Search results for: open chromatin regions

Authors: Fan Gao, Lior Pachter

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The primary tool currently used to pre-process 10X Chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices, and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Keywords: single-cell, ATAC-seq, bioinformatics, open chromatin landscape, chromatin interactome

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Sharon Yunger, Liat Altman, Yuval Garini, Yaron Shav-Tal

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Understanding the dynamics of transcription in living cells has improved since the development of quantitative fluorescence-based imaging techniques. We established a method for following transcription from a single copy gene in living cells. A gene tagged with MS2 repeats, used for mRNA tagging, in its 3' UTR was integrated into a single genomic locus. The actively transcribing gene was detected and analyzed by fluorescence in situ hybridization (FISH) and live-cell imaging. Several cell clones were created that differed in the promoter regulating the gene. Thus, comparative analysis could be obtained without the risk of different position effects at each integration site. Cells in S/G2 phases could be detected exhibiting two adjacent transcription sites on sister chromatids. A sharp reduction in the transcription levels was observed as cells progressed along the cell cycle. We hypothesized that a change in chromatin structure acts as a general mechanism during the cell cycle leading to down-regulation in the activity of some genes. We addressed this question by treating the cells with chromatin decondensing agents. Quantifying and imaging the treated cells suggests that chromatin structure plays a role both in regulating transcriptional levels along the cell cycle, as well as in limiting an active gene from reaching its maximum transcription potential at any given time. These results contribute to understanding the role of chromatin as a regulator of gene expression.

Keywords: cell cycle, living cells, nucleus, transcription

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Authors: Vincent Murray

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The chromatin structure at the transcription start sites (TSSs) of genes is very important in the control of gene expression. In order for gene expression to occur, the chromatin structure at the TSS has to be altered so that the transcriptional machinery can be assembled and RNA transcripts can be produced. In particular, the nucleosome structure and positioning around the TSS has to be changed. Bleomycin is utilized as an anti-tumor agent to treat Hodgkin's lymphoma, squamous cell carcinoma, and testicular cancer. Bleomycin produces DNA damage in human cells and DNA strand breaks, especially double-strand breaks, are thought to be responsible for the cancer chemotherapeutic activity of bleomycin. Bleomycin is a large glycopeptide with molecular weight of approximately 1500 Daltons and hence its DNA strand cleavage activity can be utilized as a probe of chromatin structure. In this project, Illumina next-generation DNA sequencing technology was used to determine the position of DNA double-strand breaks at the TSSs of genes in intact cells. In this genome-wide study, it was found that bleomycin cleavage preferentially occurred at the TSSs of actively transcribed human genes in comparison with non-transcribed genes. There was a correlation between the level of enhanced bleomycin cleavage at TSSs and the degree of transcriptional activity. In addition, bleomycin was able to determine the position of nucleosomes at the TSSs of human genes. Bleomycin analogues were also utilized as probes of chromatin structure at the TSSs of human genes. In a similar manner to bleomycin, the bleomycin analogues 6′-deoxy-BLM Z and zorbamycin preferentially cleaved at the TSSs of human genes. Interestingly this degree of enhanced TSS cleavage inversely correlated with the cytotoxicity (IC50 values) of BLM analogues. This indicated that the degree of cleavage by bleomycin analogues at the TSSs of human genes was very important in the cytotoxicity of bleomycin and analogues. It also provided a deeper insight into the mechanism of action of this cancer chemotherapeutic agent since actively transcribed genes were preferentially targeted.

Keywords: anti-cancer activity, chromatin structure, cytotoxicity, gene expression, next-generation DNA sequencing

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Authors: Hashem Dadashpoor, Sadegh Saeidi Shirvan

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While with the evolution of the economy towards a knowledge-based economy, innovation is a requirement for metropolitan regions, the adoption of an open innovation strategy is an option and a requirement for many industrial firms in these regions. Studies show that investing in research and development units cannot alone increase innovation. Within the framework of the theory of learning regions, this gap, which scholars call it the ‘innovation gap’, is filled with regional features of firms. This paper attempts to investigate the factors affecting the open innovation of firms in metropolitan regions, and it searches for these in territorial innovation models and, in particular, the theory of learning regions. In the next step, the effect of identified factors which is considered as regional learning factors in this research is analyzed on the innovation of sample firms by SPSS software using multiple linear regression. The case study of this research is constituted of industrial enterprises from two groups of food industry and auto parts in Toos industrial town in Mashhad metropolitan region. For data gathering of this research, interviews were conducted with managers of industrial firms using structured questionnaires. Based on this study, the effect of factors such as size of firms, inter-firm competition, the use of local labor force and institutional infrastructures were significant in the innovation of the firms studied, and 44% of the changes in the firms’ innovation occurred as a result of the change in these factors.

Keywords: regional knowledge networks, learning regions, interactive learning, innovation

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Authors: Maciej Sobczak, Julita Pietrzak, Tomasz Płoszaj, Agnieszka Robaszkiewicz

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Brg1, a member of SWI/SNF complex, plays a role in chromatin remodeling, therefore, regulates expression of many genes. Brg1 is an ATPase of SWI/SNF complex, thus its activity requires ATP. Through its bromodomain recognizes acetylated histone residues and evicts them, thus promoting transcriptionally active state of chromatin. One of the enzymes that is responsible for acetylation of histone residues is Ep300. It was previously shown in the literature that cooperation of Brg1 and Ep300 occurs at the promoter regions that have binding sites for E2F-family transcription factors as well as CpG islands. According to literature, approximately 20% of human cancer possess mutation in Brg1 or any other crucial SWI/SNF subunit. That phenomenon makes Brg1-Ep300 a very promising target for anti-cancer therapy. Therefore in our study, we investigated if physical interaction between Brg1 and Ep300 exists and what impact those two proteins have on key for breast cancer cells processes such as DNA damage repair and cell proliferation. Bioinformatical analysis pointed out, that genes involved in cell proliferation and DNA damage repair are overexpressed in MCF7 and MDA-MB-231 cells. Moreover, promoter regions of these genes are highly acetylated, which suggests high transcriptional activity of those sites. Notably, many of those gene possess within their promoters an E2F, Brg1 motives, as well as CpG islands and acetylated histones. Our data show that Brg1 physically interacts with Ep300, and together they regulate expression of genes involved in DNA damage repair and cell proliferation. Upon inhibiting Brg1 or Ep300, expression of vital for cancer cell survival genes such as CDK2/4, BRCA1/2, PCNA, and XRCC1 is decreased in MDA-MB-231 and MCF7 cells. Moreover, inhibition or silencing of either Brg1 or Ep300 leads to cell cycle arrest in G1. After inhibition of BRG1 or Ep300 on tested gene promoters, the repressor complex including Rb, HDAC1, and EZH2 is formed, which inhibits gene expression. These results highlight potentially significant target for targeted anticancer therapy to be introduced as a supportive therapy.

Keywords: brg1, ep300, breast cancer, epigenetics

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Authors: P. Asiabi, M. Shahhoseini, R. Favaedi, F. Hassani, N. Nassiri, B. Movaghar, L. Karimian, P. Eftekhariyazdi

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Introduction: Polycystic Ovary Syndrome is a common gynecologic disorder. Many factors including environment, metabolism, hormones and genetics are involved in etiopathogenesis of PCOS. Of genes that have altered expression in human reproductive system disorders are HOX family genes which act as transcription factors in regulation of cell proliferation, differentiation, adhesion and migration. Since recent evidences consider epigenetic factors as causative mechanisms of PCOS, evaluation of association between known epigenetic marks of acetylation/methylation of histone 3 (H3K9ac/me) with regulatory regions of these genes can represent better insight about PCOS. In the current study, cumulus cells (CCs) which have critical roles during folliculogenesis, oocyte maturation, ovulation and fertilization were aimed to monitor epigenetic alterations of HOX genes. Material and methods: CCs were collected from 20 PCOS patients and 20 fertile women (18-36 year) with male infertility problems referred to the Royan Institute to have ICSI under GnRH antagonist protocol. Informed consents were obtained from the participants. Thirty six hours after hCG injection, ovaries were punctured and cumulus oocyte complexes were dissected. Soluble chromatin were extracted from CCs and Chromatin Immune precipitation (ChIP) coupled with Real Time PCR was performed to quantify the epigenetic marks of histone H3K9 acetylation/methylation (H3K9ac/me) on regulatory regions of 15 members of HOX genes from A-D subfamily. Results: Obtained data showed significant increase of H3K9ac epigenetic mark on regulatory regions of HOXA1, HOXB2, HOXC4, HOXD1, HOXD3 and HOXD4 (P < 0.01) and HOXC5 (P < 0.05) and also significant decrease of H3K9ac into regulatory regions of HOXA2, HOXA4, HOXA5, HOXB1 and HOXB5 (P < 0.01) and HOXB3 (P<0.05) in PCOS patients vs. control group. On the other side, there was a significant decrease in incorporation of H3K9me level on regulatory region of HOXA2, HOXA3, HOXA4, HOXA5, HOXB3 and HOXC4 (P≤0.01) and HOXB5 (P < 0.05) in PCOS patients vs. control group. This epigenetic mark (H3K9me2) has significant increase on regulatory region of HOXB1, HOXB2, HOXC5, HOXD1, HOXD3 and HOXD4 (P ≤ 0.01) and HOXB4 (P < 0.05) in patients vs. control group. There were no significant changes in acetylation/methylation levels of H3K9 on regulatory regions of the other studied genes. Conclusion: Current study suggests that epigenetic alterations of HOX genes can be correlated with PCOS and consequently female infertility. This finding might offer additional definitions of PCOS, and eventually provides insight for novel treatments with epidrugs for this disease.

Keywords: epigenetic, HOX genes, PCOS, female infertility

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Authors: Jeonghwan Jeon

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Technology planning with both internal capacity and external resource is necessary for successful open innovation. Until now, many types of research have been conducted for this issue. However, technology planning for open innovation at the national level has not been researched sufficiently. This study proposes Open roadmap for open innovation at the national level. The proposed open roadmap can manage the inflow & outflow open innovation systematically. Six types of open roadmap are classified with respect to the innovation direction and characteristics. The proposed open roadmap is applied to the open innovation cases of the Roman period. The proposed open roadmap is expected to be helpful tool for technology policy planning at the national level.

Keywords: technology planning, open innovation, internal resource, external resource, technology management

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Authors: András Farkas, István Molnár, Jan Vrána, Veronika Burešová, Petr Cápal, András Cseh, Márta Molnár-Láng, Jaroslav Doležel

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Species of Aegilops played a central role in the evolution of wheat and are sources of traits related to yield quality and tolerance against biotic and abiotic stresses. These wild genes and alleles are desirable to use in crop improvement programs via introgressive hybridization. However, the success of chromosome mediated gene transfer to wheat are hampered by the pour knowledge on the genome structure of Aegilops relative to wheat and by the low number of cost-effective molecular markers specific for Aegilops chromosomes. The COS markers specific for genes conserved throughout evolution in both sequence and copy number between Triticeae/Aegilops taxa and define orthologous regions, thus enabling the comparison of regions on the chromosomes of related species. The present study compared individual chromosomes of Aegilops umbellulata (UU), Ae. comosa (MM), Ae. speltoides (SS) and Ae. caudata (CC) purified by flourescent labelling with oligonucleotid SSR repeats and biparametric flow cytometry with wheat by identifying orthologous chromosomal regions by COS markers. The linear order of bin-mapped COS markers along the wheat D chromosomes was identified by the use of chromosome-specific sequence data and virtual gene order. Syntenic regions of wheat identifying genome rearrangements differentiating the U, M, S or C genomes from the D genome of wheat were detected. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species and wheat will facilitate the targeted development of new markers specific for U, M, S and C genomic regions and will contribute to the understanding of molecular processes related to the evolution of Aegilops.

Keywords: Aegilops, cos-markers, flow-sorting, wheat

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Authors: G. Carrero, C. Contreras, M. J. Hendzel

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Linker histones or histones H1 are highly mobile nuclear proteins that regulate the organization of chromatin and limit DNA accessibility by binding to the chromatin structure (DNA and associated proteins). It is known that this binding process is driven by both slow (strong binding) and rapid (weak binding) interactions. However, the exact binding mechanism has not been fully described. Moreover, the existing models only account for one type of bound population that does not distinguish explicitly between the weakly and strongly bound proteins. Thus, we propose different systems of reaction-diffusion equations to describe explicitly the rapid and slow interactions during a FRAP (Fluorescence Recovery After Photobleaching) experiment. We perform a model comparison analysis to characterize the binding mechanism of histone H1 and provide new meaningful biophysical information on the kinetics of histone H1.

Keywords: FRAP (Fluorescence Recovery After Photobleaching), histone H1, histone H1 binding kinetics, linker histone, reaction-diffusion equation

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Authors: Hyo-Min Kim, Seokjin Ham, Mi-Joung Yoo, Minseon Kim, Tae-Young Roh

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The gastrointestinal (GI) tract of most animals, including murine, is highly compartmentalized epithelia which also provide distinct different functions of its own tissue. Nevertheless, these epithelia share certain characteristics that enhance immune responses to infections and maintain the barrier function of the intestine. GI tract epithelia also undergo regeneration not only in homeostatic conditions but also in a response to the damage. A full turnover of the murine gastrointestinal epithelium occurs every 4-5 day, a process that is regulated and maintained by a minor population of Lgr5+ adult stem cell that commonly conserved in the bottom of crypts through GI tract. Maintenance of the stem cell is somehow regulated by epigenetic factors according to recent studies. Chromatin vacancy, remodelers, histone variants and histone modifiers could affect adult stem cell fate. In this study, Lgr5-EGFP reporter mouse was used to take advantage of exploring the epigenetic dynamics among Lgr5 positive mutual stem cell in GI tract. Cells were isolated by fluorescence-activated cell sorting (FACS), gene expression levels, chromatin accessibility changes and histone modifications were analyzed. Some notable chromatin structural related epigenetic variants were detected. To identify the overall cell-cell interaction inside the stem cell niche, an extensive genome-wide analysis should be also followed. According to the results, nevertheless, we expected a broader understanding of cellular niche maintaining stem cells and epigenetic barriers through conserved stem cell in GI tract. We expect that our study could provide more evidence of adult stem cell plasticity and more chances to understand each stem cell that takes parts in certain organs.

Keywords: adult stem cell, epigenetics, LGR5 stem cell, gastrointestinal tract

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Authors: H. Nejadriahi

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This paper focuses on the performance of Iwan as one of the significant spaces in the traditional architecture of Iran. The aim of this study is to investigate on the role of Iwan in sustainability enhancement of traditional houses of different climatic regions of Iran. Iwan is considered as a semi-open space, which its form and location in the building highly depends to the climatic situation of that region. For that reason, Iwan is recognized as one of the sustainable elements in the traditional houses of Iran, which can provide more comfort with less use of energy. In this study, the history and emergence of Iwan in the traditional architecture of Iran as well as the concept of sustainability in architecture are explained briefly. Then, the change of performance or form of Iwan is analysed in different climatic regions of Iran in accordance to the sustainability concepts. The methods used in this study are descriptive and analytic. Results of this paper verify that studying the sustainability solutions in the traditional architecture of Iran, would be a valuable source of inspiration for the current designers to create an environmental and sustainable architecture for the future.

Keywords: climatic regions of Iran, Iwan, sustainability, traditional houses

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Authors: Michal Štros, Eva Polanská, Šárka Pospíšilová

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HMGB1 is an architectural protein in chromatin, acting also as a signaling molecule outside the cell. Recent reports from several laboratories provided evidence that a number of both the intracellular and extracellular functions of HMGB1 may depend on redox-sensitive cysteine residues of the protein. MALDI-TOF analysis revealed that mild oxidization of HMGB1 resulted in a conformational change of the protein due to formation of an intramolecular disulphide bond by opposing Cys23 and Cys45 residues. We have demonstrated that redox state of HMGB1 could significantly modulate the ability of the protein to bind and bend DNA. We have also shown that reduced HMGB1 could easily displace histone H1 from DNA, while oxidized HMGB1 had limited capacity for H1 displacement. Using microscale thermophoresis (MST) we have further studied mechanism of HMGB1 interaction with histone H1 in free solution or when histone H1 was bound to DNA. Our MST analysis indicated that reduced HMGB1 exhibited in free solution > 1000 higher affinity of for H1 (KD ~ 4.5 nM) than oxidized HMGB1 (KD <10 M). Finally, we present a novel mechanism for the HMGB1-mediated modulation of histone H1 binding to DNA.

Keywords: HMGB1, histone H1, redox state, interaction, cross-linking, DNA bending, DNA end-joining, microscale thermophoresis

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Authors: Alma Orucevic-Alagic, Martin Höst

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Open source communities have demonstrated that complex and enterprise grade software can be produced, supported, and maintained by self-organizing groups of developers using primarily electronic form of communication. Due to the inherent nature of open source development, a specific set of open source software development practices has evolved. While there is an ongoing research on the topic of applicability of open source development practices within a company setting, still little is known about their benefits and challenges. The objective of this research is to understand if and to what degree open source development practices observed within a mature open source community are aligned with development practices within a large software and hardware company setting. For the purpose of this case study a set of open source development practices that are present in a mature open source community has been identified. Then, development practices of a large, international, hardware and software company based in Sweden were assessed and compared to the identified open source community practices. It is shown that there are many similarities between a mature open source community and a large company setting in regard to software development practices. We also identify practices that exist in open source communities and that are not standard within a company setting, but whose implementation can result in an improved software development efficiency within the company setting.

Keywords: development practices, open source software, innersource, closed open source

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Authors: Alan C. Lin, Tran Anh Son

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This study proposes an approach to determine the undercut regions and their releasing directions for slider design of complex parts represented by the file format of STL (STereoLithography). In order to delineate the border of undercut regions, orthogonal cutting planes are firstly employed to automatically find the inner loops of a part model. To discover the facets belonging to undercut regions, attributes are then assigned to the facets of the part model based on the topological relationship of adjacent facets of each inner loop. After that, the undercut regions are separated from other facets in the model. Through the recognized facets of the undercut regions, the concept of 'visibility map (V-map)' is further applied to determine feasible releasing directions for each of the undercut regions. The undercut regions having the same releasing direction are finally grouped to form a slider in the injection mold.

Keywords: solid model, STL data, injection mold design, visibility map

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Authors: Kwame Kodua-Ntim

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The study explored the authors self-archiving to create awareness of open-access institutional repositories in universities. The qualitative approach of the study was informed by the interpretive paradigm as well as the case research design. The target population for the study was all twelve (12) open-access institutional repositories managers and administrators purposively selected from the five (5) universities in Ghana. The universities were chosen since they were the only ones listed in the Directory of Open Access Repositories. Interviews were conducted using a semi-structured interview guide and data were analyzed using thematic analysis. The study revealed that academics had some information about self-archiving in open-access institutional repositories and university libraries with open-access institutional repositories were using DSpace software. Managers and administrators of open-access institutional repositories mediated content uploaded and believed that author self-archiving could improve awareness of open-access institutional repositories. The study recommended that universities should fully implement the author’s self-archiving protocol, and academics should be trained to be able to upload research works onto open-access institutional repositories. Furthermore, the university and university library should provide rigorous policies on author self-archiving and incentives for author self-archiving in the open access institutional repositories.

Keywords: author, awareness, institutional repositories, open access, open archive, self-archiving

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Authors: Rahul Thakur, Onkar Chandel

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Red Hat is the world leader in providing open source software and solutions. A global enterprise, like Red Hat, has unique issues of connecting employees with content because of distributed offices, multiple teams spread across geographies, multiple languages, and different cultures. Employees, of a global company, create content that is distributed across departments, teams, regions, and countries. This makes finding the best content difficult since owners keep iterating on the existing content. When employees are unable to find the content, they end up creating it once again and in the process duplicating existing material and effort. Also, employees may not find the relevant content and spend time reviewing obsolete duplicate, or irrelevant content. On an average, a person spends 15 minutes/day in failed searches that might result in missed business opportunities, employee frustration, and substandard deliverables. Red Hat Knowledge Management Office (KMO) applied 'open source strategy' to solve the above problems. Under the Open Source Strategy, decisions are taken collectively. The strategy aims at accomplishing common goals with the help of communities. The objectives of this initiative were to save employees' time, get them authentic content, improve their content search experience, avoid duplicate content creation, provide context based search, improve analytics, improve content management workflows, automate content classification, and automate content upload. This session will describe open source strategy, its applicability in content management, challenges, recommended solutions, and outcome.

Keywords: content classification, content management, knowledge management, open source

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Authors: Hasan Vural

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Turkey is a favorable country to produce a great variety of agricultural products because of her different geographic and climatic conditions which have been used to divide the country into four main and seven sub regions. This classification into seven regions traditionally has been used in order to data collection and publication especially related with agricultural production. Afterwards, nine agricultural regions were considered. Recently, the governmental body which is responsible of data collection and dissemination (Turkish Institute of Statistics-TIS) has used 12 classes which include 11 sub regions and Istanbul province. This study aims to evaluate these classification efforts based on the acreage of ten main crops in a ten years time period (1996-2005). The panel data grouped in 11 subregions has been evaluated by cluster and multivariate statistical methods. It was concluded that from the agricultural production point of view, it will be rather meaningful to consider three main and eight sub-agricultural regions throughout the country.

Keywords: agricultural region, factorial analysis, cluster analysis,

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Authors: Semih Sözer

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One of the most common issues in economic systems is understanding characteristics of economic activities in cities and regions. Although there are critics to economic base models in conceptual and empirical aspects, these models are useful tools to examining the economic structure of a nation, regions or cities. This paper uses one of the methodologies of economic base models namely the location quotients model. Data for this model includes employment numbers of provinces and NUTS II regions in Turkey. Time series of data covers the years of 1990, 2000, 2003, and 2009. Aim of this study is finding which sectors are export-base and which sectors are import-base in provinces and regions. Model results show that big provinces or powerful regions (population, size etc.) mostly have basic sectors in their economic system. However, interesting facts came from different sectors in different provinces and regions in the model results.

Keywords: economic base, location quotients model, regional economics, regional development

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Authors: Chaithanya Pothuganti

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Open and semi-open spaces in educational buildings like corridors, mid landings, seating spaces, lobby, courtyards are traditionally have been the places of social communion and interaction which helps in promoting the knowledge, performance, activeness, and motivation in students. Factors like availability of land, commercialization, of educational facilities, especially in e-techno and smart schools, led to closed classrooms to accommodate students thereby lack quality open and semi-open spaces. This insufficient attention towards open space design which is a means of informal learning misses an opportunity to encourage the student’s skill development, behavior and learning skills. The core objective of this paper is to find the level of impact on student learning behavior and to identify the suitable proportions and configuration of spaces that shape the schools. In order to achieve this, different types of open spaces in schools and their impact on student’s performance in various existing models are analysed using case studies to draw some design principles. The study is limited to indoor open spaces like corridors, break out spaces and courtyards. The expected outcome of the paper is to suggest better design considerations for the development of semi-open and open spaces which functions as an element for informal learnings. Its focus is to provide further thinking on designing and development of open spaces in educational buildings.

Keywords: configuration of spaces and proportions, informal learning, open spaces, schools, student’s behavior

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Authors: Sarah Baker, Jayati Chaudhuri

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Librarians have embraced the open access movement in all disciplines but their own. They are strong advocates on college campuses and curate institutional repositories, yet there are surprisingly few open access LIS journals. Presenters evaluated the open access availability of library and information science literature. After analyzing the top 100 library science journals (the top 50 journals from Scimago and JCR) and finding very few gold open access journals, they then investigated the availability of open access articles from the top 10 closed access journals. Presenters would like to generate a conversation on what type of proactive approach librarians can take to increase open access to literature within our discipline. Librarians like their colleagues in other disciplines are not motivated to submit their articles to their institutional repositories. Presenters have found a similar reluctance from their fellow colleagues regarding open access initiatives on campus. Presenters will describe Open Access Week activities as part of a campus-wide initiative and share some faculty comments, concerns, and misconceptions that came up as a part of this dialog. Presenters will discuss their personal experiences providing access to faculty publications through the California State University Los Angeles institutional repository.

Keywords: faculty scholarship, institutional repositories, library and information science journals, open access

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Authors: Audrey Romero-Pelaez, Juan Carlos Morocho-Yunga

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The increasing amount of open educational resources (OER) published on the web for consumption in teaching and learning environments also generates a growing need to ensure the quality of these resources. The low level of OER discovery is one of the most significant drawbacks when faced with its reuse, and as a consequence, high-quality educational resources can go unnoticed. Metadata enables the discovery of resources on the web. The purpose of this study is to lay the foundations for open educational resources to achieve their first quality star within the Quality4OER Framework. In this study, we evaluate the quality of OER metadata and establish the main guidelines on metadata quality in this context.

Keywords: open educational resources, OER quality, quality metadata

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Authors: Naila Naseer

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Emotional Intelligence (EI) concept is not new yet unique and interesting. EI is a person’s ability to be aware of his/her own emotions and to manage, handle and communicate emotions with others effectively. The present study was conducted to assess the relationship between emotional intelligence and age of graduate level students at Allama Iqbal Open University (AIOU). Population consisted of Allama Iqbal Open University students (B.Ed 3rd Semester, Autumn 2007) from Rawalpindi and Islamabad regions. Total number of sample consisted of 469 participants was randomly drawn out by using table of random numbers. Bar-On EQ-i was administered on the participants through personal contact. The instrument was also validated through pilot study on a random sample of 50 participants (B.Ed students Spring 2006), who had completed their B.Ed degree successfully. Data was analyzed and tabulated in percentages, frequencies, mean, standard deviation, correlation, and scatter gram in SPSS (version 16.0 for windows). The results revealed that students with higher age group had scored low on the scale (Bar-On EQ-i). Moreover, the students in low age groups exhibited higher levels of EI as compared with old age students.

Keywords: emotional intelligence, age level, learning, emotion-related feelings

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Authors: Kars Beek, Remco Groeneveld, Sjaak Brinkkemper

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Although there is much literature available on requirement documentation in traditional software development, few studies have been conducted about this topic in open source software development. While open-source software development is becoming more important, the software development processes are often not as structured as corporate software development processes. Papers show that communities, creating open-source software, often lack structure and documentation. However, most recent studies about this topic are often ten or more years old. Therefore, this research has been conducted to determine if the lack of structure and documentation in requirement engineering is currently still the situation in these communities. Three open-source products have been chosen as subjects for conducting this research. The data for this research was gathered based on interviews, observations, and analyses of feature proposals and issue tracking tools. In this paper, we present a comparison and an analysis of the different methods used for requirements documentation to understand the current practices of requirements documentation in open source software development.

Keywords: case study, open source software, open source software development, requirement elicitation, requirement engineering

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Authors: Amy Gooden

Abstract:

Various modes of consent have been utilized in health research, but open consent has not been explored in South Africa’s AI research context. Open consent entails the sharing of data without assurances of privacy and may be seen as an attempt to marry open science with informed consent. Because all potential uses of data are unknown, it has been questioned whether consent can be informed. Instead of trying to adapt existing modes of consent, why not adopt a new perspective? This is what open consent proposes and what this research will explore in AI health research in South Africa.

Keywords: artificial intelligence, consent, health, law, research, South Africa

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Authors: Darusalam, Jorish Hulstijn, Marijn Janssen

Abstract:

Media has revealed a variety of corruption cases in the regional and local governments all over the world. Many governments pursued many anti-corruption reforms and have created a system of checks and balances. Three types of corruption are faced by citizens; administrative corruption, collusion and extortion. Accountability is one of the benchmarks for building transparent government. The public sector is required to report the results of the programs that have been implemented so that the citizen can judge whether the institution has been working such as economical, efficient and effective. Open Data is offering solutions for the implementation of good governance in organizations who want to be more transparent. In addition, Open Data can create transparency and accountability to the community. The objective of this paper is to build a framework of open data for accountability to combating corruption. This paper will investigate the relationship between open data, and accountability as part of anti-corruption initiatives. This research will investigate the impact of open data implementation on public organization.

Keywords: open data, accountability, anti-corruption, framework

Procedia PDF Downloads 336

Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

Abstract:

Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Ali E. Abbas

Abstract:

This paper highlights some of the normative issues that might result by setting independent thresholds in risk analyses and particularly with safety regions. A second objective is to explain how such regions can be specified appropriately in a meaningful way. We start with a review of the importance of setting deterministic trade-offs among target requirements. We then show how to determine safety regions for risk analysis appropriately using utility functions.

Keywords: decision analysis, thresholds, risk, reliability

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Authors: Anastasis D. Petrou

Abstract:

Innovation and strategy discussions do highlight open innovation as a new paradigm in business. Yet, a number of stumbling blocks in the form of closed innovation principles weaved into the fabric of a traditional business model stand in the way of the new paradigm’s momentum to increase value in various business contexts. The paper argues that businesses considering an engagement with the open innovation paradigm would need to take steps to improve their multiplicative, absorptive and relational capabilities, respectively. The needed improvements would amount to a business model evolutionary transformation and eventually bring about a paradigm overhaul in business. The transformation is worth staging over time to ensure that open innovation is developed across interconnected and partnered areas of strategic importance. This article develops an open innovation strategy (OIS) capabilities model, and employs examples from different industries to briefly discuss OIS’s potential to augment business value in a number of suggested areas for future research.

Keywords: close innovation, open innovation paradigm, open innovation strategy (OIS) paradigm, OIS capabilities model, multiplicative capability, absorptive capability, relational capability

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Authors: B. Raghu, Shashi Vemuri, Ch. Sreenivasa Rao

Abstract:

The survey on pesticide use pattern was carried out by interviewing farmers growing chill in open fields and poly houses based on the questionnaire prepared to assess their knowledge and practices on crop cultivation, general awareness on pesticide recommendations and use. Education levels of poly house farmers are high compared to open field farmers, where 57.14% poly house farmers are high school educated, whereas 35% open field farmers are illiterates. Majority farmers use nursery of 35 days and grow in <0.5 acre poly house in summer and rabi and < 1 acre in open field during kharif. Awareness on pesticide related issues is varying among poly house and open field farmers with some commonality, where 28.57% poly house farmers know about recommended pesticides while only 10% open field farmers are aware of this issue. However, in general, all farmers contact pesticide dealer for recommendations, poly house farmers prefer to contact scientists (35.71%) and open field farmers prefer to contact agricultural officers (33.33). Most farmers are unaware about pesticide classification and toxicity symbols on packing. Farmers are aware about endosulfan ban, but only 21.42% poly house and 11.66% open field farmers know about ban of monocrotofos on vegetables. Very few farmers know about pesticide residues and related issues, but know washing helps to reduce contamination.

Keywords: open field, pesticide usage, polyhouses, residues survey

Procedia PDF Downloads 468