6,113 research outputs found
Quantitative methods for profiling dynamic chromatin features
No full textLiving systems, from entire organisms down to the single cells constituting them are dynamic entities that continuously adapt and respond to their local environment. Cells achieve this through gene expression programs derived from static information encoded in the DNA made dynamic through chemical modifications at the chromatin level, collectively termed the epigenome. Numerous epigenetic regulators have been implicated in early embryonic developmental transitions and pluripotency. Ex vivo, the different states of pluripotency can be recapitulated by embryonic stem cells (ESCs) grown in defined media conditions. Many developmental gene promoters in ESCs display co-occurrence of the activating histone H3 lysine 4 trimethylation (H3K4me3) mark and the repressive H3K27me3 mark. This distinctive bivalent signature is considered to poise expression, allowing timely resolution to an active or inactive state depending on the signal.The distribution of histone modifications and chromatin-associated factors across the genome can be mapped using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). However, traditional ChIP-seq methods fail to quantitatively profile the nuanced global and local epigenetic rewiring that takes place in key developmental stages. This thesis addresses this limitation through the development of a quantitative multiplexed ChIP-seq technology: MINUTE (multiplexed indexed unique molecule T7 amplification end to end sequencing) ChIP. Across the three papers included in this thesis, we reveal the underpinnings of chromatin state dynamics in early mouse and human embryonic development by employing MINUTE ChIP. In Paper I, we first show that MINUTE ChIP enables accurate quantitative comparisons over a wide linear range. By employing it to characterize mouse ESCs grown in 2i and serum conditions, we find that the 2i naïve state is characterized by high global levels of H3K27me3 and low H3K4me3. At bivalent promoters, we observe that while H3K27me3 levels are stably maintained between serum and 2i, H3K4me3 levels are higher in the serum condition. Through quantitative epigenome profiling, in Paper II we find that naïve human ESCs also have broad global gain of Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 and define a previously unrecognized, naïve-specific set of bivalent promoters. Bulk and single-cell transcriptomics confirmed that naïve bivalency maintains key trophectoderm and mesoderm transcription factors in a transcriptionally poised state which is resolved to an active state upon depletion of H3K27me3. Therefore, we discovered that PRC2-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development. In paper III we show how quantitative RNA polymerase II occupancy profiles generated by MINUTE ChIP can be integrated with transient transcriptomics data to unravel genome wide transcriptional kinetics in three mESCs pluripotent states: naïve, ground and paused.Taken together, this thesis provides compelling evidence for a broad H3K27me3 hypermethylation of the genome in both naïve mouse and human ESCs and the basis for substantially revising the model for bivalency during embryonic development.List of scientific papersI. Banushree Kumar, Simon J Elsässer. Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells. Cell Reports. 2019, Vol. 28, 3274-3284.e5. https://doi.org/10.1016/j.celrep.2019.08.046 II. Banushree Kumar*, Carmen Navarro*, Nerges Winblad*, John P Schell, Cheng Zhao, Jere Weltner, Laura Baqué-Vidal, Angelo Salazar Mantero, Sophie Petropoulos, Fredrik Lanner, Simon J Elsässer. Polycomb Repressive Complex 2 shields naïve human pluripotent cells from trophectoderm differentiation. [Accepted] https://doi.org/10.1038/s41556-022-00916-w III. Rui Shao, Banushree Kumar, Katja Lidschreiber, Michael Lidschreiber, Patrick Cramer, Simon J Elsässer Distinct transcription kinetics of pluripotent cell states. Molecular Systems Biology. 2022, Vol.18, e10407. https://doi.org/10.15252/msb.202110407 </p
Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells
No full textVarious supplementary data, information and pseudocod
Bibliographics for the 983 eprints in the live archives of E-LIS : trends and status report up to 7th July 2004, based on author-self-archiving metadata
No full textThe priority for ideas and philosophy related to "Network Theory" have been traced back and documented by Braun(2004),and credit goes to Karinthy(1929).The IT has empowered to realise it, as the most practical phenomena and it is no more a humour. The OAI (Open Archives Initiatives)and ACIS (Academic Contributor Information System)are progressive in the direction ,which may lead to realise the "Collective Genius" at global level. Focus of present study is on Author-Self-Archiving (A-S-A)Metadata of the 983 Eprints in the Live Archives of the E-LIS (EPrints of Library and Information Science),which were approved till 7th July 2004.The A-S-A Metadata was used for librametric analysis. Self-explanatory bibliographics are illustrated.The highlights include: Conference papers (34%); highest approval, June 2004 (28%); published archives (76%);not refereed (52%); not in public domain (60%); highest self-archiving-author (De Robbio, Antonella).The Nos. of EPrints having single JITA domain specifications were: Theoretical and general aspects of libraries and information(27); Information use and sociology of information(80);Users,literacy and reading(13);Libraries as physical collections(30);Publishing and legal issues(57);Management(13);Industry, profession and education(36);Information sources, supports, channels(113) ; Information treatment for information services, Information functions and techniques (101); Technical services libraries, archives and museums(25); Housing technologies(1); Information technology and library technology(92); and Inter-domainery (395) i.e. having specifications of two or more than two JITA classes
Distinct transcription kinetics of pluripotent cell states
No full textMouse embryonic stem cells (mESCs) can adopt naïve, ground, and paused pluripotent states that give rise to unique transcriptomes. Here, we use transient transcriptome sequencing (TT-seq) to define both coding and non-coding transcription units (TUs) in these three pluripotent states and combine TT-seq with RNA polymerase II occupancy profiling to unravel the kinetics of RNA metabolism genome-wide. Compared to the naïve state (serum), RNA synthesis and turnover rates are globally reduced in the ground state (2i) and the paused state (mTORi). The global reduction in RNA synthesis goes along with a genome-wide decrease of polymerase elongation velocity, which is related to epigenomic features and alterations in the Pol II termination window. Our data suggest that transcription activity is the main determinant of steady state mRNA levels in the naïve state and that genome-wide changes in transcription kinetics invoke ground and paused pluripotent states
A Unified Shell model for Buoyancy-Driven Turbulence
No full textWe construct a unified shell model for stably stratified and convective turbulence. Shell model simulation of stably stratified flow in turbulent regime exhibit Bolgiano-Obukhbov (BO) scaling in which the kinetic energy spectrum varies as . However, simulation of convective turbulence shows Kolmogorov's spectrum. These results are consistent with the direct numerical simulations of Kumar {\em et al.} [Phys. Rev. E {\bf 90}, 023016 (2014)]. We also observe a dual scaling ( and ) for a limited range of parameters in stably stratified flow
Story of the Story-Teller: A Conversation with Ramendra Kumar
No full textRamendra Kumar (Ramen) is an award-winning writer, storyteller and inspirational speaker with 42 books to his name. Ramen’s writings have been published by many of the leading publishers in the county and translated into 30 languages. They have found a place in several textbooks and anthologies. He has written across all genres ranging from picture books to adult fiction, satire, poetry, travelogues, biographies and on issues related to parenting and relationships. He has been invited to literary festivals held in Denmark, Greece, Sharjah, Sri Lanka as well Indian events including the prestigious Jaipur Litfest to conduct storytelling sessions and creative writing workshops. He has also been empanelled by Pearson India Education Services as well as several schools to conduct workshops. He was nominated as a Jury Member for the Best Children’s Author Category of The Times of India’s ‘Women AutHer’ Awards 2020. Many of his stories have been showcased by popular audio streaming, apps both within and outside the country, such as Spotify, Gaatha, Talking Stories Radio – London et al.
An Engineer & an MBA, Ramen was serving as the General Manager (Corporate Communications), SAIL, Rourkela Steel Plant, when he took Voluntary Retirement to pursue his passion, in August 2020. To know more about the writer, you can visit his website www.ramendra.in & his page on Wikipedia. Dr. Sagar Kumar Sharma interviews the author and unfolds the pages of his life.
 
NOTICE!!! This person (known as Ashwin Kumar) plagiarized the text titled: "Using phenomenological research methods in qualitative health research"
No full textEDITORIAL NOTICE:
1. This publication has been removed due to detected plagiarism by the editorial.
2. If you have cited, you MUST UPDATE your reference with the following original article:
Wojnar, Danuta, and Kristen Swanson. “Phenomenology An Exploration”. Journal of holistic nursing : official journal of the American Holistic Nurses’ Association 25 (01 October 2007): 172-80; discussion 181. https://doi.org/10.1177/0898010106295172.
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3. Submitter's Profile Record (the thief, the plagiariser):
Name: Ashwin KumarURL: http://www.freewebs.com/ak2146Affiliation: University of Western Sydney, Australia.Country: AustraliaBio Statement:Dr. Ashwin Kumar,PO Box 571,Toongabbie,Sydney,Australia, NSW, 2146.Homepage: http://www.freewebs.com/ak2146Email: [email protected]
[email protected]: 0432-622-147Skype Internet Phone ID: ak2146
Dr. Ashwin Kumar (BA, MA (Distinction), PhD) is an academic researcher whose research interests and areas of expertise include: Complementary and alternative medicine (CAM), ageing and social gerontology, sociology, social anthropology, sociology of care, public health, health promotion, Indigenous health, migrant and refugee health, disability and chronic illness. Ashwin is the author of 8 books and numerous academic journal articles in the field of public health, health sociology and anthropology of health and illness. His books: The Lived Experience of Caring; The Lived Experience of Ageing; The Lived Experience of Using Complementary and Alternative Medicine; Doing Sociology; The Basics of Sociology; Plain English Writing; Research and Writing Skills and Writing Effective Essays are available at:
http://www.amazon.com/s/ref=ntt_athr_dp_sr_1?_encoding=UTF8&sort=relevancerank&search-alias=books&field-author=PhD.%20Ashwin%20Kumar
My homepage: http://www.freewebs.com/ak2146
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Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks
No full textCite this code as: Kumar, J. (2023). Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks (Version 1.0) [Computer software]. https://doi.org/10.5281/zenodo.8048530
Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks
Author: Jitendra (Jitu) Kumar ([email protected]), Oak Ridge National Laboratory
Regional and global ecological research networks, representing coordinated and standardized as well as adhoc networks of observation sites, provide valuable observations necessary for ecological modeling and synthesis studies. Studies conducted across observational networks strive to scale up their results to larger areas, trying to reach conclusions that are valid throughout regional, continental, and even global scales. Network representativeness and constituency can show how well conditions at those locations represent conditions elsewhere within a larger area containing the network and can be used to help scale-up results over larger regions.
Representativeness: Euclidean distance between two sites plotted in multivariate environmental space can be used as an inverse measure of multivariate similarity to quantify representativeness. Close sites in environmental space have a similar combination of environmental factors, and therefore are highly representative of each other.
Constituency: For any site in the network, its Constituency represent all locations that are best represented by the multivariate environmental drivers at that site.
Code Compilation:
make
Edit the ```makefile``` as needed for your platform.
CC=gcc
CFLAGS= -O3
hpea: network_representativeness.o\
utility.o
(CFLAGS) *.o -lm -o network_representativeness
.o:
(CFLAGS) -c $<
clean:
\rm *.o network_representativeness
Running the representativeness analysis:
Usage: network_representativeness -infile input data file [ASCII]
-coordsfile coordinate file name
-clustfile coordinate file name [OPTIONAL -- must be used with -siteclustfile]
-sitefile site data file name
-siteclustfile site data file name [OPTIONAL -- must be used with -clustfile]
-nsites No. of sites
-minmaxfile minmax file name
-outfile output file name
-nrows No. of rows in input data
-ncols No. of variables
-details [OPTIONAL -- turn on output representativeness for each site, default is to write network representativeness and constituency only.]
-help program usage help.
Publications using ```network_reprentativeness``` code:
Kumar, J., Coffin, A. W., Baffaut, C., Ponce-Campos, G., Witthaus, L., and Hargrove, W. W. (2023) "Quantitative Representativeness and Constituency of the Long-Term Agroecosystem Research Network, and Analysis of Complementarity with Other Existing Ecological Networks", Environmental Management (in press)
M. M. T. A. Pallandt, J. Kumar, M. Mauritz, E. A. G. Schuur, A.-M. Virkkala, G. Celis, F. M. Hoffman, and M. Göckede. Representativeness assessment of the pan-arctic eddy covariance site network and optimized future enhancements. Biogeosciences, 19(3):559--583, 2022. https://doi.org/10.5194/bg-19-559-2022
J. Kumar, F. M. Hoffman, W. W. Hargrove, and N. Collier. Understanding the representativeness of FLUXNET for upscaling carbon flux from eddy covariance measurements. Earth System Science Data Discussion, 2016:1--25, August 2016. https://doi.org/10.5194/essd-2016-36.If you use this software, please cite it as below.
Kumar, J. (2023). Multivariate Quantitative Representativeness and Constituency Analysis of Ecological Observation Networks (Version 1.0) [Computer software]. https://doi.org/10.5281/zenodo.804853
Dilip Kumar: autor-aktor
No full textDilip Kumar has been praised for his sublime dialog delivery, for his restrained gestures, and for his measured and controlled underplay of emotions in tragic stories as well as in light-hearted comedies. His debut in 1944 with Jwar Bhata (Ebb and Tide) met with less-than-flattering reviews. So did the next three films until his 1948 film, Jugnu (Firefly), which brought him recognition and success. Unlike his contemporaries such as Raj Kapoor and Dev Anand, who propelled their careers by launching their own production companies, Dilip Kumar relied on his talent, his unique approach to characterization, and his immersion in the projects he undertook. In the course of his career that spanned six decades, Kumar made only 62 films. However, his work is a textbook for other actors that followed. Not only did he bring respectability to a profession that had been shunned by the upper classes in India as a profession for “pimps and prostitutes,” but he also elevated film-acting and filmmaking to an academic discipline, making him worthy of the title ‘Professor Emeritus of Acting’. Rooted in the theoretical framework of Howard S. Becker’s work on the “production of culture” and “doing things together,” this paper discusses Kumar’s approach to acting, character development, and the level of his involvement and commitment to each of his projects. The author of this article argues that more than the creative control as a producer or a director, it is the artistic involvement and commitment of the main actors that shape great works of art in cinema. Dilip Kumar demonstrated it repeatedly.Dilip Kumar był chwalony za wysublimowane prowadzenie dialogów, opanowaną gestykulację oraz za wyważone i kontrolowane wyrażanie emocji zarówno w opowieściach tragicznych, jak też w beztroskich komediach. Jego debiut w 1944 w Jwar Bhata (Odpływy i przypływy) spotkał się z niezbyt pochlebnymi recenzjami. Podobnie było z kolejnymi trzema filmami, aż do filmu Jugnu (Świetlik) z 1948 roku, który przyniósł mu uznanie i sukces. W przeciwieństwie do swoich rówieśników, jak Raj Kapoor iDev Anand, którzy napędzali kariery, uruchamiając własne firmy produkcyjne, Dilip Kumar polegał na swoim talencie, unikalnym podejściu do charakteryzacji i zaangażowaniu w projekty, których się podjął. W ciągu swojej sześćdziesięcioletniej kariery Kumar nakręcił tylko 62 filmy. Jednak jego praca jest podręcznikowa dla młodszych aktorów. Nie tylko przyniósł szacunek zawodowi aktora, traktowanemu przez indyjskie klasy wyższe jako zawód „alfonsów i prostytutek”, ale także podniósł aktorstwo filmowe i filmowanie do dyscypliny akademickiej, co uczyniło Kumara godnym tytułu emerytowanego profesora aktorstwa. Artykuł ten, zakorzeniony w ramach teoretycznych pracy Howarda S. Beckera nad „produkcją kultury” i „robieniem rzeczy razem”, omawia podejście Kumara do aktorstwa i rozwoju postaci oraz poziom jego zaangażowania w każdy ze swoich projektów. Autor tego artykułu przekonuje, że to artystyczne zaangażowanie i poświęcenie głównych aktorów kształtują wielkie dzieła sztuki w kinie bardziej niż kontrola twórcza producenta czy reżysera. Dilip Kumar wielokrotnie to zademonstrował
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