interact with the mathematics before the lesson ended. All three teachers displayed a willingness to grow and learn as teachers. Calculus students do not always learn what their teachers think they have taught. The students in this study displayed a variety of mistaken ideas about the concept of derivative and about other mathematical topics. For example, many students had trouble distinguishing between properties of the function and properties of the derivative. Some students believed that the derivative at a point was a line, rather than the numerical value associated with the slope of a line. Students and teachers disagreed about the correct definition of the derivative, with students attributing little importance to the idea of limits.
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Johnson, William J. "The teaching methods of Jesus a guide /." Theological Research Exchange Network (TREN), 1991. http://www.tren.com.

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28

Jiang, Hao, and 姜昊. "Construction and computation methods for biological networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B50662144.

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Biological systems are complex in that they comprise large number of interacting entities, and their dynamics follow mechanic regulations for movement and biological function organization. Established computational modeling deals with studying and manipulating biologically relevant systems as a powerful approach. Inner structure and behavior of complex biological systems can be analyzed and understood by computable biological networks. In this thesis, models and computation methods are proposed for biological networks. The study of Genetic Regulatory Networks (GRNs) is an important research topic in genomic research. Several promising techniques have been proposed for capturing the behavior of gene regulations in biological systems. One of the promising models for GRNs, Boolean Network (BN) has gained a lot of attention. However, little light has been shed on the analysis of internal connection between the dynamics of biological molecules and network systems. Inference and completion problems of a BN from a given set of singleton attractors are considered to be important in understanding the relationship between dynamics of biological molecules and network systems. Discrete dynamic systems model has been recently proposed to model time-course microarray measurements of genes, but delay effect may be modeled as a realistic factor in studying GRNs. A delay discrete dynamic systems model is developed to model GRNs. Inference and analysis of networks is one of the grand challenges in modern statistical biology. Machine learning method, in particular, Support Vector Machine (SVM), has been successfully applied in predictions of internal connections embedded in networks. Kernels in conjunction with SVM demonstrate strong ability in performing various tasks such as biomedical diagnosis, function prediction and motif extractions. In biomedical diagnosis, data sets are always high dimensional which provide a challenging research problem in machine learning area. Novel kernels using distance-metric that are not common in machine learning framework are proposed for possible tumor differentiation discrimination problem. Protein function prediction problem is a hot topic in bioinformatics. The K-spectrum Kernel is among the top popular models in description of protein sequences. Taking into consideration of positive-semi-definiteness in kernel construction, Eigen-matrix translation technique is introduced in novel kernel formulation to give better prediction result. In a further step, power of Eigen-matrix translation technique in feature selection is demonstrated through mathematical formulation. Due to structure complexity of carbohydrates, the study of carbohydrate sugar chains has lagged behind compared to that of DNA and proteins. A weighted q-gram kernel is constructed in classifying glycan structures with limitations in feature extractions. A biochemically-weighted tree kernel is then proposed to enhance the ability in both classification as well as motif extractions. Finally the problem of metabolite biomarker discovery is researched. Human diseases, in particular metabolic diseases, can be directly caused by the lack of essential metabolites. Identification of metabolite biomarkers has significant importance in the study of biochemical reaction and signaling networks. A promising computational approach is proposed to identify metabolic biomarkers through integrating biomedical data and disease-specific gene expression data.
published_or_final_version
Mathematics
Doctoral
Doctor of Philosophy
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29

Seelig, Johannes. "Optical methods for nanoscale investigations in biology /." Zürich : ETH, 2006. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16856.

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30

Cherry, Amanda M. "Methods to Characterize Orofacial Development." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5484.

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In this thesis, several techniques were combined to optimize, evaluate and characterize craniofacial development in Xenopus, with additional focus on understanding the alterations made during maturation in the craniofacial region and the cartilage. Three important techniques used were: confocal microscopy in conjunction with Acridine Orange (AO) labeling, Alcian Blue (AB) labeling, and geometric morphometric analysis. I found that facial width increased across all techniques used to evaluate it. Included within this focus was the study of the development of the ceratohyal (CH) cartilage, which supported the mouth and snout. This was also found to increase width wise, in unison with facial and orofacial growth. This data may suggest a link between the face, mouth and CH growth, in which the developing cartilage elongates and widens causing the increase seen in the width and distension of the mouth.
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31

Zahir, Freshta. "Teaching Methods of Foreign Languages : Teaching and learning of Spanish language in Kabul." Thesis, Karlstads universitet, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-33821.

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Second languages which are also called foreign languages are learnt beside native spoken languages and they are learnt in a systematic way (Hinkel, 2005). Spanish and English are widely spoken around the globe and they have improved a lot in Afghanistan, especially SPanish after Spanish military existence in teh country as part of ISAF after 2001 to Afghanistan and after the establishment of some private schools where Spanish is a part of curriculum. This school was built due to the interest of Spanish embassy. As the embassy got informed that there is the Spanish department, they immidiately got interested and wanted to establish a school in Afghanistan too where Spanish will be taught as one subject in this only one school in Kabul city. Since, there are mostly non-native speaking teachers with different teaching approaches in Kabul University; the researcher therefore, conducted this study to compares English and Spanish language teachers in the university and a private school. Moreover, students’ perceptions as regards learning a second language are explored as well as their experience and motives. Data for this research is collected with the help of ready-made questionnaire which was distributed to 20 English teachers, seven Spanish teachers at the university, five teachers of Kabul international school, 50 students of Spanish department and 50 students of Kabul international school. In addition to this, five classes were observed in university and five in private school, which helped the comparison of teachers’ perceptions and factual teaching performance in the class. It was found that there are both similarities and differences among teachers of English and Spanish teachers when teaching these foreign languages. In schools these languages are taught superficially and teachers lack professional knowledge while in the university vice versa. This research also found that nearly all the staff and students in Spanish department are grown up in urban areas and none of the students while only three out of 12 Spanish teachers have visited Spain. Half of the students in school were concerned about the impact of Spanish on Afghan society while students in the university and Spanish teachers had the counter idea. Moreover, it was found that in university students were given articles, assignments and topics from magazines and newspapers apart from daily lessons for the intention that students strengthen their Spanish language while this practice was hardly visible in school classrooms. In school Spanish language was taught on lecture based where students rarely found any chance for practice of the language and most of the time was allocated for the translation of Spanish.
TEMP Afganistan
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32

Alotaibi, Sultan. "Study of Islamic Teaching Methods in Saudi Arabia." Bowling Green State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1395603595.

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Crabill, Thomas V. "Teaching Methods of a Successful College Soccer Coach." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1399642117.

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34

Quilling, Michael Lance. "Applying rhythm teaching methods in an instrumental ensemble." Kansas State University, 2017. http://hdl.handle.net/2097/38162.

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Master of Music
School of Music, Theatre, and Dance
Frederick Burrack
Finding a systematic process for teaching rhythms in the instrumental setting has presented its own set of challenges. Numerous factors such as time constraints, engagement, motivation, and various degrees of proficiency amongst the students can all play a part in the overall success of the group. This video presentation includes a teaching demonstration utilizing techniques acquired from MU680-A (Advanced Rehearsal Techniques). Using rhythm readiness sheets modeled by Dr. Jay Gilbert and specific rehearsal techniques taught by Dr. Frank Tracz, this presentation exhibits a process for teaching rhythms that increases retention of rhythmic patterns in a way that enables all students to engage in the learning process simultaneously. The lesson plan is explained in detail and the routine was repeated daily and eventually implemented into the twelve-minute warmup portion of the rehearsal. After three weeks the students were recorded and asked to reflect on their progression. A noticeable change was observed after the lesson was completed and applied to the piece. In addition, the method also revealed several hidden learning outcomes, such as facilitating independence as musicians, utilizing listening skills to distinguish how various patterns fit within an established pulse, and increasing student motivation by creating positive rehearsals with attainable goals. The result was a performance showcasing the growth of the ensemble’s overall musicianship. The rhythm readiness sheet and concept that was utilized in the teaching demonstration is credited to Dr. Jay Gilbert. The rhythm readiness sheet is not copyrighted or published, however expressed written consent was granted by Dr. Gilbert and can be found in the Appendix.
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35

Randall, John H. "Stages of faculty concern about teaching online| Relationships between faculty teaching methods and technology use in teaching." Thesis, Pepperdine University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10139810.

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As more online courses and programs are created, it is imperative institutions understand the concern of their faculty toward teaching online, the types of technology they use, and the methods they use to instruct students in order to provide appropriate resources to support them. This quantitative study measures these concerns, using the Stages of Concern Questionnaire, of full-time faculty at a small Christian liberal arts university in Southern California relative to teaching online, technology use, and teaching methods. The majority of faculty reported being unconcerned about teaching online.

The correlations conducted between faculty’s concerns about teaching online and their teaching methods showed that while some relationships exist, the strength of the relationships are weak. The same was true for the relationships between faculty’s technology use and their concern about teaching online. Additionally, analysis of variance revealed faculty who practice more student-centered teaching methods are more likely to focus on coordinating and cooperating with others regarding teaching online.

It can be concluded that the majority of faculty at the institution are not concerned about teaching online and that overall, their technology use and specific teaching methods do not contribute to their concerns about teaching online. However, it was found that faculty who are more student-centered are more likely to cooperate and coordinate with others in regards to teaching online. These findings have implications for the institution where this research was conducted. The administration can be more confident knowing that many of their faculty are not highly concerned about teaching online, therefore, may be less likely to resist teaching these types of classes. The administration now has information that shows faculty who are more student-centered are more likely to cooperate with others in regards to teaching online. These faculty may be more inclined to promote online teaching and ultimately help fulfill the strategic plans of the University.

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36

Meer, Ralph Raymond. "Rapid methods for the detection of toxigenic Clostridium perfringens." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290593.

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Clostridium perfringens may be the most widely occurring bacterial pathogen and is responsible for a variety of diseases in both humans and animals. The virulence of this organism is associated with the ability to produce an estimated 17 potential exotoxins. The production of one or more of the five major toxins (α,β,ε, and ι) is the basis for placing isolates into five toxigenic types, A through E. Enterotoxin (CPE), is not used in typing but is considered a major virulence factor. A multiplex PCR genotyping assay was developed, utilizing primers derived from sequences of cpa, cpb, etx, iA, and cpe, yielding products of 324, 196, 655, 446, and 233 bp, respectively. Template for this assay was derived from individual colonies suspended in 200 μl of HPLC-grade water, boiled for 20 min or heated in a microwave oven for 10 min at 700 W. Included in the 50 μl reaction volume was 10 μl of template, 0.15 to 0.7 μM of each primer, 0.1 mM dNTPs, 2 mM MgCl₂, and 2 units of Taq DNA polymerase. The PCR products were examined by electrophoresis in a 1.5% agarose gel stained with EtBr. Correlation of genotype with toxin phenotype in strains examined by mouse inoculation was excellent, and it was possible to provide results rapidly, usually in < 4 h. An ELISA procedure was established for detection of β toxin produced by C. perfringens types B and C. The ELISA was used to differentiate Cpb⁺ from Cpb⁻ isolates grown in overnight broth cultures and to measure β toxin in commercial fermentations of type C organisms. In addition to the above assays, preliminary work was initiated on the development of a PCR procedure for quantitation of C. perfringens in clinical or environmental samples, and involved the construction of a 233 bp homologous, competitive mimic from a restriction digest of a 323 bp PCR product generated from cpa.
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Burr, Mark Daniel 1949. "An evaluation of DNA fingerprinting methods for subtyping Salmonella." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290630.

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The use of DNA typing and fingerprinting methods to identify and discriminate strains of bacteria, including Salmonella, has increased dramatically in recent years. Traditional typing methods, including serotyping and phage typing, have often not adequately discriminated strains, nor have they always identified virulent or antibiotic resistant strains. In a literature review, DNA-based methods, including plasmid analysis, restriction fragment length polymorphism (RFLP) analysis, and polymerase chain reaction (PCR) fingerprinting methods were evaluated. Plasmid analysis, including plasmid profiles and plasmid fingerprints have been shown to be useful primarily in short-term investigations of disease outbreak. However, plasmid profiles or possession of individual plasmids have generally not been good indicators of cell phenotypes overall. RFLP fingerprinting of Salmonella utilizing probes from ribosomal DNA, insertion sequence IS200, or random sequences has been reported. Ribotypes detected with ribosomal probes have generally been shared among different serotypes, whereas IS200 profiles have tended to be more serotype-specific. AP PCR and rep-PCR primers have been shown to discriminate Salmonella isolates, but fingerprints have been more difficult to reproduce and interpret than RFLP fingerprints. Several authors have reported bands of varying intensities, and some faint bands have not been reproducible. Improved methods of resolving and detecting PCR products are necessary. In a laboratory study, 85 environmental Salmonella isolates belonging to 22 serotypes were fingerprinted by 16S RFLP ribotyping, by rep-PCR, using ERIC (enterobacterial repetitive intergenic consensus) primers, and by AP PCR. Ribotypes were shared by isolates from different serotypes. ERIC PCR and one AP PCR primer produced fingerprints that discriminated among the different isolates, but did not identify serotypes. Another AP PCR primer produced simple patterns that neither discriminated isolates, nor identified serotypes. In a second related laboratory study, computer-assisted matching of AP PCR fingerprints of several known isolates was evaluated. Aliquots of the PCR reaction were run in the same and different gels, and the fingerprints bands were scored by two technicians on a presence-absence basis, and matched by creating dendrograms. Although replicate fingerprints of an isolate appeared reproducible, they were not always scored identically. Thus, the computer was not always able to correctly match fingerprints.
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Hansen, Cristina M. "Novel methods of disease surveillance in wildlife." Thesis, University of Alaska Fairbanks, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3702799.

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Both infectious and noninfectious disease agents in wildlife impact human health and accurate research, monitoring, and diagnostic methods are necessary. The objectives of the research reported here were to develop and implement novel methods for bacterial and toxicological disease agent surveillance in wildlife. This dissertation begins with a review of tularemia, an important zoonotic disease to the state of Alaska and the Northern hemisphere. In chapter two, I show the development and implementation of broad-based PCR and quantitative PCR (qPCR) surveillance methods for bacterial DNA in tissue samples; 1298 tissue samples were assayed, numerous potential bacterial pathogens were identified and qPCR detection limits were quantified for various tissue matrices. Chapter three describes an investigation into microbial infection as a source of embryo mortality in greater white-fronted geese (Anser albifrons) in Arctic Alaska. This chapter builds upon our previously developed PCR surveillance techniques by which I demonstrated that bacterial infection is responsible for some greater white-fronted goose embryo mortality in Arctic Alaska. Chapter four describes the development and validation of a cellulose filter paper method for quantifying total mercury in whole blood. I determined that filter paper technology is useful for monitoring total mercury in whole blood, with excellent recoveries (82 - 95% of expected values) and R2 values (0.95 - 0.97) when regressed against the concentration of total mercury in whole blood, the technique generally considered as the "gold standard" for mercury detection. These methods will aid in the accurate detection of disease agents in wildlife as demonstrated by our white-fronted goose work.

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Cong, Yang, and 丛阳. "Optimization models and computational methods for systems biology." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B47752841.

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Systems biology is a comprehensive quantitative analysis of the manner in which all the components of a biological system interact functionally along with time. Mathematical modeling and computational methods are indispensable in such kind of studies, especially for interpreting and predicting the complex interactions among all the components so as to obtain some desirable system properties. System dynamics, system robustness and control method are three crucial properties in systems biology. In this thesis, the above properties are studied in four different biological systems. The outbreak and spread of infectious diseases have been questioned and studied for years. The spread mechanism and prediction about the disease could enable scientists to evaluate isolation plans to have significant effects on a particular epidemic. A differential equation model is proposed to study the dynamics of HIV spread in a network of prisons. In prisons, screening and quarantining are both efficient control manners. An optimization model is proposed to study optimal strategies for the control of HIV spread in a prison system. A primordium (plural: primordia) is an organ or tissue in its earliest recognizable stage of development. Primordial development in plants is critical to the proper positioning and development of plant organs. An optimization model and two control mechanisms are proposed to study the dynamics and robustness of primordial systems. Probabilistic Boolean Networks (PBNs) are mathematical models for studying the switching behavior in genetic regulatory networks. An algorithm is proposed to identify singleton and small attractors in PBNs which correspond to cell types and cell states. The captured problem is NP-hard in general. Our algorithm is theoretically and computationally demonstrated to be much more efficient than the naive algorithm that examines all the possible states. The goal of studying the long-term behavior of a genetic regulatory network is to study the control strategies such that the system can obtain desired properties. A control method is proposed to study multiple external interventions meanwhile minimizing the control cost. Robustness is a paramount property for living organisms. The impact degree is a measure of robustness of a metabolic system against the deletion of single or multiple reaction(s). An algorithm is proposed to study the impact degree in Escherichia coli metabolic system. Moreover, approximation method based on Branching process is proposed for estimating the impact degree of metabolic networks. The effectiveness of our method is assured by testing with real-world Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae and Homo Sapiens metabolic systems.
published_or_final_version
Mathematics
Doctoral
Doctor of Philosophy
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40

Gamalielsson, Jonas. "Developing semantic pathway comparison methods for systems biology." Thesis, Heriot-Watt University, 2009. http://hdl.handle.net/10399/2294.

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Systems biology is an emerging multi-disciplinary field in which the behaviour of complex biological systems is studied by considering the interaction of many cellular and molecular constituents rather than using a “traditional” reductionist approach where constituents are studied individually. Systems are often studied over time with the ultimate goal of developing models which can be used to understand and predict complex biological processes, such as human diseases. To support systems biology, a large number of biological pathways are being derived for many different organisms, and these are stored in various databases. This pathway collection presents an opportunity to compare and contrast pathways, and to utilise the knowledge they represent. This thesis presents some of the first algorithms that are designed to explore this opportunity. It is argued that the methods will be useful to biologists in order to assess the biological plausibility of derived pathways, compare different biological pathways for semantic similarities, and to derive putative pathways that are semantically similar to documented biological pathways. The methods will therefore extend the systems biology toolbox that biologists can use to make new biological discoveries.
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41

Ding, Jiarui. "Computational methods for systems biology data of cancer." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/58164.

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High-throughput genome sequencing and other techniques provide a cost-effective way to study cancer biology and seek precision treatment options. In this dissertation I address three challenges in cancer systems biology research: 1) predicting somatic mutations, 2) interpreting mutation functions, and 3) stratifying patients into biologically meaningful groups. Somatic single nucleotide variants are frequent therapeutically actionable mutations in cancer, e.g., the ‘hotspot’ mutations in known cancer driver genes such as EGFR, KRAS, and BRAF. However, only a small proportion of cancer patients harbour these known driver mutations. Therefore, there is a great need to systematically profile a cancer genome to identify all the somatic single nucleotide variants. I develop methods to discover these somatic mutations from cancer genomic sequencing data, taking into account the noise in high-throughput sequencing data and valuable validated genuine somatic mutations and non-somatic mutations. Of the somatic alterations acquired for each cancer patient, only a few mutations ‘drive’ the initialization and progression of cancer. To better understand the evolution of cancer, as well as to apply precision treatments, we need to assess the functions of these mutations to pinpoint the driver mutations. I address this challenge by predicting the mutations correlated with gene expression dysregulation. The method is based on hierarchical Bayes modelling of the influence of mutations on gene expression, and can predict the mutations that impact gene expression in individual patients. Although probably no two cancer genomes share exactly the same set of somatic mutations because of the stochastic nature of acquired mutations across the three billion base pairs, some cancer patients share common driver mutations or disrupted pathways. These patients may have similar prognoses and potentially benefit from the same kind of treatment options. I develop an efficient clustering algorithm to cluster high-throughput and high-dimensional bio- logical datasets, with the potential to put cancer patients into biologically meaningful groups for treatment selection.
Science, Faculty of
Computer Science, Department of
Graduate
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42

Francis, Black Alison. "Understanding the teaching of biology at A level." Thesis, University of Oxford, 2005. http://ora.ox.ac.uk/objects/uuid:7a7828b8-bbdb-4246-aa5d-7836e314460d.

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This research focuses on uncovering, from the perspectives of practitioners themselves, the practical knowledge and understanding that shapes three teachers' successful teaching of biology at A level. Adopting a case study approach, it investigates the ways in which these biology teachers characterise their successful teaching of the subject at A level. It also explores the subject matter knowledge and understanding that shapes and accounts for these characterisations without making assumptions about the nature of this knowledge. Data are collected through the non-participant observation of a connected series of the teachers' A level biology lessons as well as informant-style interviewing following the observed lessons. The findings suggest that the main aim of the teachers' successful teaching of biology at A level is to ensure their students achieve examination success. In light of this, their teaching can be characterised in terms of three central features. First, they believe that to achieve this aim their students only need to know the substantive dimension of biological knowledge - they do not consider knowing the syntactic dimension to be a prerequisite to examination success. Second, they believe that their students need to conceptualise this substantive biological knowledge in several patterned ways. Third, they believe that the best way to encourage their students to develop and retain these specific conceptualisations is by adopting carefully controlled and highly structured teacher-centred pedagogical strategies. The teachers' characterisations appear to be shaped and accounted for by specific conceptions of biology which provide an overall structure to substantive biological knowledge - a structure that is determined by various guiding principles. This research provides a first attempt to map out the practical knowledge and understanding that shapes the successful teaching of biology at A level from the perspectives of teachers themselves. The ways in which these teachers characterise their teaching differ significantly from the ways in which such teaching is described in most of the extant literature in science education on teaching and learning. This study suggests that the teachers, far from lacking in knowledge, skills and understanding, are highly skilled practitioners who respond to the local and national contexts in which they work and, taking account of these, shape their subject matter teaching accordingly such that their main aim - student examination success - is achievable. This study highlights the discrepancy between academic writing in science education on practice and practice itself. The thesis ends with a consideration of the implications of the study for the research agenda in science education, the school science curriculum and the curriculum for teacher education in both preparing and supporting the professional development of science teachers.
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43

Fuxelius, Hans-Henrik. "Methods and Applications in Comparative Bacterial Genomics." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8398.

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Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution frequencies. The software was applied to the genomes of six Chlamydia trachomatis strains to identify the most rapidly evolving genes. Five genes were chosen for genotyping, and close to a 3-fold higher discrimination capacity was achieved than that of serotypes. With GenComp as the backbone, a massive comparative analysis were performed on the variable gene set in the Rickettsiaceae, which includes Rickettsia prowazekii and Orientia tsutsugamushi, the agents of epidemic and scrub typhus, respectively. O. tsutsugamushi has the most exceptional bacterial genome identified to date; the 2.2 Mb genome is 200-fold more repeated than the 1.1 Mb R. prowazekii genome due to an extensive proliferation of conjugative type IV secretion systems and associated genes. GenComp identified 688 core genes that are conserved across 7 closely related Rickettsia genomes along with a set of 469 variably present genes with homologs in other species. The analysis indicates that up to 70% of the extensively degraded and variably present genes represent mobile genetic elements and genes putatively acquired by horizontal gene transfer. This explains the paradox of the high pseudogene load in the small Rickettsia genomes. This study demonstrates that GenComp provides an efficient system for pseudogene identification and may help distinguish genes from spurious ORFs in the many pan-genome sequencing projects going on worldwide.
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Ollivier, Julien. "Scalable methods for modelling complex biochemical networks." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=104586.

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In cells, complex networks of interacting biomolecules process both environmental and endogenous signals to control gene expression and other cellular processes. This poses a challenge to researchers who attempt to develop mathematical and computational models of biochemical networks that reflect this complexity. In this thesis, I propose methods that help manage complexity by exploiting the finding that, as for other biological systems, cellular networks are characterized by a modularity that appears at all levels of organization.The first part of this work focuses on the modular properties of proteins and how their function can be characterized through their structure and allosteric properties. I develop a modular rule-based framework and formal modelling language that describes the computations performed by allosteric proteins and that is rooted in biophysical principles. Rule-based modelling conventionally addresses the problem of combinatorial complexity, whereby protein interactions can generate a combinatorial explosion of protein complex states. However, I explore how these same interactions can potentially require a combinatorial number of parameters to describe them. I demonstrate that my rule-based framework effectively addresses this problem of regulatory complexity, and describes allosteric proteins and networks in a unified, consistent, and modular fashion. I use the framework in three applications. First, I show that allostery can make macromolecular assembly more efficacious when a protein that joins two separable parts of a complex is present in excessively high concentrations. Second, I demonstrate that I can straightforwardly analyze the complex cooperative interactions that arise when competitive ligands bind to a multimeric protein. Third, I analyze a new model of G protein-coupled receptor signalling and demonstrate that it explains the functional selectivity of these receptors while being parsimonious in the number of parameters used. Overall, I find that my rule-based modelling framework, implemented as the Allosteric Network Compiler software tool, can ease of modelling and analysis of complex allosteric interactions.If cellular networks are modular, this implies that small sub-systems can be studied in isolation, provided that external inputs and perturbations to the system can be modelled appropriately. However, cellular networks are subject to both intrinsic noise, which is endogenous to the system, but also extrinsic noise, arising from noisy inputs. Furthermore, many inputs may be dynamic, whether due to experimental protocols or perhaps reflecting the cyclic process of cell division. This motivates my development, in the second part of this work, of efficient stochastic simulation algorithms for biochemical networks that can accommodate time-varying biochemical parameters. Starting from Gillespie's well-known First Reaction Method and Gibson and Bruck's Next Reaction Method, I develop two new algorithms that allow time-varying inputs of arbitrary functional form while scaling well to systems comprising many biochemical reactions. I analyze their scaling properties and find that a modified First Reaction Method may scale better than a modified Next Reaction Method in some applications.The third and last part of this thesis introduces a new software tool, Facile, that eases the creation, update and simulation of biochemical network models. Models created through a simple and intuitive textual language are automatically converted into a form usable by downstream tools, for example ordinary differential equations for simulation by Matlab. Also, Facile conveniently accommodates mathematical and time-varying expressions in rate laws.
Au niveau cellulaire, des réseaux complexes d'interaction biomoléculaire traitent les signaux tant environnementaux qu'endogènes dans le but de contrôler l'expression génétique ainsi que d'autres processus cellulaires. Ceci est un défi pour les chercheurs qui veulent concevoir des modèles mathématiques et calculatoires des réseaux biochimiques. Dans cette thèse, je propose des méthodes qui facilitent la gestion de cette complexité en exploitant la constatation que, tout comme d'autres systèmes biologiques, les réseaux cellulaires se caractérisent par une modularité qui transparaît à tous les niveaux d'organisation.Dans la première partie, je mets l'accent sur les propriétés modulaires des protéines et sur la façon de caractériser leur fonction, compte tenu de leur structure et de leurs propriétés allostériques. J'ai mis au point un cadre modulaire à base de règles ainsi qu'un langage formel de modélisation qui permet de décrire les calculs effectués par les protéines allostériques et qui découle de principes biophysiques. La modélisation à base de règles s'adresse conventionnellement au problème de la complexité combinatoire, où les interactions entre les protéines peuvent générer une explosion combinatoire d'états des complexes protéiques. J'examine, cependant, comment il peut s'avérer nécessaire d'utiliser un nombre combinatoire de paramètres pour décrire ces mêmes interactions. Je démontre que notre cadre à base de règles peut régler efficacement ce problème de la complexité régulatoire, et permet de décrire les protéines et les réseaux allostériques de façon unifiée, cohérente et modulaire. J'utilise le cadre développé dans trois applications. Tout d'abord, je montre que l'allostérie peut rendre l'assemblage macromoléculaire plus efficace lorsqu'une protéine qui unit deux parties distinctes d'un complexe protéique est présente en concentration excessive. Deuxièmement, je démontre qu'il est relativement simple d'analyser les interactions coopératives complexes qui surviennent lorsque des ligands compétitifs se lient à une protéine multimérique. En troisième lieu, j'analyse un nouveau modèle de la signalisation des récepteurs couplés aux protéines G qui explique leur sélectivité fonctionnelle tout en limitant le nombre des paramètres utilisés. Globalement, je montre que ce cadre basé sur des règles, qui est implémenté dans le logiciel ‘Allosteric Network Compiler', peut faciliter la modélisation et l'analyse d'interactions allostériques complexes.Si les réseaux cellulaires sont modulaires, il en résulte que des sous-systèmes peuvent être étudiés séparément, à la condition que les entrées et les perturbations externes du système puissent être modélisées adéquatement. Cependant, ces réseaux sont soumis à l'influence du bruit intrinsèque, qui est endogène au système, mais également au bruit extrinsèque, venant des entrées bruyantes. De plus, de nombreuses entrées peuvent être dynamiques. Cela motive, dans la deuxième partie de ce travail, le développement d'algorithmes efficients de simulation stochastique pour les réseaux biochimiques qui peuvent tenir compte de paramètres biochimiques dynamiques. En me fondant sur la méthode maintenant célèbre de Gillespie, d'appellation ‘First Reaction Method', et sur celle de Gibson et Bruck, la ‘Next Reaction Method', j'ai développé deux nouveaux algorithmes qui permettent des entrées dynamiques de forme fonctionnelle arbitraire tout en s'échelonnant bien sur les systèmes qui comportent de nombreuses réactions biochimiques. J'analyse leurs propriétés d'échelonnement et je constate que, pour certaines applications, la ‘First Reaction Method' modifiée s'échelonne mieux que la ‘Next Reaction Method' modifiée.La troisième et dernière partie cette thèse est la présentation d'un nouvel outil informatique, Facile, qui simplifie la création, la mise à jour et la simulation de modèles de réseaux biochimiques.
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45

Hatcher, Anthony. "Comparison of Micrscan Identification and Susceptibility Testing Methods for Streptococcus Dysgalactiae to Conventional Biochemical Reactions and Kirby-Bauer Susceptibility Testing Methods." TopSCHOLAR®, 1994. http://digitalcommons.wku.edu/theses/970.

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A total of 100 isolates of Streptococcus dysgalact iae from bovine mastitis infections was used to evaluate and compare the biochemical reactions of the gram positive Combo Type 6 panel on the MicroScan autoSCANR system to a conventional procedure for identification of streptococci. Of the 100 isolates, 83.3% was identified as "Very Rare Biotype" by the MicroScan and classified as S. dysgalactiae by conventional methods. Of the remaining 16.7%, MicroScan identified 3.3% as Streptococcus morbillorum, 3.3% as Aerococcus viridians, 3.3% as Streptococcus constellatum/milleri, 1.7% as Streptococcus agalactiae, 1.7% as Streptococcus mitis, 1.7% as Streptococcus sanguis, and 1.7% as Streptococcus intermidis/rni 1 leri. The identification of bacteria other than Very Rare Biotype can be attributed to code profiles listed in the MicroScan which demonstrate biochemical reactions similar to S. dysgalact iae. The antimicrobial susceptibility of 94 S. dysgalactiae isolates to 16 antibiotics was determined by the MicroScan system. Of the antibiotics tested, each demonstrated greater than 85% susceptibility against the 94 strains of S. dysgalactiae. Of the 16 antibiotics used in the MicroScan, nine were compared to the standard Kirby-Bauer method and/or results obtained from the literature. S. dysgalactiae was reported as sensitive to penicillin on 89.4% of the strains tested by the MicroScan, 98.4% by the Kirby-Bauer method, and 98.0% by the literature references. In testing 94 strains for susceptibility to gentamicin by two methods, MicroScan resulted in 98.0% comparability to literature values but 83.6% to the Kirby-Bauer technique. The other antibiotics tested on the MicroScan and compared to the Kirby-Bauer and/or literature values illustrated a comparison of greater than 90%. In this study, 36 isolates of S. dysgalactiae demonstrating resistance to tetracycline, single, and multiple antibiotics were analyzed for plasmids. The evidence of plasmids was not detected as analyzed by agarose gel electrophoresis. All 100 isolates of S. dysgalactiae, with the exception of one, were tested serologically for the presence of C antigen. Each isolate tested was classified as a Group C streptococci. Each of the 100 isolates was stored in 5% sheep red blood cells at -20°C for one year. Each isolate was revived, with the exception of one, and demonstrated characteristic streptococcal colony morphology. The storage recovery rate was 99% and is an acceptable storage method for streptococci.
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46

Dimont, Emmanuel. "Methods for the Analysis of Differential Composition of Gene Expression." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226062.

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Modern next-generation sequencing and microarray-based assays have empowered the computational biologist to measure various aspects of biological activity. This has led to the growth of genomics, transcriptomics and proteomics as fields of study of the complete set of DNA, RNA and proteins in living cells respectively. One major challenge in the analysis of this data, however, has been the widespread lack of sufficiently large sample sizes due to the high cost of new emerging technologies, making statistical inference difficult. In addition, due to the hierarchical nature of the various types of data, it is important to correctly integrate them to make meaningful biological discoveries and better informed decisions for the successful treatment of disease. In this dissertation I propose: (1) a novel method for more powerful statistical testing of differential digital gene expression between two conditions, (2) a framework for the integration of multi-level biologic data, demonstrated with the compositional analysis of gene expression and its link to promoter structure, and (3) an extension to a more complex generalized linear modeling framework, demonstrated with the compositional analysis of gene expression and its link to pathway structure adjusted for confounding covariates.
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47

Huakau, John Tupou. "New methods for analysis of epidemiological data using capture-recapture methods." Thesis, University of Auckland, 2002. http://wwwlib.umi.com/dissertations/fullcit/3085723.

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Capture-recapture methods take their origins from animal abundance estimation, where they were used to estimate the unknown size of the animal population under study. In the late 1940s and again in the late 1960s and early 1970s these same capture-recapture methods were modified and applied to epidemiological list data. Since then through their continued use, in particular in the 1990s, these methods have become popular for the estimation of the completeness of disease registries and for the estimation of the unknown total size of human disease populations. In this thesis we investigate new methods for the analysis of epidemiological list data using capture-recapture methods. In particular we compare two standard methods used to estimate the unknown total population size, and examine new methods which incorporate list mismatch errors and model-selection uncertainty into the process for the estimation of the unknown total population size and its associated confidence interval. We study the use of modified tag loss methods from animal abundance estimation to allow for list mismatch errors in the epidemio-logical list data. We also explore the use of a weighted average method, the use of Bootstrap methods, and the use of a Bayesian model averaging method for incorporating model-selection uncertainty into the estimate of the unknown total population size and its associated confidence interval. In addition we use two previously unanalysed Diabetes studies to illustrate the methods examined and a well-known Spina Bifida Study for simulation purposes. This thesis finds that ignoring list mismatch errors will lead to biased estimates of the unknown total population size and that the list mismatch methods considered here result in a useful adjustment. The adjustment also approximately agrees with the results obtained using a complex matching algorithm. As for the incorporation of model-selection uncertainty, we find that confidence intervals which incorporate model-selection uncertainty are wider and more appropriate than confidence intervals that do not. Hence we recommend the use of tag loss methods to adjust for list mismatch errors and the use of methods that incorporate model-selection uncertainty into both point and interval estimates of the unknown total population size.
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48

Fillion, Bergeron Marianne. "Plasmid isolation and purification by electrofiltration and comparison of different direct colony sequencing methods and PCR-based sequencing methods." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6050.

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We have designed an electrophoresis system that can purify plasmid DNA from a culture without centrifugation. This system is based on electrofiltration where bacterial cell lysates are loaded in one chamber and the purified plasmid DNA is recovered in an adjacent chamber. These two chambers are separated by a membrane made of regenerated cellulose, which allows plasmid DNA to migrate to the recovery chamber while retaining most contaminants in the loading chamber. Unfortunately, even with the optimization of the parameters involved in the electrofiltration, the only DNA that can pass through the middle membrane still has some contaminants, which prevent sequencing of the plasmid. Our results have shown that a pure plasmid cannot cross a membrane with pores small enough to prevent the migration of most of the contaminants. Only a plasmid complexed with some contaminants can cross a small pore membrane. In parallel, we have compared six direct sequencing methods that do not require any plasmid purification prior to the sequencing reaction. We compared the reliability, quality of sequences, time required, and cost of these six methods. We found that the best method was that of Zhang et al. (1999). This method is fast, reliable, produces good quality sequences and is inexpensive. The performance of this method is due to the amount of ABI's ready reaction mix used, the pre-sequencing heating step to lyse the cell, the large volume of the PCR sequencing reaction and the addition of BSA.
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49

Chounlamany, Kongsy, and Bounchanh Khounphilaphanh. "New methods of teaching? : refroming education in Lao PDR." Doctoral thesis, Umeå universitet, Pedagogiska institutionen, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-40938.

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This thesis is about the recent education reform in Laos as a global and a local process. When the economy was deteriorating in Lao People’s Democratic Republic (PDR), the so called New Economic Mechanism (NEM) was introduced and the country opened up for global donors and markets. This also had an effect on the education system. To get hold of financial support there were demands on Lao PDR to replace the previous strong centralised governing of education with more decentralised strategies. There were further demands to replace teacher-led lessons and rote learning with more student-centred classroom practices. The research questions asked in this thesis are: How are education reform and the new methods of teaching governed in policy and through the formal education organisations from ministry level to school level? How do teachers and students in teacher education respond to the education reform and the new methods of teaching? What attention is put to gender and ethnic minorities in these matters? The thesis is inspired by Gita Steiner-Khamsi’s global perspectives on education reform; consensus, conflict and culturalist perspectives. It is also based on a local understanding taking its starting point in a pragmatic approach and a mosaic epistemology and a qualitative inductive methodological approach. The empirical findings are based on 36 documents that govern the education reform, 119 individual interviews with teachers and students in social science and science at teacher education, some observations and a contextual analysis of education, gender and ethnicity in Laos. The findings show that there is a consensus with the international community about bringing education to all people in Lao PDR. However, the political understanding is in conflict between neoliberal and socialist traditions. Democratic centralism is the foundation which built the governing system in Laos; information flows up through the system and decisions down. Even though the system leaves 20 percent autonomy to teachers to develop local curricula in line with the new methods of teaching, there are yet no major signs that such curricula exist. Teacher educators and teacher students understand new methods of teaching mainly as group learning and individual learning with only small variations between the two subjects. According to current policy the goal is to improve access to education for females and ethnic minority students. The ethnic minority students regarded individual studies as difficult because of language problems. They preferred group learning because they could be supported in language issues. Females also felt supported in group learning. However, because of old gender traditions especially females from the dominating Lao Loum group also found individual learning supportive. In individual learning females got opportunities to show individual capacities without being constrained by societal norms. The thesis ends up in a pragmatic tradition where possibilities and constraints with the education reform in Lao PDR are commented on.
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50

Jacober, Rochelle Ann. "Effectiveness of three methods of teaching breast self-examination." Thesis, The University of Arizona, 1987. http://hdl.handle.net/10150/276598.

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A quasi-experimental design was used in this study to determine if guided practice would result in higher breast cancer knowledge scores, higher breast self-examination (BSE) knowledge scores and higher intent to practice scores then modeling alone or teaching without modeling or guided practice. Fifty-eight women participated in the study. There were 19 women in the guided practice group, 22 in the modeling group and 17 in the control group. A pre-test, post-test format was used. ANCOVA was used to statistically control for the variance in pre-test scores. Descriptive statistics were used to analyze demographic data. The results showed that all methods of teaching resulted in higher breast cancer and BSE knowledge scores and in higher intent to practice scores. There were no statistically significant differences between the groups. Nursing research need to continue in this area to find the most effective method of teaching women breast self-examination.
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