Journal articles on the topic 'Curated landscapes'
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Wheler, Jennifer, J. Jack Lee, and Razelle Kurzrock. "Unique Molecular Landscapes in Cancer: Implications for Individualized, Curated Drug Combinations." Cancer Research 74, no. 24 (October 17, 2014): 7181–84. http://dx.doi.org/10.1158/0008-5472.can-14-2329.
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Williams, Roy Trevor, Jenny Mackness, and Simone Gumtau. "Footprints of emergence." International Review of Research in Open and Distributed Learning 13, no. 4 (September 12, 2012): 49. http://dx.doi.org/10.19173/irrodl.v13i4.1267.
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<p>It is ironic that the management of education has become more closed while learning has become more open, particularly over the past 10-20 years. The curriculum has become more instrumental, predictive, standardized, and micro-managed in the belief that this supports employability as well as the management of educational processes, resources, and value. Meanwhile, people have embraced interactive, participatory, collaborative, and innovative networks for living and learning. To respond to these challenges, we need to develop <em>practical tools to help us describe these new forms of learning</em> which are multivariate, self-organised, complex, adaptive, and unpredictable. We draw on complexity theory and our experience as researchers, designers, and participants in open and interactive learning to go beyond conventional approaches. We develop a 3D model of landscapes of learning for exploring the relationship between prescribed and emergent learning in any given curriculum. We do this by repeatedly testing our descriptive landscapes (or footprints) against theory, research, and practice across a range of case studies. By doing this, we have not only come up with a practical tool which can be used by curriculum designers, but also realised that the curriculum itself can usefully be treated as emergent, depending on the dynamics<br />between prescribed and emergent learning and how the learning landscape is curated.</p>
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Keefer, Natalie, and Michelle Haj-Broussard. "Language in Educational Contexts." Journal of Culture and Values in Education 3, no. 2 (December 22, 2020): 1–12. http://dx.doi.org/10.46303/jcve.2020.9.
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The purpose of this special issue is to provide a space for scholars to disseminate theory and research about the influence of language in educational contexts. In this issue, we curated articles that address topics related to how language serves as a defining or decisive factor in education and schooling. In our introduction to this special issue, we provide an interpretive overview of the articles and offer an explanation of their relevance for understanding the complex nature of contemporary education. Salient topics include: critical analysis of discourse, linguistic landscapes, Natural Semantic Metalanguage, language ideology, politics and educational funding, funds of knowledge/identity, and definitional caveats related to language learning pedagogies in divergent contexts.
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Thomason, Allison Karmel. "The Sense-scapes of Neo-Assyrian Capital Cities: Royal Authority and Bodily Experience." Cambridge Archaeological Journal 26, no. 2 (February 3, 2016): 243–64. http://dx.doi.org/10.1017/s0959774315000578.
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This study approaches the material world of the Neo-Assyrian period in Mesopotamia from the theoretical and methodological standpoint of the field of sensory archaeology. Analysis of relevant royal inscriptions, administrative tablets, bas-reliefs and artefacts excavated from the palaces in the Assyrian capital cities of Nimrud, Khorsabad and Nineveh demonstrates that the Assyrian kings and their courtly advisors participated in activities of biopolitics. The study identifies several phenomena and features of the Assyrian world, including palaces that served as sensorial envelopes, commensal feasts, travelling processions, water-control projects and libation rituals that the Neo-Assyrian royal authority deployed in attempts to control sensory experiences. At the same time, the study reconstructs the sensory experiences of Assyrian bodies as they passed through royally curated structures and landscapes.
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Li, Qiuyuan, Yan Jiang, Nan Song, Bin Zhou, Zhao Li, and Lei Lin. "An Immune-Related Genetic Feature Depicted the Heterogeneous Nature of Lung Adenocarcinoma and Squamous Cell Carcinoma and Their Distinctive Predicted Drug Responses." Oxidative Medicine and Cellular Longevity 2022 (August 27, 2022): 1–23. http://dx.doi.org/10.1155/2022/8447083.
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One of the primary causes of global cancer-associated mortality is lung cancer (LC). Current improvements in the management of LC rely mainly on the advancement of patient stratification, both molecularly and clinically, to achieve the maximal therapeutic benefit, while most LC screening protocols remain underdeveloped. In this research, we first employed two algorithms (ESTIMATE and xCell) to calculate the immune/stromal infiltration scores. This helped identify the altered immune infiltration landscapes in lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Afterward, based on their immune-related characteristics, we successfully stratified the LUAD and LUSC into 2 and 3 clusters, respectively. Different from the conventional bioinformatic approaches that start from the investigation of differential expression of single genes, differentially enriched curated gene sets identified through gene set variation analyses (GSVA) were curated, and gene names were reconstructed afterward. Furthermore, weighted gene correlation network analyses (WGCNA) were used to reveal hub genes highly connected with the clustering process. Actual expression levels of critical hub genes among different clusters were compared and so were the functional pathways these genes enriched into. Lastly, a computational method was applied to predict and compare the responses of each cluster to primary therapeutic agents. The heterogeneity presented in our study, along with the drug responses expected for identified clusters, may shed light on future exploration of combination immunochemotherapy that facilitates the optimization of individualized therapy.
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Laming, Alice, Michael-Shawn Fletcher, Anthony Romano, Russell Mullett, Simon Connor, Michela Mariani, S. Yoshi Maezumi, and Patricia S. Gadd. "The Curse of Conservation: Empirical Evidence Demonstrating That Changes in Land-Use Legislation Drove Catastrophic Bushfires in Southeast Australia." Fire 5, no. 6 (October 26, 2022): 175. http://dx.doi.org/10.3390/fire5060175.
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Protecting “wilderness” and removing human involvement in “nature” was a core pillar of the modern conservation movement through the 20th century. Conservation approaches and legislation informed by this narrative fail to recognise that Aboriginal people have long valued, used, and shaped most landscapes on Earth. Aboriginal people curated open and fire-safe Country for millennia with fire in what are now forested and fire-prone regions. Settler land holders recognised the importance of this and mimicked these practices. The Land Conservation Act of 1970 in Victoria, Australia, prohibited burning by settler land holders in an effort to protect natural landscapes. We present a 120-year record of vegetation and fire regime change from Gunaikurnai Country, southeast Australia. Our data demonstrate that catastrophic bushfires first impacted the local area immediately following the prohibition of settler burning in 1970, which allowed a rapid increase in flammable eucalypts that resulted in the onset of catastrophic bushfires. Our data corroborate local narratives on the root causes of the current bushfire crisis. Perpetuation of the wilderness myth in conservation may worsen this crisis, and it is time to listen to and learn from Indigenous and local people, and to empower these communities to drive research and management agendas.
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Abraham, Anna. "How We Tell Apart Fiction from Reality." American Journal of Psychology 135, no. 1 (April 1, 2022): 1–18. http://dx.doi.org/10.5406/19398298.135.1.01.
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Abstract The human ability to tell apart reality from fiction is intriguing. Through a range of media, such as novels and movies, we are able to readily engage in fictional worlds and experience alternative realities. Yet even when we are completely immersed and emotionally engaged within these worlds, we have little difficulty in leaving the fictional landscapes and getting back to the day-to-day of our own world. How are we able to do this? How do we acquire our understanding of our real world? How is this similar to and different from the development of our knowledge of fictional worlds? In exploring these questions, this article makes the case for a novel multilevel explanation (called BLINCS) of our implicit understanding of the reality–fiction distinction, namely that it is derived from the fact that the worlds of fiction, relative to reality, are bounded, inference-light, curated, and sparse.
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Hart, Thomas C., and Timothy H. Ives. "Preliminary Starch Grain Evidence of Ancient Stone Tool Use at the Early Archaic (9,000 B.P.) Site of Sandy Hill, Mashantucket, Connecticut." Ethnobiology Letters 4 (September 2, 2013): 87–95. http://dx.doi.org/10.14237/ebl.4.2013.57.
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Early Archaic subsistence strategies of New England remain poorly understood despite their importance in helping researchers understand how people adapt to changing landscapes following the end of the last glacial maximum (21,000-14,000 B.P.). Excavations at the Mashantucket Pequot Reservation in Mashantucket, Connecticut during the 1990s revealed a large, semi-sedentary village nestled alongside a complex wetland ecosystem. In this paper, we present preliminary starch grain analysis of several stone tools recovered and curated from these excavations. The results of this study indicate that both transitory and reserve starch grains are preserved on these artifacts and that at least one of the artifacts may have been used for leaf or stem processing. The results of this study also demonstrate the potential for future research in which paired macrobotanical and residue analysis will allow for a better understanding of subsistence practices at the site and during the early Archaic in general.
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Corcoran-Tadd, Athena. "<> rainy days 2017." Tempo 72, no. 284 (March 20, 2018): 81–83. http://dx.doi.org/10.1017/s0040298217001334.
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Questioning whether new music is ‘losing touch’, Lydia Rilling, in her first edition as artistic director of Luxembourg's rainy days festival, curated a programme which sought, via an exploration of ‘the emotional landscapes of contemporary music’, to ‘reveal’ that this is not the case. The festival's scope extended beyond concerts to sound installations, pre- and post-concert talks, an (all female-presented) conference dedicated to the festival topic, a newly affiliated composition academy, and a closing ‘bal contemporain’ which paired Frank Zappa and Alexander Schubert with onion soup, while composers, musicologists and curators let loose after such extensive reflection upon the question that had been posed at every turn, emblazoned on the yellow telephone book-sized festival programmes (from which all quotations in this review are taken), echoed on individual concert programmes, interrogating the listener from the tickets’ fine print: how does it feel?
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Borić, Dušan, Nikola Borovinić, Ljiljana Đuričić, Jelena Bulatović, Katarina Gerometta, Dragana Filipović, Ethel Allué, Zvezdana Vušović-Lučić, and Emanuela Cristiani. "Spearheading into the Neolithic: Last Foragers and First Farmers in the Dinaric Alps of Montenegro." European Journal of Archaeology 22, no. 4 (June 26, 2019): 470–98. http://dx.doi.org/10.1017/eaa.2019.14.
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This article presents a summary of new evidence for the Mesolithic in the Dinaric Alps of Montenegro. The region is one of the best areas in south-eastern Europe to study Early Holocene foragers and the nature of the transition to Neolithic lifeways at the end of the seventh and the beginning of the sixth millennium cal bc thanks to the existence of biodiverse landscapes and numerous karstic features. We argue that harpoons found at two different sites in this regional context represent a curated technology that has its roots in a local Mesolithic cultural tradition. The continued use of this standardized hunting tool kit in the Neolithic provides an important indication about the character of the Mesolithic–Neolithic transition. We also use this regional case study to address wider questions concerning the visibility and modes of Mesolithic occupation in south-eastern Europe as a whole.
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Flynn, Jullien M., Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G. Clark, Cédric Feschotte, and Arian F. Smit. "RepeatModeler2 for automated genomic discovery of transposable element families." Proceedings of the National Academy of Sciences 117, no. 17 (April 16, 2020): 9451–57. http://dx.doi.org/10.1073/pnas.1921046117.
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The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, http://www.repeatmasker.org/RepeatModeler/).
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Xiang, Renshen, Yuhang Ge, Wei Song, Jun Ren, Can Kong, and Tao Fu. "Pyroptosis Patterns Characterized by Distinct Tumor Microenvironment Infiltration Landscapes in Gastric Cancer." Genes 12, no. 10 (September 28, 2021): 1535. http://dx.doi.org/10.3390/genes12101535.
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Background: The potential role of pyroptosis in tumor microenvironment (TME) reprogramming and immunotherapy has received increasing attention. As most studies have concentrated on a single TME cell type or a single pyroptosis regulator (PR), the overall TME cell-infiltrating characteristics mediated by the integrated roles of multiple PRs have not been comprehensively recognized. Methods: This study curated 33 PRs and conducted consensus clustering to identify distinct pyroptosis patterns in gastric cancer (GC) patients. A single-sample gene set enrichment analysis algorithm was used to quantify the infiltration density of TME immune cells and the enrichment scores of well-defined biological signatures. The pyroptosis patterns of individuals were quantified using a principal component analysis algorithm called the pyroptosis score (PS). Results: Three distinct pyroptosis patterns with significant survival differences were identified from 1422 GC samples; these patterns were closely associated with three TME cell-infiltrating landscapes—namely, the immune-inflamed, immune-excluded, and immune-desert phenotypes. The PS model generated on the basis of the pyroptosis pattern-related signature genes could accurately predict the TME status, existing molecular subtypes, genetic variation, therapeutic response, and clinical outcome; among which, a relatively high PS was highly consistent with immune activation, molecular subtypes with survival advantages, high tumor mutation burden, high microsatellite instability, and other favorable characteristics. In particular, from the Cancer Genome Atlas database, the PS model exhibited significant prognostic relevance in a pan-cancer analysis, and patients with a relatively high PS exhibited durable therapeutic advantages and better prognostic benefits in anti-PD1/L1 therapy. Conclusions: This study demonstrates that pyroptosis is prominently correlated with TME diversity and complexity, and quantification of the pyroptosis patterns of individuals will enhance our cognition of TME infiltration landscapes and help in formulating more effective immunotherapeutic strategies.
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Nicolson, Norman G., Reju Korah, and Tobias Carling. "Adrenocortical cancer cell line mutational profile reveals aggressive genetic background." Journal of Molecular Endocrinology 62, no. 4 (May 2019): 179–86. http://dx.doi.org/10.1530/jme-18-0262.
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Adrenocortical carcinomas are rare tumors with poor prognosis and limited treatment options. Although widely used as in vitro models to test novel therapeutic strategies, the adrenocortical carcinoma-derived cell lines NCI-H295R and SW-13 have only partially been described genetically. Our aim was to characterize the mutational landscape of these cells to improve their experimental utility and map them to clinical subtypes of adrenocortical carcinoma. Genomic DNA from NCI-H295R and SW-13 cells was subjected to whole-exome sequencing. Variants were filtered for non-synonymous mutations and curated for validated adrenocortical and pan-cancer driver gene mutations. Genes mutated in the cell lines were mapped using gene ontology and protein pathway tools to determine signaling effects and compared to mutational and clinical characteristics of 92 adrenocortical carcinoma cases from The Cancer Genome Atlas. NCI-H295R and SW-13 cells carried 1325 and 1836 non-synonymous variants, respectively. Of these, 61 and 76 were known cancer driver genes, of which 32 were shared between cell lines. Variant interaction analyses demonstrated dominant TP53 dysregulation in both cell lines complemented by distinct WNT (NCI-H295R) and chromatin remodeling (SW-13) pathway perturbations. Both cell lines genetically resemble more aggressive adrenocortical carcinomas with worse prognosis, for which development of targeted therapies is most critical. Careful incorporation of the genetic landscapes outlined in this study will further the in vitro utility of these cell lines in testing for novel therapeutic approaches for adrenocortical malignancy.
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Micieli-Voutsinas, Jacque, and Julia Cavicchi. "Toxic landfills, survivor trees, and dust cloud memories: More-than-human ecologies of 9/11 memory." Environment and Planning D: Society and Space 37, no. 3 (January 15, 2019): 504–22. http://dx.doi.org/10.1177/0263775818820325.
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The symbolic power of grass, trees, flowers, stones, water, and other everyday objects to evoke more-than-human experiences is a cornerstone of memorial practice. As survivors of traumatic events, nonhuman elements have long been preserved in, even added to, memorial landscapes for their representational capacities to “say what cannot be said.” Beyond their mobilization as passive symbols, the plants themselves also exert a “creative presence” that equally shapes memorial sites, wherein ecologies of memory are negotiated and coconstituted through human and nonhuman lives. In foregrounding ecologies of “9/11” memory and memorialization, this essay draws on more-than-human approaches that emphasize how both human and nonhuman matter and memory emerge from and transform each other in and around lower Manhattan. At the World Trade Center, both human and nonhuman experiences of violence and violation are implicated in the “ecologies of memory” preserved and curated at the site. Focusing on ecologies of 9/11 commemoration, we argue that spatially fixed narratives of trauma obfuscate the environmentally diffuse human victims of the September 11th terror attacks, as well as how nonhuman actors coconstitute, contradict, and transform these memorial spaces. We argue that these memorial spaces employ the affective power of nonhuman actors to reproduce exclusionary narratives of cultural trauma, while obscuring very real environmentally diffuse human victims and ongoing harms, domestically and abroad. As a result of these negotiations, divergent forms of “slow violence” are rendered visible within the memorial landscape.
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frisk, henrik, and miya yoshida. "new communications technology in the context of interactive sound art: an empirical analysis." Organised Sound 10, no. 2 (August 2005): 121–27. http://dx.doi.org/10.1017/s1355771805000762.
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in this article we discuss the notion of ‘interaction’, ‘participation’ and ‘the public’ in artistic work, specifically within the context of the exhibition the invisible landscapes (curated by miya yoshida, malmö konstmuseum, 2003) and ethersound (created by henrik frisk), a sound installation displayed in that exhibition. in this work the audience is invited to participate in the creation of new sound events by sending text messages from their mobile phones. thus, our discussion is focused on the space and the mode of participation opened up by new communication technology. based on our experiences of that project, we introduce and explain what we believe are relations of creative production and a different kind of creativity that may emerge from active interaction. we also attempt to describe what we believe an implementation of active public participation can lead to.we are combining two modes of thinking in this article; one is inspired by a discourse of cultural theories and the other by reflection on our experience of the event. the latter is, by definition, rather subject centred and expansive based on individual observation. we examine and analyse the phenomenon of ‘participation’ whilst playing ethersound as a process of creative production, and seek to reflect upon the power of the co-operative practice and its relation to participation and creativity.
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Prakash, Harish, R. Suresh Kumar, Bibhuti Lahkar, Raman Sukumar, Abi T. Vanak, and Maria Thaker. "Animal movement ecology in India: insights from 2011–2021 and prospective for the future." PeerJ 10 (December 13, 2022): e14401. http://dx.doi.org/10.7717/peerj.14401.
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The field of animal movement ecology has advanced by leaps and bounds in the past few decades with the advent of sophisticated technology, advanced analytical tools, and multiple frameworks and paradigms to address key ecological problems. Unlike the longer history and faster growth of the field in North America, Europe, and Africa, movement ecology in Asia has only recently been gaining momentum. Here, we provide a review of the field from studies based in India over the last 11 years (2011–2021) curated from the database, Scopus, and search engine, Google Scholar. We identify current directions in the research objectives, taxa studied, tracking technology and the biogeographic regions in which animals were tracked, considering the years since the last systematic review of movement ecology research in the country. As an indication of the growing interest in this field, there has been a rapid increase in the number of publications over the last decade. Class Mammalia continues to dominate the taxa tracked, with tiger and leopard being the most common species studied across publications. Invertebrates and other small and medium-sized animals, as well as aquatic animals, in comparison, are understudied and remain among the important target taxa for tracking in future studies. As in the previous three decades, researchers have focussed on characterising home ranges and habitat use of animals. There is, however, a notable shift to examine the movement decision of animals in human-modified landscapes, although efforts to use movement ecology to understand impacts of climate change remain missing. Given the biogeographic and taxonomic diversity of India, and the fact that the interface between anthropogenic activity and wildlife interactions is increasing, we suggest ways in which the field of movement ecology can be expanded to facilitate ecological insights and conservation efforts. With the advancement of affordable technologies and the availability of analytical tools, the potential to expand the field of movement ecology, shift research foci, and gain new insights is now prime.
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Salama, Ashraf M., and Anna Katharina Grichting. "Edge, Center, and Spine: Exploring the Multi-Dimentionality of Contemporary Landscapes in Middle Eastern Cities." International Journal of Architectural Research: ArchNet-IJAR 9, no. 2 (July 13, 2015): 113. http://dx.doi.org/10.26687/archnet-ijar.v9i2.791.
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This paper offers an overview of landscape interventions in three Middle Eastern cities and a positional interpretation of the way in which different landscape typologies can contribute to their socio-spatial and environmental contexts. The paper identifies three levels of contribution of contemporary landscape – edge, center, and spine - corresponding to three landscape typologies: the edge typology is a linear coastal landscape that acts as an interface between the city and the sea; the central typology is a city park that reactivates or regenerates a fragment of the city and communities that surround it; and the spine is an ecological infrastructure – a wadi - that articulates and curates the natural and constructed flow of water creating productive landscapes and public spaces. In undertaking the discussion and analysis, a multi-layered general methodology was employed. First, to induct generalities on three projects identified a literature review and analysis of development and technical review reports is conducted in order to elucidate a considerable number of issues underlying each landscape typology while classifying them under three main sub-headings that include contextual background, evolutionary design and planning aspects, and key spatial design features. Second, to deduct particularities concerning the contribution of each typology, critical discussion, reflection, and reference to some empirical studies are carried out with the intention of unveiling the contribution of each typology to its context and to the city within which it exists.
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Chitrabongs, Chittawadi. "Curartistry: Curating Everyday Artistry in Bangkok." Nakhara : Journal of Environmental Design and Planning 21, no. 1 (June 10, 2022): 208. http://dx.doi.org/10.54028/nj202221208.
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How can architecture be taught internationally, beyond the neocolonialist tendency of European-based international exchange programs? Curartistry, a method of curating everyday artistry in Bangkok, is used to achieve bilateral exchanges in art and architectural education between teachers and students of different nationalities. We offer interpretations of late-nineteenth-century and post-war ideas of “everyday life,” based especially on Charles Baudelaire’s “The Painter of Modern Life,” Henry Lefebvre’s “Critique of Everyday Life,” Maurice Blanchot and Susan Hanson’s “Everyday Speech,” and Walter Benjamin’s “On Some Motifs in Baudelaire.” Their ideas grew out of their experiences in Western European metropolises, and continue to reflect similar conditions in twenty-first-century Bangkok. In addition to these literary works, Henry W. Lawrence’s City Trees: A Historical Geography from the Renaissance through the Nineteenth Century has been useful in the development of our workshop entitled, “Curartistry: Trees in Bangkok.”
Curartistry is a practice in which particular elements of a city are researched and recorded in drawing and photography. We invite students to visit overlooked sites, landscapes, and trees in Bangkok, and then to write and rewrite until a particular object or installation emerges from redrafting their experiences. These records lead to the proposal of projects, whether artistically, architecturally or otherwise crafted. Once a proposal takes on the form of a project, its existence as a project, rather than as a finished artwork or artefact, is what lends the project criteria for judging it. Outcomes from these projects typically take the form of an elementary installation or exhibition, presented by individual students to guest critics.
In this article, we discuss the processes of work, and how everyday artistry in Bangkok is curated in relation to the selected ideas of “everyday life” that transcend time and place, as well as the construction of our method of work. Curartistry is a key way in which we are addressing fundamental issues of city life such as social inequality, nature, ecological crises, labour, and materiality. The final outcomes often address a number of issues, such as the intense relationship between nature and city, dramatic effects in light and colour, transplantation, or tree names in relation to Thai beliefs in fortune. It is hoped that this attempt to systematically document the subjective experiences of urban life will be read as a contribution to global architectural education.
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Lahelma, Marja. "Curator: Mai Britt Guleng: Harald Sohlberg. Infinite Landscapes." Kunst og Kultur 102, no. 01 (April 1, 2019): 77–79. http://dx.doi.org/10.18261/issn.1504-3029-2019-01-06.
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Stourac, Jan, Juraj Dubrava, Milos Musil, Jana Horackova, Jiri Damborsky, Stanislav Mazurenko, and David Bednar. "FireProtDB: database of manually curated protein stability data." Nucleic Acids Research 49, no. D1 (November 9, 2020): D319—D324. http://dx.doi.org/10.1093/nar/gkaa981.
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Abstract The majority of naturally occurring proteins have evolved to function under mild conditions inside the living organisms. One of the critical obstacles for the use of proteins in biotechnological applications is their insufficient stability at elevated temperatures or in the presence of salts. Since experimental screening for stabilizing mutations is typically laborious and expensive, in silico predictors are often used for narrowing down the mutational landscape. The recent advances in machine learning and artificial intelligence further facilitate the development of such computational tools. However, the accuracy of these predictors strongly depends on the quality and amount of data used for training and testing, which have often been reported as the current bottleneck of the approach. To address this problem, we present a novel database of experimental thermostability data for single-point mutants FireProtDB. The database combines the published datasets, data extracted manually from the recent literature, and the data collected in our laboratory. Its user interface is designed to facilitate both types of the expected use: (i) the interactive explorations of individual entries on the level of a protein or mutation and (ii) the construction of highly customized and machine learning-friendly datasets using advanced searching and filtering. The database is freely available at https://loschmidt.chemi.muni.cz/fireprotdb.
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Flanagan, Pamela. "The curated representation of Saga Norén: Interweaving narratives of fashion and interiors." Film, Fashion & Consumption 9, no. 1 (May 1, 2020): 99–124. http://dx.doi.org/10.1386/ffc_00014_1.
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Abstract Nordic Noir dramas have dominated the landscape of contemporary television, transforming the crime genre beyond the traditional English-speaking productions whilst forging a path for female protagonists to dominate. This article seeks to analyse the relationship between the narrative, fashion and interiors through the main female protagonist Saga Noren (Sofia Helin) in Bron/Broen (The Bridge) (2011‐18), the Danish-Swedish production of the Nordic Noir drama.
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Tumuluru, Sravya, James Godfrey, Jovian Yu, Alan Cooper, Xiufen Chen, Gerben Duns, Sonali M. Smith, Christian Steidl, and Justin Kline. "Integrative Genomic Analysis Uncovers Unique Diffuse Large B Cell Lymphoma (DLBCL) Immune Environments and Identifies Associations with Specific Oncogenic Alterations." Blood 138, Supplement 1 (November 5, 2021): 449. http://dx.doi.org/10.1182/blood-2021-153724.
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Abstract Introduction: Most patients diagnosed with diffuse large B cell lymphoma (DLBCL) are cured with combination chemoimmunotherapy, but 40% will develop relapsed or refractory (r/r) disease, which is often associated with a poor clinical outcome. PD-1 blockade therapy has been investigated in r/r DLBCL; however, response rates in unselected DLBCL patients are disappointing, highlighting the need for deeper understanding of DLBCL immune landscapes, as well as mechanisms that regulate the immune response to checkpoint blockade therapy (CBT) in this disease. In solid cancers, tumor-cell intrinsic oncogenic signaling strongly influences the immune environment and impacts clinical response to CBT. Despite the recent publication of large-scale genomic datasets in DLBCL, the impact of oncogenic signaling on the immune environment remains to be fully elucidated. In this study, we aimed to characterize immune landscapes associated with DLBCL, as well as the role of lymphoma-intrinsic alterations on shaping the immune environment in this disease. Methods: Using gene set variation analysis (GSVA) in a large cohort of primary DLBCLs (n = ~900), a sample-wise enrichment score was generated for gene sets associated with tumor infiltrating lymphocytes. Gene sets were manually curated to include signatures relating to IFNγ response, T helper cell subsets, CD8 + T cell exhaustion, macrophages, and dendritic cells. A DLBCL cell-of-origin (COO) signature was also included in the GSVA to control for the transcriptional and genomic effects of COO. Samples were hierarchically clustered into related groups. Multispectral immunofluorescence (mIF) for canonical T cell markers was used to confirm GSVA clustering. To mechanistically validate our findings, CRISPR/Cas9 gene editing was used to modulate candidate oncogenes and tumor suppressors genes (TSGs) in the syngeneic A20 murine lymphoma model. Results: GSVA performed on transcriptomes from a large genomic DLBCL dataset revealed four distinct DLBCL immune clusters, termed "ABC hot", "ABC cold", "GCB hot" and "GCB cold", defined by differential expression scores of immune related gene sets (Fig 1A). Concordant with our previous work, DLBCLs with PD-L1 gene amplifications, which are associated with a "T-cell inflamed" tumor microenvironment, were enriched in the "ABC hot" cluster (Fig 1B). Conversely, double hit signature DLBCLs, known to be associated with decreased immune cell infiltration and a GCB COO, were enriched in "GCB cold" DLBCLs (Fig 1C). In an internal cohort of diagnostic DLBCL samples (n = 90) for whom RNA sequencing (RNAseq) and FFPE tissue were available, mIF analysis showed that both "ABC hot" and "GCB hot" DLBCLs had significantly higher ratios of CD8 + T cells to lymphoma cells compared to cold DLBCLs. "ABC hot" DLBCLs also had a significantly higher CD4 + T cell to lymphoma cell ratio (Fig 1D). Importantly, several mutations that correlated with particular DLBCL immune clusters were identified. The "ABC cold" cluster was significantly enriched for loss-of-function (LOF) mutations in TMEM30A and MYD88, whereas LOF mutations in ATM and FOXO1 were commonly observed in "GCB cold" DLBCLs. Finally, LOF mutations in SOCS1 and B2M were significantly enriched in "GCB hot" DLBCLs (Fig 1E, 1F). As LOF SOCS1 mutations were strongly associated with "GCB hot" DLBCLs and are also prevalent in other CBT-sensitive lymphomas, we hypothesized that SOCS1 LOF mutations would enhance lymphoma cell vulnerability to CBT due to increased IFNγ sensitivity resulting from unopposed JAK/STAT activation. To test this hypothesis, we generated Socs1 deficient A20 lymphoma cells. Compared to A20 WT, A20 Socs1-/- cells were characterized by increased pStat1 levels upon IFNγ stimulation (Fig 1G). Interestingly, A20 Socs1-/- tumors showed increased sensitivity to α-PD1 therapy compared to A20 WT in syngeneic hosts. Together, these data suggest that tumor-cell intrinsic JAK/STAT activation via SOCS1 -/- increases lymphoma cell sensitivity to IFNγ and α-PD1 therapy (Fig 1H). Conclusion: We have developed a novel immunogenomic platform to define the role of tumor-cell intrinsic alterations on the immune landscape of DLBCL. Confirmatory studies using in vitro and in vivo models validated the effect of key oncogenes and TSGs on the tumor microenvironment, and suggest these candidate genes may impact response to CBT in DLBCL. Figure 1 Figure 1. Disclosures Smith: Alexion, AstraZeneca Rare Disease: Other: Study investigator; Celgene, Genetech, AbbVie: Consultancy. Steidl: Trillium Therapeutics: Research Funding; Curis Inc.: Consultancy; Epizyme: Research Funding; Seattle Genetics: Consultancy; Bayer: Consultancy; AbbVie: Consultancy; Bristol-Myers Squibb: Research Funding. Kline: Seagen: Membership on an entity's Board of Directors or advisory committees; Morphosys: Consultancy, Membership on an entity's Board of Directors or advisory committees; Kite/Gilead: Speakers Bureau; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy, Research Funding; Verastem: Research Funding; SecuraBio: Membership on an entity's Board of Directors or advisory committees; Regeneron: Membership on an entity's Board of Directors or advisory committees.
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Ratliff, Jeffrey, Jason Crowell, Stacey L. Clardy, and Ted Burns. "Innovations in on-demand audio education." Neurology 94, no. 14 (March 4, 2020): 621–24. http://dx.doi.org/10.1212/wnl.0000000000009221.
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The evolution of broadcast audio has been rapidly changing over the past 10–15 years with the advent of podcasts in the early 2000s. As with other media, podcast audio has been adapted for use within medical and specifically neurology education in the form of the Neurology Podcast since 2007. As podcasts were an initial step in the field of on-demand media, further technological evolution has resulted in increasing customization of a listener's audio experience. We believe a historical inflection point has been reached with the increasingly mainstream adoption of virtual assistant technology which allows for consumption of brief on-demand self-curated audio productions. As editors of the Neurology Podcast, we have introduced a new audio product to this technological landscape, the Neurology Minute. In doing so, we hope that curated on-demand educational audio will become a part of the daily routine of many practicing neurologists as we move into this new technological age.
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Alrifai, Taha, Natasha Edwin, Dale L. Bixby, Adam John Hockenberry, Emmanuel Okeke, Brett Mahon, Duane C. Hassane, Sari Heitner Enschede, Melissa Larson, and Jamile M. Shammo. "Assessing the Role of BCOR/BCORL1 and Other Historically Low-Frequency Somatic Mutations in Myelodysplastic Syndromes." Blood 138, Supplement 1 (November 5, 2021): 4647. http://dx.doi.org/10.1182/blood-2021-147470.
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Abstract Background: Myelodysplastic syndromes (MDS) represent a heterogeneous group of malignancies that are characterized by aberrant hematopoiesis and consequently abnormal blood counts. Patients with MDS have an increased likelihood of developing acute myeloid leukemia (AML). Next generation sequencing (NGS) is currently being used to study the genetic landscapes of diverse cancer types in finer detail than has previously been possible, owing to its ease-of-use and widespread availability. Crucially, the accuracy and broad breadth of genomic coverage provided by NGS approaches may permit the study of mutations that are rare in MDS patients, yet well studied in AML or other cancer types. Based on the fact that much less is known about particular rare somatic mutations in MDS, we decided to investigate 6 genes. IDH1 and IDH2 are targetable in patients with AML. Mutations in JAK2 are found in high proportions in patients with myeloproliferative neoplasms (MPNs) or MDS/MPN overlap neoplasms. Finally, other mutations in genes such as BCOR, BCORL1, and MUTYH also occur in MDS patients with appreciable-but generally low-frequencies such that their overall impact on MDS patients is largely unknown. Methods: We utilized the Tempus LENS platform to retrospectively characterize 236 MDS patients who underwent genomic-testing with the Tempus|xT assay (DNA-seq of 595-648 genes at 500x coverage; full transcriptome RNA-seq; data accessed on 06/28/2021). The patient population was 28% female, with a median age of 71.6 years. Mutations identified included germline and/or somatic single nucleotide variants (though we only considered somatic variants in this study), insertions/deletions and copy number variations (gains defined as ≥8 copies). For a subset of patients processed at Rush University Medical Center (RUMC), we additionally performed a curated clinical investigation into laboratory variables, prognostic data, treatment history and outcomes data. Results: Within the Tempus MDS dataset, we observed a range of mutation frequencies. In total, 58 patients had mutations in at least one of either: JAK2, BCOR, IDH2, IDH1, BCORL1, and MUTYH. When comparing the observed frequencies against values that have previously been reported, mutations in these 6 genes occurred with higher frequency in our dataset while most other mutations were in accordance with the relative frequencies reported by other sources (Table 1). We observed the largest deviation from expectation for BCOR. Whereas prior reports list this mutation as occurring with a frequency of <5%, greater than 10% of the records we analyzed contained a mutation in either BCOR (n=24, 10.16%) or BCORL1 (n=6, 2.54%). Four records in the dataset had mutations in both BCOR and BCORL1; a total of 26 records (11%) thus contained mutations in one of these two genes. Of these 26 patients, 50% were female and the median age was 70 years. The most commonly observed co-mutations with BCOR/BCORL1 were-in order of frequency-RUNX1 (50%), ASXL1 (23%), DNMT3A (23%), SF3B1 (19%), and STAG2 (19%). Additional data were derived from detailed clinical investigation into a limited subset of 4 patients who were treated at RUMC and who had mutations in either BCOR or BCORL1. Revised International Prognostic Scoring System (IPSS-R) scores were: high/very high (2) and low (2). Three of the four patients displayed complex karyotypes and three of the four progressed to AML. Conclusions: We identified a higher frequency of BCOR/BCORL1 mutations among patients with MDS than has been previously reported. At the same time, most other mutation frequencies were in relative accordance with existing reports. We observed complex cytogenetic abnormalities in 75% of patients for which we had extensive clinical information. Our data suggest an association between BCOR/BCORL1 mutations and complex karyotypes, a finding that may establish a prognostic role of BCOR/BCORL1 and have potential therapeutic implications. This hypothesis is, however, subject to further investigation and will require larger sample sizes that are likely to become available with the rapidly increasing utilization of next generation sequencing techniques and availability of high-quality, curated clinical information. Figure 1 Figure 1. Disclosures Hockenberry: Tempus Labs, Inc: Current Employment, Current holder of stock options in a privately-held company. Okeke: Tempus Labs, Inc: Current Employment. Mahon: Tempus Labs, Inc: Current Employment. Hassane: Tempus Labs, Inc: Current Employment. Enschede: Tempus Labs, Inc: Current Employment, Current holder of stock options in a privately-held company. Shammo: Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; Astra zeneca: Research Funding; CTI pharma: Research Funding; Stemline therapeutics: Research Funding; Kartos Pharma: Research Funding; Takeda: Consultancy, Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company, Honoraria, Research Funding; Abbvie: Current holder of individual stocks in a privately-held company, Research Funding; Baxter: Current holder of stock options in a privately-held company; sanofi: Consultancy, Honoraria, Speakers Bureau; NS Pharma: Membership on an entity's Board of Directors or advisory committees; Incyte: Consultancy, Honoraria, Research Funding, Speakers Bureau; BMS: Consultancy, Honoraria, Research Funding, Speakers Bureau; Apellis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Alexion: Consultancy, Honoraria, Research Funding, Speakers Bureau.
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Jain, Neha, Kathleen F. Mittendorf, Marilyn Holt, Michele Lenoue-Newton, Ian Maurer, Clinton Miller, Matthew Stachowiak, et al. "The My Cancer Genome clinical trial data model and trial curation workflow." Journal of the American Medical Informatics Association 27, no. 7 (June 1, 2020): 1057–66. http://dx.doi.org/10.1093/jamia/ocaa066.
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Abstract Objective As clinical trials evolve in complexity, clinical trial data models that can capture relevant trial data in meaningful, structured annotations and computable forms are needed to support accrual. Material and Methods We have developed a clinical trial information model, curation information system, and a standard operating procedure for consistent and accurate annotation of cancer clinical trials. Clinical trial documents are pulled into the curation system from publicly available sources. Using a web-based interface, a curator creates structured assertions related to disease-biomarker eligibility criteria, therapeutic context, and treatment cohorts by leveraging our data model features. These structured assertions are published on the My Cancer Genome (MCG) website. Results To date, over 5000 oncology trials have been manually curated. All trial assertion data are available for public view on the MCG website. Querying our structured knowledge base, we performed a landscape analysis to assess the top diseases, biomarker alterations, and drugs featured across all cancer trials. Discussion Beyond curating commonly captured elements, such as disease and biomarker eligibility criteria, we have expanded our model to support the curation of trial interventions and therapeutic context (ie, neoadjuvant, metastatic, etc.), and the respective biomarker-disease treatment cohorts. To the best of our knowledge, this is the first effort to capture these fields in a structured format. Conclusion This paper makes a significant contribution to the field of biomedical informatics and knowledge dissemination for precision oncology via the MCG website. Key words knowledge representation, My Cancer Genome, precision oncology, knowledge curation, cancer informatics, clinical trial data model
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Poll, Brian G., Lihe Chen, Chung-Lin Chou, Viswanathan Raghuram, and Mark A. Knepper. "Landscape of GPCR expression along the mouse nephron." American Journal of Physiology-Renal Physiology 321, no. 1 (July 1, 2021): F50—F68. http://dx.doi.org/10.1152/ajprenal.00077.2021.
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Kidney transport and other renal functions are regulated by multiple G protein-coupled receptors (GPCRs) expressed along the renal tubule. The rapid, recent appearance of comprehensive unbiased gene expression data in the various renal tubule segments, chiefly RNA sequencing and protein mass spectrometry data, has provided a means of identifying patterns of GPCR expression along the renal tubule. To allow for comprehensive mapping, we first curated a comprehensive list of GPCRs in the genomes of mice, rats, and humans ( https://hpcwebapps.cit.nih.gov/ESBL/Database/GPCRs/ ) using multiple online data sources. We used this list to mine segment-specific and cell type-specific expression data from RNA-sequencing studies in microdissected mouse tubule segments to identify GPCRs that are selectively expressed in discrete tubule segments. Comparisons of these mapped mouse GPCRs with other omics datasets as well as functional data from isolated perfused tubule and micropuncture studies confirmed patterns of expression for well-known receptors and identified poorly studied GPCRs that are likely to play roles in the regulation of renal tubule function. Thus, we provide data resources for GPCR expression across the renal tubule, highlighting both well-known GPCRs and understudied receptors to provide guidance for future studies.
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LI, Yuhan. "CURATED VIEWSHEDS— LANDSCAPE PLANNING AND DESIGN OF THE MOUNT KUMGANG INTERNATIONAL TOURIST ZONE ON THE KOREAN PENINSULA." Landscape Architecture Frontiers 7, no. 5 (2019): 156. http://dx.doi.org/10.15302/j-laf-1-050008.
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Atkinson, John A. "Ben Lawers, an archaeological landscape in time." Scottish Archaeological Internet Reports, no. 62 (2016): 1–285. http://dx.doi.org/10.9750/issn.2056-7421.2016.62.1-285.
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This volume presents the results of archaeological investigations between 1996 and 2005, carried out as part of the Ben Lawers Historic Landscape Project, a multi-disciplinary project based on north Loch Tayside in the Central Highlands of Scotland (NGR: NN 63763 41298). Archaeological surveys and excavations formed the core of the Ben Lawers Project, but many other disciplines also contributed to researching this landscape. Some of these partner projects are reported here, while others have been presented elsewhere (Tipping et al 2009), and some have formed part of doctoral research projects (Watters 2007). The results of the 13 field seasons, particularly the nine evaluation and excavation seasons, together with the results of the partner projects, specialist studies and scientific analyses, have provided a body of evidence which permits the story of the land of Lawers to be told. The historical continuum in that story can be used to curate and manage this landscape for generations to come.
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Yang, Jing, Jonathan Hale, and Toby Blackman. "How do buildings talk? Embodied experience in the Rolex Learning Centre." Architectural Research Quarterly 25, no. 1 (March 2021): 83–92. http://dx.doi.org/10.1017/s1359135521000129.
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The Venice Architecture Biennale in 2010, curated by Japanese architect Kazuyo Sejima, co-founder of Tokyo-based practice SANAA, included a remarkable twenty-four-minute 3D film by the German director Wim Wenders depicting the practice’s Rolex Learning Centre in Switzerland. Entitled If Buildings Could Talk, the film ran in a continuous loop, without a tangible beginning or end, much like the building itself. Invited by SANAA to develop the film, Wenders found himself confronted with a new type of space that he had no prior experience of, and no vocabulary to describe: ‘The Rolex Learning Centre’, said Wenders during a talk given at the Biennale, ‘is more landscape than building.’
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Valente, Rossana. "Guy D. R. Sanders, Jennifer Palinkas, Ioulia Tzonou-Herbst, with James Herbst. Ancient Corinth: Site Guide, 7th Edition. pp. 208, with col. plates. 2018. Princeton NJ: The American School of Classical Studies at Athens. ISBN 978-0-87661-661-1, hardcover." Journal of Greek Archaeology 5 (January 1, 2020): 625–29. http://dx.doi.org/10.32028/jga.v5i.470.
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Since the beginning of the excavations in Ancient Corinth by the American School of Classical Studies at Athens in 1896, a multi-period, intricate stratigraphy of the urban landscape of this site has been unravelled. This century-long history of excavations in Ancient Corinth has been previously disseminated by six editions of the site guide published by the American School of Classical Studies at Athens. Previous editions were curated by the ASCSA director Rhys Carpenter in 1928 and in 1933; the scholar Charles Morgan in 1936; Oscar Broneer in 1947 and 1951, whose 1951 edition was revisited by Robert Scranton in 1954; and, finally, Corinth director Henry Robinson in 1960.
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Logan, Zachari, and Wayne Baerwaldt. "Interview with guest editor Wayne Baerwaldt." Public 31, no. 62 (December 1, 2020): 182–90. http://dx.doi.org/10.1386/public_00046_1.
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The interview with curator and guest editor Wayne Baerwaldt and artist, Zachari Logan pertains to questions about the nature of Logan’s visual art practice in relation to gender, sexuality and intersecting issues of queer embodiment and landscape.
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Hoffos, David, and Margo Henry. "Art." Public 31, no. 62 (December 1, 2020): 240. http://dx.doi.org/10.1386/public_00053_5.
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The interview with curator and guest editor Wayne Baerwaldt and artist, Zachari Logan pertains to questions about the nature of Logan’s visual art practice in relation to gender, sexuality and intersecting issues of queer embodiment and landscape.
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Jain, Neha M., Marilyn Holt, Christine Micheel, and Mia Levy. "Landscape Analysis of Breast Cancer and Acute Myeloid Leukemia Trials Using the My Cancer Genome Clinical Trial Data Model." JCO Clinical Cancer Informatics, no. 5 (September 2021): 975–84. http://dx.doi.org/10.1200/cci.21.00082.
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PURPOSE The field of oncology is expanding rapidly. New trials are opening as an increasing number of therapeutic agents are being investigated before they can become approved therapies. Aggregate views of these data, particularly data associated with diseases, biomarkers, and drugs, can be helpful in understanding the trends in current research as well as existing gaps in cancer care. METHODS In this paper, we performed a landscape analysis for breast cancer and acute myeloid leukemia related trials with structured, curated data from clinical trials using the My Cancer Genome clinical trial knowledgebase. RESULTS We have performed detailed analytics on breast cancer (N = 1,128) and acute myeloid leukemia trial sets (N = 483) to highlight the top biomarkers, drug classes, and drugs—thereby supporting a full view of biomarkers, biomarker groups, and drugs that are currently being explored in these respective diseases. CONCLUSION Analysis and data visualization of the cancer clinical trial landscape can inform strategic planning for new trial designs and trial activation at a particular site.
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Baas, Jeroen, Michiel Schotten, Andrew Plume, Grégoire Côté, and Reza Karimi. "Scopus as a curated, high-quality bibliometric data source for academic research in quantitative science studies." Quantitative Science Studies 1, no. 1 (February 2020): 377–86. http://dx.doi.org/10.1162/qss_a_00019.
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Scopus is among the largest curated abstract and citation databases, with a wide global and regional coverage of scientific journals, conference proceedings, and books, while ensuring only the highest quality data are indexed through rigorous content selection and re-evaluation by an independent Content Selection and Advisory Board. Additionally, extensive quality assurance processes continuously monitor and improve all data elements in Scopus. Besides enriched metadata records of scientific articles, Scopus offers comprehensive author and institution profiles, obtained from advanced profiling algorithms and manual curation, ensuring high precision and recall. The trustworthiness of Scopus has led to its use as bibliometric data source for large-scale analyses in research assessments, research landscape studies, science policy evaluations, and university rankings. Scopus data have been offered for free for selected studies by the academic research community, such as through application programming interfaces, which have led to many publications employing Scopus data to investigate topics such as researcher mobility, network visualizations, and spatial bibliometrics. In June 2019, the International Center for the Study of Research was launched, with an advisory board consisting of bibliometricians, aiming to work with the scientometric research community and offering a virtual laboratory where researchers will be able to utilize Scopus data.
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Li, Xing, Almudena Martinez-Fernandez, Katherine A. Hartjes, Jean-Pierre A. Kocher, Timothy M. Olson, Andre Terzic, and Timothy J. Nelson. "Transcriptional atlas of cardiogenesis maps congenital heart disease interactome." Physiological Genomics 46, no. 13 (July 1, 2014): 482–95. http://dx.doi.org/10.1152/physiolgenomics.00015.2014.
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Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease.
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Davis, Allan Peter, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Jolene Wiegers, Thomas C. Wiegers, and Carolyn J. Mattingly. "Comparative Toxicogenomics Database (CTD): update 2021." Nucleic Acids Research 49, no. D1 (October 17, 2020): D1138—D1143. http://dx.doi.org/10.1093/nar/gkaa891.
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Abstract The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures to advance understanding about human health. Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions. In this biennial update, we report a 20% increase in CTD curated content and now provide 45 million toxicogenomic relationships for over 16 300 chemicals, 51 300 genes, 5500 phenotypes, 7200 diseases and 163 000 exposure events, from 600 comparative species. Furthermore, we increase the functionality of chemical–phenotype content with new data-tabs on CTD Disease pages (to help fill in knowledge gaps for environmental health) and new phenotype search parameters (for Batch Query and Venn analysis tools). As well, we introduce new CTD Anatomy pages that allow users to uniquely explore and analyze chemical–phenotype interactions from an anatomical perspective. Finally, we have enhanced CTD Chemical pages with new literature-based chemical synonyms (to improve querying) and added 1600 amino acid-based compounds (to increase chemical landscape). Together, these updates continue to augment CTD as a powerful resource for generating testable hypotheses about the etiologies and molecular mechanisms underlying environmentally influenced diseases.
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Smith, Huhana. "Hei Wai Ora: A Photo Essay." International Journal of Cultural Property 15, no. 2 (May 2008): 181–88. http://dx.doi.org/10.1017/s0940739108080119.
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The images presented document aspects of progress and growth for a significant wetland and coastal restoration project taking place at Kuku, Horowhenua, southwest coast of North Island, Aotearoa, New Zealand. The work is undertaken by representatives from various hapū known as Ngäti Te Rangitäwhia, Te Mateawa, Ngäti Manu, and Ngäti Kapumanawawhiti ki Kuku, who are affiliates of a larger tribal group, or iwi, Ngäti Tükorehe. The research project (undertaken while working as senior curator Mätauranga Mäori at the Museum of New Zealand Te Papa Tongarewa, Wellington) links cultural landscape issues and activities to the concerns for cultural property as revered taonga with special qualities within museum collections. The term taonga is relevant to understanding culturally venerated items within museum holdings while honoring their associated peoples, tribal lands, and waterways from where they derive. As significant cultural material, taonga are valued because of their associations. Cultural landscapes are also well regarded as land-, sea-, and water-based taonga—an encompassing term that denotes their intrinsic value and intricate natural, cultural, and spiritual interrelationships. As museum professionals rethink cultural property issues in different ways, the academic research has also embraced the concept of land- and water-based taonga to bolster ecological, cultural, and spiritual contexts that persist in ancestral lands in tribal tenure.
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Pérez, Serge, François Bonnardel, Frédérique Lisacek, Anne Imberty, Sylvie Ricard Blum, and Olga Makshakova. "GAG-DB, the New Interface of the Three-Dimensional Landscape of Glycosaminoglycans." Biomolecules 10, no. 12 (December 11, 2020): 1660. http://dx.doi.org/10.3390/biom10121660.
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Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG and GAG-protein complexes determined by X-ray single-crystal diffraction methods, X-ray fiber diffractometry, solution NMR spectroscopy, and scattering data often associated with molecular modeling. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to the description of the bound glycan ligands using simple graphical representation and numerical format for cross-referencing to other databases in glycoscience and functional data. GAG-DB provides detailed information on GAGs, their bound protein ligands, and features their interactions using several open access applications. Binding covers interactions between monosaccharides and protein monosaccharide units and the evaluation of quaternary structure. GAG-DB is freely available.
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Hoskins, Emily L., Eric Samorodnitsky, Michele R. Wing, Julie W. Reeser, Julia Hopkins, Karthikeyan Murugesan, Zheng Kuang, et al. "Abstract 761: Pan-cancer landscape and impact of PD-L1 and PD-L2 structural variation." Cancer Research 82, no. 12_Supplement (June 15, 2022): 761. http://dx.doi.org/10.1158/1538-7445.am2022-761.
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Abstract Purpose PD-1 receptor and ligand interactions are the target of immunotherapies across 16 cancer types. Biomarkers that predict response to immunotherapy are microsatellite instability, tumor mutational burden and PD-L1 immunohistochemistry. Structural variations in PD-L1 (CD274) and PD-L2 (PDCD1LG2) have been observed across cancer, but the full landscape is unknown. Here we describe the genomic landscape of PD-L1 and PD-L2 structural variation, their potential impact on the tumor microenvironment and evidence that patients with these alterations can benefit from immunotherapy. Methods We analyzed sequencing data from cancer cases with PD-L1 (CD274) and PD-L2 (PDCD1LG2) structural variations across published data, The Cancer Genome Atlas (TCGA) and the Oncology Research Information Exchange Network. From TCGA we obtained copy number status through cBioPortal, gene expression using TCGABiolinks and PD-L1 structural variations identified by Kataoka et al. Gene fusions were detected in ORIEN using STAR-Fusion and Arriba. To evaluate immune signature enrichment we ran software ImSig on gene expression data, using Mann-Whitney tests to determine significant results. We curated literature of patients with structural variations in PD-L1 or PD-L2 receiving PD-1 immunotherapy. Findings From 18 studies and datasets we curated 319 cases with structural variations in PD-L1 and PD-L2. We observed breakpoint ‘hotspots’ in the untranslated regions (UTRs) of both genes including 70 duplications, 48 deletions, 78 inversions and 106 translocations. Leveraging TCGA, we found that PD-L1 amplified tumors had significantly upregulated PD-L1 expression and signatures for interferon signaling and immune cell proliferation, compared to PD-L1 copy neutral tumors, each p < 0.001. Similarly, in PD-L1 rearranged tumors we observed upregulation in PD-L1 expression and signatures for interferon signaling, macrophages, monocytes, T cells and immune cell proliferation, all p < 0.001 compared to PD-L1 copy neutral tumors. Further, retrospective review of 7 studies including patients with structural variations in PD-L1 or PD-L2 revealed >50% (43/77) response rate to immunotherapy. Implications Our evaluation of PD-L1 and PD-L2 structural variations show that the 3’ UTR is affected in hotspots involving a variety of structural variations. Our findings from TCGA suggest PD-L1 structural variation may play a role in driving expression of PD-L1 and immune dysregulation. Enriched interferon signaling in PD-L1 rearranged tumors is of interest as interferon exposure is known to drive PD-L1 and PD-L2 expression. Retrospective evidence from curated studies suggest that this genomic alteration could help identify candidates for PD-1 inhibitors. Based on these findings we propose further study to optimize detection of PD-L1 and PD-L2 structural variation in cancer and design of a pan-cancer prospective clinical trial to target these alterations. Citation Format: Emily L. Hoskins, Eric Samorodnitsky, Michele R. Wing, Julie W. Reeser, Julia Hopkins, Karthikeyan Murugesan, Zheng Kuang, Leah Stein, Zach Risch, Raven Vella, Serifat Adebola, Lianbo Yu, Anoosha Paruchuri, Richard S. Huang, Lee A. Albacker, Sameek Roychowdhury. Pan-cancer landscape and impact of PD-L1 and PD-L2 structural variation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 761.
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Vadala, Jeffrey R., and Debra S. Walker. "The Rapid Rise and Fall of Cerros, Belize: A Generational Approach to Chronology." Latin American Antiquity 31, no. 1 (March 2020): 143–62. http://dx.doi.org/10.1017/laq.2019.102.
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In this article, we use the precision of Bayesian modeled radiocarbon dates to reconstruct a generational history of Late Preclassic (300 BC–AD 250) Cerros (Cerro Maya), Belize. This research was made possible by long-curated excavation records and material remains now housed at the Florida Museum of Natural History, Gainesville. Our interpretations build on earlier research and refine the temporal resolution significantly, enabling us to view site development from the perspective of adjacent generations sharing a lived experience. Here we examine material evidence of their collective actions as they built new buildings and renovated aging ones, characterizing their roles in inventing a visual future for the Late Preclassic Maya port that engaged ancestral actions while reinventing the landscape.
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Burrai, Francesco, and Giovanni Salis. "Umanizzazione delle cure: curare con l'arte." Giornale di Clinica Nefrologica e Dialisi 32, no. 1 (June 30, 2020): 92–95. http://dx.doi.org/10.33393/gcnd.2020.2154.
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Art can be a way, together with Nature, to intercept that landscape and inner climate characterized by the rhythm of silence. That dimension of iridescent calm imbued with creative and vital energy, which pushes towards a universal, seductive, profound sphere. Man can, with courage, abandon himself in this harmony and melody of thoughts that suggest a vast and visionary possibility. Each person has the inner possibility to be Art, to get out of the continuous distortions of daily life, to produce a metamorphosis of one’s life. Art triggers the unconscious side of seeing, a rhythmic, dynamic principle, on which every gesture of maximum spontaneity depends, not touched by the artificial, by masks of fugacity and by false personalities. Without Art, it seems that part of real life is missing. The deep artistic power is fluid, without space or time, pulsating with new forms and substance and creating a new personal identity, contiguous to the real world, which inspires new desires. Many diseases of today and yesterday are produced by the lack of expressiveness or by the repression of personal creativity. Art produces well-being because it is the transformation of unconscious expressive energies, so life for our health.
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Begley, Dale A., Debbie M. Krupke, Steven Neuhauser, John Sundberg, and Carol J. Bult. "Abstract 1190: MMHCdb: A knowledgebase for the evolving landscape of mouse models of human cancer." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1190. http://dx.doi.org/10.1158/1538-7445.am2022-1190.
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Abstract The laboratory mouse is the premier mammalian model organism for interrogating the genetic and molecular basis of human cancer and for preclinical investigations into targets for the prevention and treatment of cancer. The distributed and heterogenous nature of information about these model systems makes it difficult for researchers to integrate and interpret the information to determine the state of the field and to identify the most relevant models for basic and preclinical research. The Mouse Models of Human Cancer database (http://tumor.informatics.jax.org) is an expertly curated knowledgebase about genetically defined mouse strains and Patient Derived Xenograft (PDX) models of human cancer. Data in MMHCdb are obtained from peer-reviewed scientific publications and direct data submissions from individual investigators and large-scale programs. MMHCdb is built on FAIR data management principles (Findable, Accessible, Interoperable, Reusable). The enforcement of metadata standards and official gene, allele and strain nomenclature ensure accurate and comprehensive search results for cancer models. MMHCdb has long represented data from spontaneous or endogenously induced tumors from genetically defined mice and for PDXs which have been the foundation of basic cancer research and preclinical studies for decades. MMHCdb has expanded to include cancer models such as Diversity Outbred and Collaborative Cross mice which are ideally suited for research into the relationship of genetic variation with cancer susceptibility and for modeling the genetics of variability in treatment responses. The MMHCdb contains over 109,266 curated tumor frequency records for over 8,275 mouse strains. Tumor types in the database have been indexed to over 21,000 literature citations. PDX models and data available in MMHCdb are also accessible from the Patient Derived Cancer Models resource at EMBL-EBI which currently provides information for over 4,000 PDXs (https://cancermodels.org).MMHCdb is supported by NCI R01 CA089713 Citation Format: Dale A. Begley, Debbie M. Krupke, Steven Neuhauser, John Sundberg, Carol J. Bult. MMHCdb: A knowledgebase for the evolving landscape of mouse models of human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1190.
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Cox, Chris, James Gopsill, and Ben Hicks. "DEMYSTIFYING DIGITAL X." Proceedings of the Design Society 1 (July 27, 2021): 911–22. http://dx.doi.org/10.1017/pds.2021.91.
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AbstractThe rapid pace of development in Digital Engineering has led to an explosion of ideas and new practice in how it can support Engineering Design and Manufacture. You may have heard of the terms Digital Transformation, Digital Twin, Digital Thread, Digital Tapestry and Digital Footprint amongst many other forms of “Digital X” but how have these come about and how do they come together to provide the landscape of what Digitalisation has to offer?In this paper, we analyse the emergence, definition, use and co-occurrence of “Digital X” terminology from an academic dataset of 19,627 papers curated from Scopus. The results reveal that these terms are being used without being fully contextualised in terms of a hierarchy or equivalent to effectively articulate the Digital landscape.Through this analysis, an emerging “Digital X” framework is proposed, with evidence given to support suggested links, and knowledge gaps highlighted for further investigation. Once this framework is complete, a rich lexicon describing the Digital Landscape will pave the way for the future in Digital Engineering.
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Dai, Yulin, Ruifeng Hu, Astrid Marilyn Manuel, Andi Liu, Peilin Jia, and Zhongming Zhao. "CSEA-DB: an omnibus for human complex trait and cell type associations." Nucleic Acids Research 49, no. D1 (November 19, 2020): D862—D870. http://dx.doi.org/10.1093/nar/gkaa1064.
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Abstract During the past decade, genome-wide association studies (GWAS) have identified many genetic variants with susceptibility to several thousands of complex diseases or traits. The genetic regulation of gene expression is highly tissue-specific and cell type-specific. Recently, single-cell technology has paved the way to dissect cellular heterogeneity in human tissues. Here, we present a reference database for GWAS trait-associated cell type-specificity, named Cell type-Specific Enrichment Analysis DataBase (CSEA-DB, available at https://bioinfo.uth.edu/CSEADB/). Specifically, we curated total of 5120 GWAS summary statistics data for a wide range of human traits and diseases followed by rigorous quality control. We further collected >900 000 cells from the leading consortia such as Human Cell Landscape, Human Cell Atlas, and extensive literature mining, including 752 tissue cell types from 71 adult and fetal tissues across 11 human organ systems. The tissues and cell types were annotated with Uberon and Cell Ontology. By applying our deTS algorithm, we conducted 10 250 480 times of trait-cell type associations, reporting a total of 598 (11.68%) GWAS traits with at least one significantly associated cell type. In summary, CSEA-DB could serve as a repository of association map for human complex traits and their underlying cell types, manually curated GWAS, and single-cell transcriptome resources.
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Taniguchi, Hiroaki, Yasunori Suzuki, and Yukikazu Natori. "The Evolving Landscape of Cancer Stem Cells and Ways to Overcome Cancer Heterogeneity." Cancers 11, no. 4 (April 14, 2019): 532. http://dx.doi.org/10.3390/cancers11040532.
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Cancer stem cells (CSCs) with therapeutic resistance and plasticity can be found in various types of tumors and are recognized as attractive targets for treatments. As CSCs are derived from tissue stem or progenitor cells, and/or dedifferentiated mature cells, their signal transduction pathways are critical in the regulation of CSCs; chronic inflammation causes the accumulation of genetic mutations and aberrant epigenetic changes in these cells, potentially leading to the production of CSCs. However, the nature of CSCs appears to be stronger than the treatments of the past. To improve the treatments targeting CSCs, it is important to inhibit several molecules on the signaling cascades in CSCs simultaneously, and to overcome cancer heterogeneity caused by the plasticity. To select suitable target molecules for CSCs, we have to explore the landscape of CSCs from the perspective of cancer stemness and signaling systems, based on the curated databases of cancer-related genes. We have been studying the integration of a broad range of knowledge and experiences from cancer biology, and also from other interdisciplinary basic sciences. In this review, we have introduced the concept of developing novel strategies targeting CSCs.
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Stampter, Paul. "Cows and Curates: the story of the land and livings of Christ Church, Oxford." Landscape History 42, no. 2 (July 3, 2021): 144–45. http://dx.doi.org/10.1080/01433768.2021.1999025.
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Macko-Podgórni, Alicja, Gabriela Machaj, and Dariusz Grzebelus. "A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome." Genes 12, no. 6 (June 3, 2021): 859. http://dx.doi.org/10.3390/genes12060859.
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Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.
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Kostovicova, Denisa, Rachel Kerr, Ivor Sokolić, Tiffany Fairey, Henry Redwood, and Jelena Subotić. "The “Digital Turn” in Transitional Justice Research: Evaluating Image and Text as Data in the Western Balkans." Comparative Southeast European Studies 70, no. 1 (March 1, 2022): 24–46. http://dx.doi.org/10.1515/soeu-2021-0055.
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Abstract The “digital turn” has transformed the landscape of transitional justice research. A wealth of data has been created through social media channels, and new digitisation tools have made existing data more easily accessible. This article discusses the ethical and methodological dimensions of using digital data and novel technologies in transitional justice research based on innovative research using digital archives, digitised transcripts, social media (Facebook) content and digital images. The authors review and evaluate how, in each of these domains, new digital technologies have enabled scholars to expand empirical evidence to understand the mechanics of transitional justice by analysing how data is produced and curated, to interrogate ethical dilemmas involved in those processes and to shift the focus from the ability of transitional justice to fulfil normative goals to how transitional justice is enacted and articulated as a process.
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Hadad, Rémi. "Ruin dynamics: Architectural destruction and the production of sedentary space at the dawn of the Neolithic revolution." Journal of Social Archaeology 19, no. 1 (September 5, 2018): 3–26. http://dx.doi.org/10.1177/1469605318794241.
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Monumental architecture in Levantine sites such as Jerf el-Ahmar, Göbekli Tepe, or Jericho appears to play an important role in place-making practices and in the organization of a possibly hierarchical sociopolitical life at the very beginning of the Neolithic. This paper focuses on an underdeveloped aspect of this phenomenon: all these buildings were ritually destroyed in a highly spectacular and costly fashion. Their ruins were purposefully curated and accumulated. Far from being static remains, these structures are the meaningful result of the dynamic re-production of monumental space and of its inscription in the landscape. Understanding these actions calls for decentering the dominant vision of architectural valuation associated primarily with ideas of “creation” or “heritage.” Architectural destruction, I shall finally claim, may well be more significant than construction for understanding the Neolithic consolidation of sedentism in the Near East.
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Li, Feng, Tan Wu, Yanjun Xu, Qun Dong, Jing Xiao, Yingqi Xu, Qian Li, et al. "A comprehensive overview of oncogenic pathways in human cancer." Briefings in Bioinformatics 21, no. 3 (May 31, 2019): 957–69. http://dx.doi.org/10.1093/bib/bbz046.
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Abstract Alterations of biological pathways can lead to oncogenesis. An overview of these oncogenic pathways would be highly valuable for researchers to reveal the pathogenic mechanism and develop novel therapeutic approaches for cancers. Here, we reviewed approximately 8500 literatures and documented experimentally validated cancer-pathway associations as benchmarking data set. This data resource includes 4709 manually curated relationships between 1557 paths and 49 cancers with 2427 upstream regulators in 7 species. Based on this resource, we first summarized the cancer-pathway associations and revealed some commonly deregulated pathways across tumor types. Then, we systematically analyzed these oncogenic pathways by integrating TCGA pan-cancer data sets. Multi-omics analysis showed oncogenic pathways may play different roles across tumor types under different omics contexts. We also charted the survival relevance landscape of oncogenic pathways in 26 tumor types, identified dominant omics features and found survival relevance for oncogenic pathways varied in tumor types and omics levels. Moreover, we predicted upstream regulators and constructed a hierarchical network model to understand the pathogenic mechanism of human cancers underlying oncogenic pathway context. Finally, we developed `CPAD’ (freely available at http://bio-bigdata.hrbmu.edu.cn/CPAD/), an online resource for exploring oncogenic pathways in human cancers, that integrated manually curated cancer-pathway associations, TCGA pan-cancer multi-omics data sets, drug–target data, drug sensitivity and multi-omics data for cancer cell lines. In summary, our study provides a comprehensive characterization of oncogenic pathways and also presents a valuable resource for investigating the pathogenesis of human cancer.