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Mandolessi S. Memory in the digital age. Open Res Eur 2024; 3:123. [PMID: 37736290 PMCID: PMC10509603 DOI: 10.12688/openreseurope.16228.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 09/23/2023]
Abstract
This article explores the configuration of collective memory under the impact of the digital turn. In recent debates, there has been a marked tendency to interpret 'digital memory' as a new type of memory, which is radically different from the traditional conceptualization. Even leading authors in the field claim that the digital revolution implies the end of collective memory. However, I argue that despite the transformations that memory undergoes in the digital age, these changes do not imply a new ontology of memory but rather a materialization of the theoretical claims made by Memory Studies since the field's inception. To support this hypothesis, I analyze digital memory in relation to three topics: first, I focus on the problematic definition of collective memory to demonstrate how the digital realm allows us to rethink the social nature of memory through a different concept of the social. By contrasting Halbwachs' notion of the social, which forms the basis of memory studies, with the alternative proposal of Gabriel Tarde, I argue that the latter enables us to refine the concept of the 'collective' that we have inherited from the founding figure of memory studies. Second, I delve into the new ontology of the digital archive showing how it materializes one of the defining features of collective memory: its mobile, dynamic, and procedural nature. Lastly, I address the inversion of the dialectic between memory and forgetting to highlight the specificity of these practices in the digital environment. I demonstrate how these changes effectively implement, surpassing older technologies, the concept of collective memory as a distributed and dynamic technological process that shapes our shared representations of the past.
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Affiliation(s)
- Silvana Mandolessi
- Cultural Studies, KU Leuven Association, Leuven, Flanders, 3000, Belgium
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2
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Cordova M. Looking for Ted: black trips, "psychedelic" humanism, and silence. Front Psychol 2023; 14:1198371. [PMID: 37941757 PMCID: PMC10629115 DOI: 10.3389/fpsyg.2023.1198371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/15/2023] [Indexed: 11/10/2023] Open
Affiliation(s)
- Michael Cordova
- The University of Texas at Austin, Austin, TX, United States
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3
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Muhajarine N, Dixon J, Dyck E, Clifford J, Chassé P, Gupta SD, Christopherson-Cote C. Capturing and Documenting the Wider Health Impacts of the COVID-19 Pandemic Through the Remember Rebuild Saskatchewan Initiative: Protocol for a Mixed Methods Interdisciplinary Project. JMIR Res Protoc 2023; 12:e46643. [PMID: 37279056 DOI: 10.2196/46643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND In the Canadian province of Saskatchewan, the global COVID-19 pandemic appeared amidst existing social health challenges in food insecurity, housing precarity and homelessness, poor mental health, and substance misuse. These chronic features intersected with the pandemic, producing a moment in time when the urgency of COVID-19 brought attention to underlying shortcomings in public health services. OBJECTIVE The objectives of the program of research are (1) to identify and measure relationships between the pandemic and wider health and social impacts, namely, food insecurity, housing precarity and homelessness, and mental health and substance use in Saskatchewan, and (2) to create an oral history of the pandemic in Saskatchewan in an accessible digital public archive. METHODS We are using a mixed methods approach to identify the impacts of the pandemic on specific equity-seeking groups and areas of social health concern by developing cross-sectional population-based surveys and producing results based on statistical analysis. We augmented the quantitative analysis by conducting qualitative interviews and oral histories to generate more granular details of people's experiences of the pandemic. We are focusing on frontline workers, other service providers, and individuals within equity-seeking groups. We are capturing digital evidence and social media posts; we are collecting and organizing key threads using a free open-source research tool, Zotero, to trace the digital evidence of the pandemic in Saskatchewan. This study is approved by the Research Ethics Board at the University of Saskatchewan (Beh-1945). RESULTS Funding for this program of research was received in March and April 2022. Survey data were collected between July and November 2022. The collection of oral histories began in June 2022 and concluded in March 2023. In total, 30 oral histories have been collected at the time of this writing. Qualitative interviews began in April 2022 and will continue until March 2024. Survey analysis began in January 2023, and results are expected to be published in mid-2023. All data and stories collected in this work are archived for preservation and freely accessible on the Remember Rebuild Saskatchewan project's website. We will share results in academic journals and conferences, town halls and community gatherings, social and digital media reports, and through collaborative exhibitions with public library systems. CONCLUSIONS The pandemic's ephemeral nature poses a risk of us "forgetting" this moment and the attendant social inequities. These challenges inspired a novel fusion among health researchers, historians, librarians, and service providers in the creation of the Remember Rebuild Saskatchewan project, which focuses on preserving the legacy of the pandemic and capturing data to support an equitable recovery in Saskatchewan. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/46643.
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Affiliation(s)
- Nazeem Muhajarine
- Department of Community Health and Epidemiology, Saskatchewan Population Health and Evaluation Research Unit, University of Saskatchewan, Saskatoon, SK, Canada
| | - James Dixon
- Saskatchewan Population Health and Evaluation Research Unit, University of Saskatchewan, Saskatoon, SK, Canada
| | - Erika Dyck
- Department of History, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jim Clifford
- Department of History, College of Arts and Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Patrick Chassé
- Saskatchewan Population Health and Evaluation Research Unit, University of Saskatchewan, Saskatoon, SK, Canada
| | - Suvadra Datta Gupta
- Saskatchewan Population Health and Evaluation Research Unit, University of Saskatchewan, Saskatoon, SK, Canada
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4
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Clarke N, Barnett C. Archiving the COVID-19 pandemic in Mass Observation and Middletown. Hist Human Sci 2023; 36:3-25. [PMID: 37153715 PMCID: PMC10151920 DOI: 10.1177/09526951231152139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The COVID-19 pandemic generated debates about how pandemics should be known. There was much discussion of what role the human sciences could play in knowing - and governing - the pandemic. In this article, we focus on attempts to know the pandemic through diaries, other biographical writing, and related forms like mass photography. In particular, we focus on the archiving of such forms by Mass Observation in the UK and the Everyday Life in Middletown (EDLM) project in the USA, and initial analyses of such material by scholars from across the human sciences. Our main argument is that archiving the pandemic was informed by, and needs viewing through, the history of the human sciences - including the distinctive histories and human sciences of Mass Observation and Middletown. The article finishes by introducing a Special Section that engages with archiving the pandemic in two senses: the archiving of diaries and related forms by Mass Observation and the EDLM project, and the archiving of initial encounters between researchers and this material by History of the Human Sciences. The Special Section seeks to know the pandemic from the human sciences in the present and to archive knowing the pandemic from the human sciences for the future.
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Rübel O, Tritt A, Ly R, Dichter BK, Ghosh S, Niu L, Baker P, Soltesz I, Ng L, Svoboda K, Frank L, Bouchard KE. The Neurodata Without Borders ecosystem for neurophysiological data science. eLife 2022; 11:e78362. [PMID: 36193886 PMCID: PMC9531949 DOI: 10.7554/elife.78362] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/13/2022] [Indexed: 01/21/2023] Open
Abstract
The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB's impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.
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Affiliation(s)
- Oliver Rübel
- Scientific Data Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Andrew Tritt
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Ryan Ly
- Scientific Data Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | | | - Satrajit Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical SchoolBostonUnited States
| | | | - Pamela Baker
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford UniversityStanfordUnited States
| | - Lydia Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Karel Svoboda
- Allen Institute for Brain ScienceSeattleUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Loren Frank
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Kavli Institute for Fundamental NeuroscienceSan FranciscoUnited States
- Departments of Physiology and Psychiatry University of California, San FranciscoSan FranciscoUnited States
| | - Kristofer E Bouchard
- Scientific Data Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Kavli Institute for Fundamental NeuroscienceSan FranciscoUnited States
- Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, University of California, BerkeleyBerkeleyUnited States
- Weill NeurohubBerkeleyUnited States
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Abstract
In the 1960s, scientists fascinated by the behavior of free-living animals founded research projects that expanded into multi-generation investigations. This paper charts the history of three scientists' projects to uncover the varied reasons for investing in a "long-term" perspective when studying animal behavior: Kenneth Armitage's study of marmots in the Rocky Mountains, Jeanne Altmann's analysis of baboons in Kenya, and Timothy Hugh Clutton-Brock's studies (among others) of red deer on the island of Rhum and meerkats in the Kalahari. The desire to study the behavior of the same group of animals over extended periods of time, I argue, came from different methodological traditions - population biology, primatology, and sociobiology - even as each saw themselves as contributing to the legacy of ethology. As scientists embraced and combined these approaches, a small number of long-running behavioral ecology projects like these grew from short pilot projects into decades-long centers of intellectual gravity within behavioral ecology as a discipline. By attending to time as well as place, we can see how this long-term perspective was crucial to their success; they measured evolutionary changes over generations of animals and their data provided insights into how the animals they studied were adapting (or not) to changing local and global environmental factors.
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Affiliation(s)
- Erika Lorraine Milam
- Charles C. and Emily R. Gillispie Professor in the History of Science, Department of History, Princeton University
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Borrego S, Vivar I, Molina A. Air- and dustborne fungi in repositories of the National Archive of the Republic of Cuba. Microb Cell 2022; 9:103-122. [PMID: 35647176 PMCID: PMC9113668 DOI: 10.15698/mic2022.05.776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022]
Abstract
This study has as objectives to determine the concentration and diversity of the air- and dustborne mycobiota in seven National Archive of the Republic of Cuba repositories, and to assess the potential risk of biodeterioration that isolated taxa may have. In the indoor and outdoor environmental microbiological samplings a SAS biocollector was used and the indoor/outdoor (I/O) ratio was determined for each repository. The settled dust was collected during six months. Sørensen's coefficient of similarity (QS) was calculated to compare the isolated taxa among the three studied niches (indoor air, dust, outdoor air). The biodegradation potential of the isolated taxa was determined by semi-quantitative tests. The concentrations in the air of repositories with natural cross-ventilation ranged from 225.2-750.3 CFU m-3, while in the Map library with air-conditioning the concentration was significantly lower. The I/O ratios ranged from 0.1-1.7 revealing different environmental qualities. The maximum settled dust load was 22.8 mg/m2/day with a top fungal concentration of 6000 CFU g-1. 14 and eleven genera were detected in the air and dust respectively with predominance of the genera Aspergillus, Cladosporium and Penicillium. A QS of 0.8 was obtained between the indoor and the outdoor environments with eleven taxa similar evidencing the incidence of outdoors on the indoor mycobiota. The isolated taxa showed several biodeteriogenic attributes highlighting twelve and 14 taxa from indoor air and dust respectively with positive results for the five tests performed. This demonstrates the potential risk that fungal environmental represent for the preserved documentary heritage.
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Affiliation(s)
- Sofia Borrego
- Conservation Preventive Laboratory, National Archive of the Republic of Cuba, Havana, Cuba
| | - Isbel Vivar
- Conservation Preventive Laboratory, National Archive of the Republic of Cuba, Havana, Cuba
| | - Alian Molina
- Conservation Preventive Laboratory, National Archive of the Republic of Cuba, Havana, Cuba
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8
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Roberts SL, Kirk JL, Muir DCG, Wiklund JA, Evans MS, Gleason A, Tam A, Drevnick PE, Dastoor A, Ryjkov A, Yang F, Wang X, Lawson G, Pilote M, Keating J, Barst BD, Ahad JME, Cooke CA. Quantification of Spatial and Temporal Trends in Atmospheric Mercury Deposition across Canada over the Past 30 Years. Environ Sci Technol 2021; 55:15766-15775. [PMID: 34792335 DOI: 10.1021/acs.est.1c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mercury (Hg) is a pollutant of concern across Canada and transboundary anthropogenic Hg sources presently account for over 95% of national anthropogenic Hg deposition. This study applies novel statistical analyses of 82 high-resolution dated lake sediment cores collected from 19 regions across Canada, including nearby point sources and in remote regions and spanning a full west-east geographical range of ∼4900 km (south of 60°N and between 132 and 64°W) to quantify the recent (1990-2018) spatial and temporal trends in anthropogenic atmospheric Hg deposition. Temporal trend analysis shows significant synchronous decreasing trends in post-1990 anthropogenic Hg fluxes in western Canada in contrast to increasing trends in the east, with spatial patterns largely driven by longitude and proximity to known point source(s). Recent sediment-derived Hg fluxes agreed well with the available wet deposition monitoring. Sediment-derived atmospheric Hg deposition rates also compared well to the modeled values derived from the Hg model, when lake sites located nearby (<100 km) point sources were omitted due to difficulties in comparison between the sediment-derived and modeled values at deposition "hot spots". This highlights the applicability of multi-core approaches to quantify spatio-temporal changes in Hg deposition over broad geographic ranges and assess the effectiveness of regional and global Hg emission reductions to address global Hg pollution concerns.
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Affiliation(s)
- Sarah L Roberts
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Jane L Kirk
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Derek C G Muir
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Johan A Wiklund
- Biology Department, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Marlene S Evans
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - Amber Gleason
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Allison Tam
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Paul E Drevnick
- Alberta Environment and Parks, 3535 Research Road NW, Calgary, Alberta T2L 2K8, Canada
- National Institute of Scientific Research, Centre Eau Terre Environment, 490 rue de la Couronne, Québec, Québec G1K 9A9, Canada
| | - Ashu Dastoor
- Air Quality Research Division, Environment and Climate Change Canada, Québec H9P 1J3, Canada
| | - Andrei Ryjkov
- Air Quality Research Division, Environment and Climate Change Canada, Québec H9P 1J3, Canada
| | - Fan Yang
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Xiaowa Wang
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Greg Lawson
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Burlington, Ontario L7R 4A6, Canada
| | - Martin Pilote
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montréal, Québec H2Y 2E7, Canada
| | - Jonathan Keating
- Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Saskatoon, Saskatchewan S7N 3H5, Canada
| | - Benjamin D Barst
- National Institute of Scientific Research, Centre Eau Terre Environment, 490 rue de la Couronne, Québec, Québec G1K 9A9, Canada
- Water and Environment Research Center, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States
| | - Jason M E Ahad
- Geological Survey of Canada─Québec Division, Québec G1K 9A9, Canada
| | - Colin A Cooke
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
- Alberta Environment and Parks, 9888 Jasper Ave, Edmonton, Alberta T5J 5C6, Canada
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Alcantara DR, Jones CI, Altmann DM, Boyton RJ, Haniffa M, Newport MJ. Multiplexed gene expression analysis of HLA class II-associated podoconiosis implicates chronic immune activation in its pathogenesis. Trans R Soc Trop Med Hyg 2021; 114:926-936. [PMID: 33099652 PMCID: PMC7738654 DOI: 10.1093/trstmh/traa107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/25/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023] Open
Abstract
Background Podoconiosis is a tropical lymphoedema of the leg resulting from barefoot exposure to irritant volcanic soils. Approximately 4 million people are affected, mainly in African highland regions. The pathogenesis of this neglected tropical disease is still largely unknown, although HLA class II (HLAII) polymorphisms are associated with the disease. Methods NanoString technology was used to assess expression of 579 immune-related genes in formalin-fixed and paraffin-embedded lymph node archival samples from podoconiosis patients and unaffected controls. Results Forty-eight genes were upregulated and 21 downregulated in podoconiosis samples compared with controls. Gene ontology analysis showed differentially expressed genes to be closely related to major histocompatibility complex protein, cytokine and TNF receptor binding genes. Pathway enrichment analysis revealed involvement of lymphocyte activation, adaptive immunity, cytokine signalling, antigen processing and the IL-12 pathways. Conclusions This exploratory study reports a multiplex gene expression analysis in podoconiosis and shows upregulation of pro-inflammatory transcripts compatible with the notion of local, chronic immune activation in this HLAII-associated disease. Implicated pathways will inform future research into podoconiosis immunopathogenesis.
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Affiliation(s)
- Diana R Alcantara
- Brighton and Sussex Centre for Global Health Research, Department of Global Health & Infection, Brighton & Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PX, UK
| | - Christopher I Jones
- Department of Primary Care and Public Health, Brighton & Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PX, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Faculty of Medicine, Hammersmith Hospital, Imperial College London, London W12 0NN, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Faculty of Medicine, Hammersmith Hospital, Imperial College London, London W12 0NN, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Melanie J Newport
- Brighton and Sussex Centre for Global Health Research, Department of Global Health & Infection, Brighton & Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PX, UK
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Williams J. Plantation Botany: Slavery and the Infrastructure of Government Science in the St. Vincent Botanic Garden, 1765-1820 s*. Ber Wiss 2021; 44:137-158. [PMID: 33891702 DOI: 10.1002/bewi.202100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This essay examines the aims, labor regime, and workers of the St. Vincent botanic garden to highlight differences in the infrastructure of government-funded botany across the British empire. It argues that slavery was a foundational element of society and natural history in the Anglo-Caribbean, and the St. Vincent botanic garden was both put into the service of slavery and transformed by it. When viewed from the Caribbean context and the perspective of enslaved workers, the St. Vincent garden's affiliation with imperial improvement becomes less salient than its support of the status quo of slavery as a system and labor regime. The garden was dependent on enslaved laborers, yet the conditions of work and contemporary prejudices led superintendents to see them as undifferentiated labor. The politics of the archive make it impossible for historians to reconstruct the experiences of the garden's enslaved workers as individuals, including the specific labor that they performed or skills that they possessed. Plantation slavery's appropriation of and influence on the infrastructure of colonial botany through the St. Vincent botanic garden suggests that historians should center the local logics of the societies where scientific knowledge making took place to reveal the many meanings of science.
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Affiliation(s)
- J'Nese Williams
- Mellon Fellow of Scholars in the Humanities, Stanford Humanities Center, Lecturer, Department of History, Stanford University
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Shaklai S, Gilad-Bachrach R, Yom-Tov E, Stern N. Detecting Impending Stroke From Cognitive Traits Evident in Internet Searches: Analysis of Archival Data. J Med Internet Res 2021; 23:e27084. [PMID: 34047699 PMCID: PMC8196360 DOI: 10.2196/27084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/03/2021] [Accepted: 05/04/2021] [Indexed: 01/13/2023] Open
Abstract
Background Cerebrovascular disease is a leading cause of mortality and disability. Common risk assessment tools for stroke are based on the Framingham equation, which relies on traditional cardiovascular risk factors to predict an acute event in the near decade. However, no tools are currently available to predict a near/impending stroke, which might alert patients at risk to seek immediate preventive action (eg, anticoagulants for atrial fibrillation, control of hypertension). Objective Here, we propose that an algorithm based on internet search queries can identify people at increased risk for a near stroke event. Methods We analyzed queries submitted to the Bing search engine by 285 people who self-identified as having undergone a stroke event and 1195 controls with regard to attributes previously shown to reflect cognitive function. Controls included random people 60 years and above, or those of similar age who queried for one of nine control conditions. Results The model performed well against all comparator groups with an area under the receiver operating characteristic curve of 0.985 or higher and a true positive rate (at a 1% false-positive rate) above 80% for separating patients from each of the controls. The predictive power rose as the stroke date approached and if data were acquired beginning 120 days prior to the event. Good prediction accuracy was obtained for a prospective cohort of users collected 1 year later. The most predictive attributes of the model were associated with cognitive function, including the use of common queries, repetition of queries, appearance of spelling mistakes, and number of queries per session. Conclusions The proposed algorithm offers a screening test for a near stroke event. After clinical validation, this algorithm may enable the administration of rapid preventive intervention. Moreover, it could be applied inexpensively, continuously, and on a large scale with the aim of reducing stroke events.
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Affiliation(s)
- Sigal Shaklai
- Institute of Endocrinology, Metabolism and Hypertension, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol Center for Epigenetics of Aging and Metabolism, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ran Gilad-Bachrach
- Faculty of Bio-Medical Engineering, Tel Aviv University, Tel Aviv, Israel.,Edmond J Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Elad Yom-Tov
- Microsoft Research, Herzeliya, Israel.,Faculty of Industrial Engineering and Management, Technion, Haifa, Israel
| | - Naftali Stern
- Institute of Endocrinology, Metabolism and Hypertension, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Sagol Center for Epigenetics of Aging and Metabolism, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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Morioka T, Blyth BJ, Imaoka T, Nishimura M, Takeshita H, Shimomura T, Ohtake J, Ishida A, Schofield P, Grosche B, Kulka U, Shimada Y, Yamada Y, Kakinuma S. Establishing the Japan-Store house of animal radiobiology experiments (J-SHARE), a large-scale necropsy and histopathology archive providing international access to important radiobiology data. Int J Radiat Biol 2019; 95:1372-1377. [PMID: 31145030 DOI: 10.1080/09553002.2019.1625458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Purpose: Projects evaluating the effects of radiation, within the National Institutes of Quantum and Radiological Science and Technology (QST), National Institute of Radiological Sciences (NIRS), have focused on risk analyses for life shortening and cancer prevalence using laboratory animals. Genetic and epigenetic alterations in radiation-induced tumors have been also analyzed with the aim of better understanding mechanisms of radiation carcinogenesis. As well as the economic and practical limitations of repeating such large-scale experiments, ethical considerations make it vital that we store and share the pathological data and samples of the animal experiments for future use. We are now constructing such an archive called the Japan-Storehouse of Animal Radiobiology Experiments (J-SHARE). Methods: J-SHARE records include information such as detailed experimental protocols, necropsy records and photographs of organs at necropsy. For each animal organs and tumor tissues are dissected, and parts are stored as frozen samples at -80 °C. Samples fixed with formalin are also embedded in paraffin blocks for histopathological analyses. Digital copies of stained tissues are being systematically saved using a virtual slide system linked to original records by barcodes. Embedded and frozen tissues are available for molecular analysis. Conclusion: Similar archive systems for radiation biology have also been under construction in the USA and Europe, the Northwestern University Radiation Archive (NURA), and STORE at the BfS, respectively. The J-SHARE will be linked with the sister-archives and made available for collaborative research to institutions and universities all over the world.
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Affiliation(s)
- Takamitsu Morioka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Benjamin J Blyth
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Tatsuhiko Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | - Mayumi Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
| | | | - Takeo Shimomura
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Jun Ohtake
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Atsuro Ishida
- Department of Information Technology, NIRS, QST , Chiba , Japan
| | - Paul Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge , UK
| | - Bernd Grosche
- Federal Office for Radiation Protection, Radiation and Health , Oberschleissheim , Germany
| | - Ulrike Kulka
- Federal Office for Radiation Protection, Radiation and Health , Oberschleissheim , Germany
| | | | - Yutaka Yamada
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan.,Fukushima Project Headquarters, NIRS, QST , Chiba , Japan
| | - Shizuko Kakinuma
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology , Chiba , Japan
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13
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Khayambashi S. Blood and Guts in Living Color: A Study of the Internet Death Video Community. Omega (Westport) 2019; 83:390-406. [PMID: 31177945 DOI: 10.1177/0030222819855883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Journalism has taken on a new form in the age of new media, allowing anyone to not only report the news, but to provide visual proof of it, uncensored and freely available. When this visual proof began to allow people to see death in its entirety, various communities began to form to not just view these videos but to also ensure their availability and continuation. This essay is about those communities and how they operate.
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14
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Abstract
Studies of ionizing radiation effects through the archiving of data began with standardizing medical treatments in the early 1900s shortly after the discovery of X-rays. Once the breadth of the delayed effects of ionizing radiation was recognized, the need for long-term follow up became apparent. There are now many human archives of data from nuclear disasters and accidents, occupational exposures, and medical procedures. Planned animal irradiation experiments began around the time of the Cold War and included a variety of doses, fractions, dose rates, and types of ionizing radiation. The goal of most of these studies was to supplement information coming from human data through carefully planned experimental conditions and immediate and uninterrupted data collection. This review aims to highlight major archives and databases that have shaped the field of radiation biology and provide a broad range of the types of datasets currently available. By preserving all of these data and tissue sets, radiation biologists can combine databases and conduct large-scale analyses of detailed existing data and perform new assays with cutting edge scientific approaches.
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Affiliation(s)
- Alia Zander
- Feinberg School of Medicine, Radiation Oncology, Northwestern University , Chicago , IL , USA
| | - Tatjana Paunesku
- Feinberg School of Medicine, Radiation Oncology, Northwestern University , Chicago , IL , USA
| | - Gayle Woloschak
- Feinberg School of Medicine, Radiation Oncology, Northwestern University , Chicago , IL , USA
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15
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Gimenez I, Gaillard CL. [From the intimate to intimacy in social sciences]. Soins 2018; 63:36-39. [PMID: 30551752 DOI: 10.1016/j.soin.2018.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Intimacy, situated in time and space and dependent on material conditions, is a recent subject of study in social sciences. It constitutes a category of analysis which provides information on the power relationships running through it. The right to intimacy, seized upon by vulnerable populations, then enables certain practices to be claimed and politicized.
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Affiliation(s)
- Irène Gimenez
- IEP de Lyon, 14, avenue Berthelot, 69365 Lyon cedex 07, France
| | - Claire-Lise Gaillard
- Université Paris-1-Panthéon-Sorbonne, 12, place du Panthéon, 75231 Paris cedex 05, France.
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16
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Abstract
The author brings to light previously unpublished material from the part of the Melanie Klein archive that deals with the subject of Klein's last, posthumously published paper "On the sense of loneliness". Here are found four differing versions of the loneliness paper, written between 1958 and 1960, and prepared for spoken presentations to different audiences. The author gives evidence from Klein's copious additional notes that she intended to write a whole book or monograph dealing with the topic of loneliness from a psychoanalytic point of view. At the time of Klein's death, as well as elaborating her own thinking on the topic of loneliness, she was gathering and incorporating the comments of a number of close colleagues on her work. Previously unpublished letters to Klein from Wilfred Bion and Elliott Jaques are included in this paper, as are extracts from Klein's own notes, organized under a number of headings. Without attempting to analyse the material in any depth, the author suggests that some of the themes Klein was working on may have had particular relevance for her personally in what turned out to be the very last months of her life.
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Affiliation(s)
- Jane Milton
- British Psychoanalytical Society, London, UK
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17
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Bell KC, Carlson CJ, Phillips AJ. Parasite Collections: Overlooked Resources for Integrative Research and Conservation. Trends Parasitol 2018; 34:637-639. [PMID: 29759934 DOI: 10.1016/j.pt.2018.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 10/16/2022]
Abstract
Parasite natural history collections form vital scientific infrastructure that play a substantial role in increasing awareness of the importance of parasites to ecosystems, conservation assessments, science, and society. These collections support novel investigations that integrate across taxa, time, and space, and should be cultivated to advance organismal-based science. Promoting and supporting parasite collections will ensure their ongoing stability and accessibility.
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Affiliation(s)
- Kayce C Bell
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Colin J Carlson
- Department of Biology, Georgetown University, Washington, DC, USA; National Socio-Environmental Synthesis Center (SESYNC), University of Maryland, Annapolis, MD, USA
| | - Anna J Phillips
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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18
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Powell H, Morrison H, Callard F. Wandering Minds: Tracing Inner Worlds Through a Historical-Geographical Art Installation. GeoHumanities 2018; 4:132-156. [PMID: 29888738 PMCID: PMC5972649 DOI: 10.1080/2373566x.2018.1441736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 01/15/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
The human act of wandering across landscapes and cityscapes has carved the research interests of scholars in cultural, urban, and historical geography, as well as in the humanities. Here we call for-and take the first steps toward-a historical geography of wandering that is pursued in the head rather than with the legs. We do so through analyzing how our audiovisual installation on mind wandering opened up epistemological and ontological questions facing historical geographies of the mind. This installation both modeled mind wandering as conceptualized at different historical moments and aimed to induce mental perambulation in its visitors. In so doing, it was intended both to stage and to disrupt relations between body and mind, the internal and external, attention and inattention, motion and stillness-and, importantly, between the archival and that which resists archival capture. We reflect on how we interspersed traditional scholarly historical and geographical enquiry with methods gleaned from creative practices. In particular, we consider the challenges that such practices pose for how we conceptualize archives-not least when the focus of attention comprises fugitive mental phenomena.
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19
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Selimovic-Hamza S, Bouzalas IG, Vandevelde M, Oevermann A, Seuberlich T. Detection of Astrovirus in Historical Cases of European Sporadic Bovine Encephalitis, Switzerland 1958-1976. Front Vet Sci 2016; 3:91. [PMID: 27781208 PMCID: PMC5058262 DOI: 10.3389/fvets.2016.00091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/27/2016] [Indexed: 11/17/2022] Open
Abstract
European sporadic bovine encephalitis is a frequent diagnosis in neurologically diseased cattle, but its etiology remained unresolved. Using in situ hybridization, we have detected a recently discovered neurotropic bovine astrovirus in historical tissues in a high proportion of brain samples of affected cattle. Our results suggest that astroviruses were already involved in the pathogenesis of the disease several decades ago, but have gone undetected.
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Affiliation(s)
- Senija Selimovic-Hamza
- DCR-VPH, Division of Neurological Sciences, NeuroCenter, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ilias G Bouzalas
- DCR-VPH, Division of Neurological Sciences, NeuroCenter, University of Bern , Bern , Switzerland
| | - Marc Vandevelde
- DCR-VPH, Division of Neurological Sciences, NeuroCenter, University of Bern , Bern , Switzerland
| | - Anna Oevermann
- DCR-VPH, Division of Neurological Sciences, NeuroCenter, University of Bern , Bern , Switzerland
| | - Torsten Seuberlich
- DCR-VPH, Division of Neurological Sciences, NeuroCenter, University of Bern , Bern , Switzerland
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20
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Müller B. [Eleven thesis on the archive of scientific research, for a new patrimonial and scientific policy]. Rev Synth 2015; 136:449-476. [PMID: 26746647 DOI: 10.1007/s11873-015-0287-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Abstracting the main content of a recent report on the bad state of the archives of scientific research, this paper puts forward eleven thesis likely to feed, in this time of numeric transition to a new documentary regime and to a new patrimonial policy. The recent numeric conditions impose to set new archival pratices, more proactive, anticipative and prospective. Archives of scientific research must be thought in a double memorial and scientific dimension, and not only as a patrimonial or historical one.
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Affiliation(s)
- Bertrand Müller
- Centre Maurice-Halbwachs, 48 boulevard Jourdan, 75014, Paris, France.
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21
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Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics 2014; 15:369. [PMID: 25494900 PMCID: PMC4272562 DOI: 10.1186/s12859-014-0369-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/30/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. RESULTS We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. CONCLUSIONS The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.
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Affiliation(s)
- Frank T Bergmann
- Modelling of Biological Processes, BioQUANT/COS, University of Heidelberg, INF 267, Heidelberg, 69120, Germany.
| | - Richard Adams
- ResearchSpace, 24 Fountainhall Road, Edinburgh, EH9 2LW, UK.
| | - Stuart Moodie
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Current affiliation: Eight Pillars Ltd, 19 Redford Walk, Edinburgh, EH13 0AG, UK.
| | - Jonathan Cooper
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, UK.
| | - Mihai Glont
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | | | - Michael Hucka
- Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Camille Laibe
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Andrew K Miller
- Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand.
| | - David P Nickerson
- Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand.
| | - Brett G Olivier
- Systems Bioinformatics, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands.
| | - Nicolas Rodriguez
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, 98195, WA, USA.
| | - Martin Scharm
- Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany.
| | - Stian Soiland-Reyes
- School of Computer Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Dagmar Waltemath
- Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, Rostock, 18057, Germany.
| | - Florent Yvon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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22
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Spriggs RV, Willis AE. TRANS PROF DB: A new resource for sharing translational profiles. Translation (Austin) 2014; 2:e965615. [PMID: 26779411 PMCID: PMC4696474 DOI: 10.4161/2169074x.2014.965615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/07/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022]
Abstract
The translational efficiency of individual mRNAs can be measured on a genome-wide scale using translational profiling techniques. Data from such experiments are an enormously important resource in the quest to understand the impact of cellular state on gene expression. To improve our understanding of these data, we have created TRANS PROF DB, a manually curated resource containing the translational status of human mRNAs under defined conditions. Results are provided at the level of an annotated conclusion for each gene, e.g. "Translation up-regulated", and also, where available, in a rawer form such as the normalized analyzed microarray output. TRANS PROF DB aims to provide a central resource for the sharing of translational profiles to facilitate reuse of published data and to enable meta-analyses across data sets. As the database expands, it will provide an easily searchable archive of publicly available translational profiling data sets. We encourage all researchers to deposit their translational profiling data into TRANS PROF DB to enable us to create a truly comprehensive resource. TRANS PROF DB is available without restriction at mrctools.mrctox.le.ac.uk/TRANS_PROF_DB.
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23
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Abstract
Increasing radiology studies has led to the emergence of new requirements for management medical information, mainly affecting the storage of digital images. Today, it is a necessary interaction between workflow management and legal rules that govern it, to allow an efficient control of medical technology and associated costs. Another important topic that is growing in importance within the healthcare sector is compliance, which includes the retention of studies, information security, and patient privacy. Previously, we conducted a series of extensive analysis and measurements of pre-existing operating conditions. These studies and projects have been described in other papers. The first phase: hardware and software installation and initial tests were completed in March 2006. The storage phase was built step by step until the PACS-INR was totally completed. Two important aspects were considered in the integration of components: (1) the reliability and performance of the system to transfer and display DICOM images, and (2) the availability of data backups for disaster recovery and downtime scenarios. This paper describes the high-availability model for a large-scale PACS to support the storage and retrieve of data using CAS and DAS technologies to provide an open storage platform. This solution offers a simple framework that integrates and automates the information at low cost and minimum risk. Likewise, the model allows an optimized use of the information infrastructure in the clinical environment. The tests of the model include massive data migration, openness, scalability, and standard compatibility to avoid locking data into a proprietary technology.
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Affiliation(s)
- Josefina Gutiérrez-Martínez
- Subdirección de Investigación Tecnológica, Instituto Nacional de Rehabilitación, Av. México- Xochimilco No. 289, Col. Arenal de Guadalupe, Tlalpan, 14389, México, Federal District, Mexico.
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24
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Abstract
Archives operating under the International Nucleotide Sequence Database Collaboration currently preserve all submitted sequences equally, but rapid increases in the rate of global sequence production will soon require differentiated treatment of DNA sequences submitted for archiving. Here, we propose a graded system in which the ease of reproduction of a sequencing-based experiment and the relative availability of a sample for resequencing define the level of lossy compression applied to stored data.
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Affiliation(s)
- Guy Cochrane
- EMBL-Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Charles E Cook
- EMBL-Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Ewan Birney
- EMBL-Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
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25
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Abstract
Systematic reviews have become increasingly critical to informing healthcare policy; however, they remain a time-consuming and labor-intensive activity. The extraction of data from constituent studies comprises a significant portion of this effort, an activity which is often needlessly duplicated, such as when attempting to update a previously conducted review or in reviews of overlapping topics.In order to address these inefficiencies, and to improve the speed and quality of healthcare policy- and decision-making, we have initiated the development of the Systematic Review Data Repository, an open collaborative Web-based repository of systematic review data. As envisioned, this resource would serve as both a central archive and data extraction tool, shared among and freely accessible to organizations producing systematic reviews worldwide. A suite of easy-to-use software tools with a Web frontend would enable researchers to seamlessly search for and incorporate previously deposited data into their own reviews, as well as contribute their own.In developing this resource, we identified a number of technical and non-technical challenges, as well as devised a number of potential solutions, including proposals for systems and software tools to assure data quality, stratify and control user access effectively and flexibly accommodate all manner of study data, as well as means by which to govern and foster adoption of this new resource.Herein we provide an account of the rationale and development of the Systematic Review Data Repository thus far, as well as outline its future trajectory.
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Affiliation(s)
- Stanley Ip
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Nira Hadar
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Sarah Keefe
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Christopher Parkin
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Ramon Iovin
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Ethan M Balk
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
| | - Joseph Lau
- Tufts Evidence-based Practice Center, Tufts Medical Center, Boston, MA 02111, USA
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26
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Persons KR, Hangiandreou NJ, Charboneau NT, Charboneau J, James E, Douglas BR, Salmon AP, Knudsen JM, Erickson BJ. Evaluation of irreversible JPEG compression for a clinical ultrasound practice. J Digit Imaging 2002; 15:15-21. [PMID: 12134210 PMCID: PMC3946084 DOI: 10.1007/s10278-002-0003-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A prior ultrasound study indicated that images with low to moderate levels of JPEG and wavelet compression were acceptable for diagnostic purposes. The purpose of this study is to validate this prior finding using the Joint Photographic Experts Group (JPEG) baseline compression algorithm, at a compression ratio of approximately 10:1, on a sufficiently large number of grayscale and color ultrasound images to attain a statistically significant result. The practical goal of this study is to determine if it is feasible for radiologists to use irreversibly compressed images as an integral part of the day to day ultrasound practice (ie, perform primary diagnosis with, and store irreversibly compressed images in the ultrasound PACS archive). In this study, 5 Radiologists were asked to review 300 grayscale and color static ultrasound images selected from 4 major anatomic groups. Each image was compressed and decompressed using the JPEG baseline compression algorithm at a fixed quality factor resulting in an average compression ratio of approximately 9:1. The images were presented in pairs (original and compressed) in a blinded fashion on a PACS workstation in the ultrasound reading areas, and radiologists were asked to pick which image they preferred in terms of diagnostic utility and their degree of certainty (on a scale from 1 to 4). Of the 1499 total readings, 50.17% (95% confidence intervals at 47.6%, and 52.7%) indicated a preference for the original image in the pair, and 49.83% (95% confidence intervals at 47.3%, and 52.0%) indicated a preference for the compressed image. These findings led the authors to conclude that static color and gray-scale ultrasound images compressed with JPEG at approximately 9:1 are statistically indistinguishable from the originals for primary diagnostic purposes. Based on the authors laboratory experience with compression and the results of this and other prior studies, JPEG compression is now being applied to all ultrasound images in the authors' radiology practice before reading. No image quality-related issues have been encountered after 12 months of operation (approximately 48000 examinations).
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Affiliation(s)
- Kenneth R Persons
- Departments of Information Services and Diagnostic Radiology, Mayo Clinic and Foundation, Rochester, MN 55905, USA.
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27
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Abstract
The need for long-term storage requires the future migration of image data from a PACS to its successor system. This paper considers the cost of such migration It is proposed that storage of data as "documents" in DICOM Part 10 formats on industry-standard media could reduce the time and cost of data migration relative to on-line DICOM transfer. The relation to present efforts in developing document-oriented electronic patient records is discussed. DICOM Part 10 files are found to be a sufficient representation of image documents, but additional software tools will be needed to reach its full potential. There is a significant cost benefit of the document storage method, but it is one of many factors which must be balanced in the selection of a PACS.
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Affiliation(s)
- F Behlen
- University of Chicago, Department or Radiology, IL 60637, USA
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