The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C. These efforts have culminated in two web-based resources from our lab—Factorbook and SCREEN—for the exploration of epigenomic data for both human and mouse. Factorbook is a peak-centric resource presenting data such as motif enrichment and histone modification profiles for transcription factor binding sites computed from ENCODE ChIP-seq data. SCREEN provides an encyclopedia of ~2 million regulatory elements, including promoters and enhancers, identified using ENCODE ChIP-seq and DNase data, with an extensive UI for searching and visualization. While we have successfully utilized the thousands of available ENCODE ChIP-seq experiments to build the Encyclopedia and visualizers, we have also struggled with the practical and theoretical inability to assay every possible experiment on every possible biosample under every conceivable biological scenario. We have used machine learning techniques to predict TF binding sites and enhancers location, and demonstrate machine learning is critical to help decipher functional regions of the genome.

The objectives of this study were to investigate existing theory regarding the conceptual learning of young learners and to determine what core concepts Grade 5 learners need to learn. An empirical investigation as to whether these learners were familiar with the mother tongue words for the identified core concepts in syllabuses and textbooks, and to investigate whether they could recede these concepts into English (the medium of instruction in their classrooms) was also undertaken. The role of conceptual awareness in learning was discussed based on Piaget's, Vygotsky's and Clark's theory. They explain how concepts and knowledge are acquired and also how language affects this process. Learners are required to know the concepts of what they learn and should recede the information or concepts into the language used for a specific learning task. In the case of this study it was English. The study revealed that many learners who were investigated in this study did not possess the knowledge to encode many of the core or broader concepts in Tshivenda, their mother tongue. Learners also seemed to learn some concepts and the English encoding for them simultaneously. The findings showed, however, that most learners in Grade 5 could not recede many of the concepts that they possessed in L1 into English the Mol. It was clear that many learners in this study were not ready to switch from mother tongue instruction to English Mol in Grade 5. Their lack of conceptual awareness coupled with the lack of adequate English proficiency to learn the subjects in English may have been influenced by a number of possible reasons. Some reasons that were suggested were the following: a lack of prior knowledge of concepts that occur in Grade 5 syllabuses and textbooks; poorly trained teachers who are unable to assist learners to create links between existing knowledge and new knowledge; poor socio-economic circumstances and illiteracy and teachers who may lack English proficiency and cannot teach all subjects confidently in English. Some implications for the findings were suggested such as the following: if teachers are aware of the demands made on the conceptual framework of learners and the possible limitations that• they have regarding their conceptual readiness to learn, intervention is possible. Much can be done regarding the strategies that teachers may employ to enrich, expand, reconstruct, revisit or adapt concepts for learning. Such strategies include visual scaffolding, an enriched conceptual and language programme and a planned and structured approach to teaching language across the curriculum. / Thesis (M.A. (Applied Language and Literary Studies))--Potchefstroom University for Christian Higher Education, 2001

The objectives of this study were to investigate existing theory regarding the conceptual learning of young learners and to determine what core concepts Grade 5 learners need to learn. An empirical investigation as to whether these learners were familiar with the mother tongue words for the identified core concepts in syllabuses and textbooks, and to investigate whether they could recede these concepts into English (the medium of instruction in their classrooms) was also undertaken. The role of conceptual awareness in learning was discussed based on Piaget's, Vygotsky's and Clark's theory. They explain how concepts and knowledge are acquired and also how language affects this process. Learners are required to know the concepts of what they learn and should recede the information or concepts into the language used for a specific learning task. In the case of this study it was English. The study revealed that many learners who were investigated in this study did not possess the knowledge to encode many of the core or broader concepts in Tshivenda, their mother tongue. Learners also seemed to learn some concepts and the English encoding for them simultaneously. The findings showed, however, that most learners in Grade 5 could not recede many of the concepts that they possessed in L1 into English the Mol. It was clear that many learners in this study were not ready to switch from mother tongue instruction to English Mol in Grade 5. Their lack of conceptual awareness coupled with the lack of adequate English proficiency to learn the subjects in English may have been influenced by a number of possible reasons. Some reasons that were suggested were the following: a lack of prior knowledge of concepts that occur in Grade 5 syllabuses and textbooks; poorly trained teachers who are unable to assist learners to create links between existing knowledge and new knowledge; poor socio-economic circumstances and illiteracy and teachers who may lack English proficiency and cannot teach all subjects confidently in English. Some implications for the findings were suggested such as the following: if teachers are aware of the demands made on the conceptual framework of learners and the possible limitations that• they have regarding their conceptual readiness to learn, intervention is possible. Much can be done regarding the strategies that teachers may employ to enrich, expand, reconstruct, revisit or adapt concepts for learning. Such strategies include visual scaffolding, an enriched conceptual and language programme and a planned and structured approach to teaching language across the curriculum. / Thesis (M.A. (Applied Language and Literary Studies))--Potchefstroom University for Christian Higher Education, 2001

Over the last decade there has been a great effort to annotate noncoding regions of the genome, particularly those that regulate gene expression. These regulatory elements contain binding sites for transcription factors (TF), which interact with one another and transcriptional machinery to initiate, enhance, or repress gene expression. The Encyclopedia of DNA Elements (ENCODE) consortium has generated thousands of epigenomic datasets, such as DNase-seq and ChIP-seq experiments, with the goal of defining such regions. By integrating these assays, we developed the Registry of candidate Regulatory Elements (cREs), a collection of putative regulatory regions across human and mouse. In total, we identified over 1.3M human and 400k mouse cREs each annotated with cell-type specific signatures (e.g. promoter-like, enhancer-like) in over 400 human and 100 mouse biosamples. We then demonstrated the biological utility of these regions by analyzing cell type enrichments for genetic variants reported by genome wide association studies (GWAS). To search and visualize these cREs, we developed the online database SCREEN (search candidate regulatory elements by ENCODE). After defining cREs, we next sought to determine their potential gene targets. To compare target gene prediction methods, we developed a comprehensive benchmark of enhancer-gene links by curating ChIA-PET, Hi-C and eQTL datasets. We then used this benchmark to evaluate unsupervised linking approaches such as the correlation of epigenomic signal. We determined that these methods have low overall performance and do not outperform simply selecting the closest gene. We then developed a supervised Random Forest model which had notably better performance than unsupervised methods. We demonstrated that this model can be applied across cell types and can be used to predict target genes for GWAS associated variants. Finally, we used the registry of cREs to annotate variants associated with psychiatric disorders. We found that these "psych SNPs" are enriched in cREs active in brain tissue and likely target genes involved in neural development pathways. We also demonstrated that psych SNPs overlap binding sites for TFs involved in neural and immune pathways. Finally, by identifying psych SNPs with allele imbalance in chromatin accessibility, we highlighted specific cases of psych SNPs altering TF binding motifs resulting in the disruption of TF binding. Overall, we demonstrated our collection of putative regulatory regions, the Registry of cREs, can be used to understand the potential biological function of noncoding variation and develop hypotheses for future testing.

Submitted by JÚLIO HEBER SILVA (julioheber@yahoo.com.br) on 2017-03-24T17:48:37Z No. of bitstreams: 2 Dissertação - Alan Henrique Ferreira Silva - 2016.pdf: 10881029 bytes, checksum: 1c411277f8b103cc8a55709053ed7f9b (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-03-27T15:13:01Z (GMT) No. of bitstreams: 2 Dissertação - Alan Henrique Ferreira Silva - 2016.pdf: 10881029 bytes, checksum: 1c411277f8b103cc8a55709053ed7f9b (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-03-27T15:13:01Z (GMT). No. of bitstreams: 2 Dissertação - Alan Henrique Ferreira Silva - 2016.pdf: 10881029 bytes, checksum: 1c411277f8b103cc8a55709053ed7f9b (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-03-31 / This work proposes method to encode and decode imas using conformal mapping. Conformal mapping modifies domains without modifyung physical characteristics between them. Real images are processed between these domains using encoding keys, also called transforming functions. The advantage of this methodology is the ability to carry the message as an encoded image in printed media for posterior-decoding. / Este trabalho propõe método que utiliza transformações conformes para codificar e decodificar imagens. As transformações conformes modificam os domínios em estudos sem modificar as características físicas entre eles. As imagens reais são transformadas entre estes domínios utilizando chaves, que são funções transformadoras. o diferencial desta metodologia é a capacidade de transportar a mensagem contida na imagem em meio impresso codificado e depois, decodificá-la.

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無線寬頻網路（Mobile Internet Broadband Network）的出現對於無線通訊產業、傳播媒體產業與影音內容產業產生了相當程度的影響，而數位化的科技發展更帶來通訊、傳播及平面媒體產業融合的可能性，無線寬頻影音串流（Mobile Internet Video Streaming）是一架構在此無線通訊媒體匯流後的新產物，透過觀察和分析它的演進發展，可以說明和解釋網路新媒體匯流造成傳統影音產業價值鏈的改變。 吾人將以無線通訊之影音播放技術之演進與發展，以及相對最先發生變化之影音產業經營環境，產生之影響，做產業價值鏈分析研究，進而了解產業經營環境之改變，新的價值創造流程及技術平台的關聯性。並藉由日本NTT DOCOMO之經驗，及對其供應商之觀察，了解台灣產業發展之可能趨勢，及策略建議藍圖。 本研究採P.W. Bane、S.P. Bradley & D.J. Collis (1998)三人提出之寬頻產業五層模式作為分析工具。五層模式分為內容(content)、包裝(package)、傳輸網路(transmission)、操作(manipulation) 及終端設備(terminal)五層架構。主要目的為以整體網路頻寬及技術演進的觀點進行分析五層間價值消長之關係，及整體網路之價值之改變。 我們發現在新的技術導入既有影音市場，由於網路之雙向特性，會產生網路效應及網路外部性，這些地方將產生新的價值所在，而擁有網路外部性的影音操作平台可獲得較高的價值。完整而消費者導向的影音操作平台，將首先累積產業之價值所在，影音操作平台的擁有者將成為產業的領導者，最終將成為標準的制定者。 影音內容的價值獲得來自網路外部性是經由更多人與內容來源(內容提供者)互動，造成下一次消費或其他使用者的外部性以及生產外部性，這樣的外部性是由虛擬連結產生．價值聚集於內容包裝層。 無線寬頻影音操作平台是服務成功的關鍵，有效的整合價值鏈及應用是必須在產業發展前完成，而完整的影音操作平台包含：內容製作壓縮平台、串流平台、訊息平台、及手機之用戶播放平台。 我們發現，新的技術導入市場，需要事先將價值鏈重新定義，整合出可行之新的商業模式，再依據新的價值鏈，新的服務流程去整合新的操作平台，投入服務後，由於是消費者導向的服務設計，可以降低消費者對新科技及新服務的學習門檻及進入障礙，而獲得市場認同。 / “Unlimited boundary & Ubiquitous content” Because of the improving the bandwidth & compression technology of mobile Internet, there are a very extremely industrial convergency in communication, broadcasting, & video audio content industry. There are several new technology including streaming, MPEG, multi media message, 3G which push the whole world going to a new Ubiquitous environment & totally change the old value chain of video audio industry, but we still have no ideal where it should go & what will happen next. We will try to research the technical evolution of video broadcasting which really influence our movie, TV industry. It will change the customer behavior of watching TV, or going to the movie. We especially want to find out where is the new value in the mobile Internet multi media industry. We will use the 5 liars analysis model of broadband industry (P.W. Bane、S.P. Bradley & D.J. Collis (1998))as our basic methodology to find out how the three vertical industries became a new 5 horizontal industries, which are content, package, transmission, manipulation, & terminal. We also want to know how they work internally & externally. We find that the video audio manipulation platform will become the key solution for this value chain, because of its network externality & network effect. The content providers also very important to provide the quality of contents to service the end customers. How to consolidate a new valuable services process & user friendly interface is the big issue here for whom will invest a large of money to creat the new mobile internet portal & new audio vedio manipulation platform. They must think not only the user interface of handset, but also the mechanism of profit sharing between these different providers who never work together in the history.