139 results on '"Wilson, Mandy"'
Search Results
102. Strengths and limitations of the federal guidance on synthetic DNA
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Adam, Laura, primary, Kozar, Michael, additional, Letort, Gaelle, additional, Mirat, Olivier, additional, Srivastava, Arunima, additional, Stewart, Tyler, additional, Wilson, Mandy L, additional, and Peccoud, Jean, additional
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- 2011
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103. Community organizing: introduction to themed section.
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Taylor, Marilyn and Wilson, Mandy
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COMMUNITY development , *COMMUNITY life , *SOCIAL groups , *SOCIAL psychology - Abstract
The article reports on the resurgence of community organizing in Great Britain. The high profile of Citizens UK have attracted the attention of politicians, trades unions and faith organizations. The government that came to power in 2010 made a commitment to train 5000 community organizers through a four-year Community Organizers Program.
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- 2015
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104. Impact of Community Work: How to Gather Evidence.
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Wilson, Mandy
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IMPACT (Mechanics) , *COMMUNITIES , *NONFICTION - Published
- 2022
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105. `I am the Prince of Pain, for I am a Princess in the Brain': Liminal Transgender Identities, Narratives and the Elimination of Ambiguities
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Wilson, Mandy, primary
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- 2002
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106. Heart and soul: how to reconcile your spirituality and sexuality
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Wilson, Mandy
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Coming out (Homosexuality) -- Methods ,Homosexuality -- Management ,Acquiescence (Psychology) -- Management ,Lesbians -- Beliefs, opinions and attitudes ,Company business management ,Women's issues/gender studies - Abstract
I remember the first time someone told me I was going to hell--it was my reflection glaring at me from the bathroom mirror, reeling from my first lesbian kiss. The [...]
- Published
- 2012
107. Book reviews
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Skorupski, John, primary, Wilson, Mandy, additional, Day, William B., additional, Bolger, Audrey, additional, Rubinstein, Robert L., additional, Graburn, Nelson H., additional, Ensel, Remco, additional, Nardini, Gloria, additional, Cohn, Michael, additional, and Northcote, Jeremy, additional
- Published
- 1999
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108. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs.
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Yizhi Cai, Wilson, Mandy L., and Peccoud, Jean
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- 2010
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109. 'I am the Prince of Pain, for I am a Princess in the Brain': Liminal Transgender Identities, Narratives and the Elimination of Ambiguities.
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Wilson, Mandy
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TRANSGENDER identity , *TRANSSEXUALISM , *GENDER identity , *GENDER transition , *GENDER-nonconforming people - Abstract
This article explores the formation and construction of transgendered identities, 'the various ontological and public narratives in which actors plot or find themselves' (Somers and Gibson, 1994: 67). Research I have conducted in Perth, Western Australia, shows that while a multiplicity of gendered identities circulate in various spaces and places, there is also a pressing need for many transgendered persons to ultimately define themselves within existing and recognizable 'normal' gender boundaries: instead of marking difference, many seem to eliminate it. Often identity goes from being 'liminal' and multiple where males can be females, females can be males, and public gender categories are temporarily and spatially suspended, to being ultimately singular, recognizable and stable (as demanded by wider medical, sociocultural and public understandings of gender). Here, I investigate what Victor Turner (expanding on the work of Arnold Van Gennep, 1960) has called the 'The Liminal Period' (1967). Following and building on the arguments initially proposed by Anne Bolin who focused on transsexual rites of transition in the USA (1988), I look at the theory of liminality in relation to transgendered rites de passage in Perth. While recognizing the large body of work from queer studies,¹ which turns its gaze toward social practices that organize a society and sexualize the 'bodies, desires, acts, identities, social relations, knowledges, culture and social institutions' (Seidman, 1996: 13), I choose instead to draw on and apply particular concepts proposed by anthropologist, Mary Douglas (1966, 1970). Employing her notions of purity and danger to relevant questions in this article, I explore how cultures understand, interpret and deal with variance and anomaly. [ABSTRACT FROM AUTHOR]
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- 2002
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110. Reflecting on micro‐ethics to center the voices of Aboriginal peoples experiencing homelessness.
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Brown, Alice V., Vieira, Emma, Oakley, Jackie, Bagshaw, Dorothy, Egan, Patrick, Southalan, Louise, Andrews, Lindey, Jones, Jocelyn, Morrison, Daniel, and Wilson, Mandy
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HOMELESS persons , *INDIGENOUS peoples , *INDIGENOUS rights , *RESEARCH personnel , *OLDER people - Abstract
This article shares the micro‐ethical lessons from those researching alongside Aboriginal people experiencing homelessness and Aboriginal Elders in Perth, Western Australia. The article is written from the perspective of the first and second author who are two non‐Aboriginal researchers being mentored in Aboriginal culture. From this positioning, it offers reflections and practical insights into researching “in the right spirit” with Aboriginal communities. More specifically, it shares lessons in negotiating community roles within community‐driven research, the importance in forming relationship with Aboriginal culture as antidote to research fatigue, practical ways to work with Aboriginal communities when they have a history of being exploited in research, navigating fair and ethical payment for involvement, and ways to clearly communicate research with them. It also shares the cultural importance and benefits of working closely with Aboriginal Elders when engaging in research with Aboriginal communities, including their ability to better negotiate project scope with community, and the value in making sense of the research findings alongside them. [ABSTRACT FROM AUTHOR]
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- 2024
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111. No Shortcuts: Organizing for Power in the New Gilded Age.
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Wilson, Mandy and Downing, Helen Wallis
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COMMUNITY organization , *SOCIAL movements , *NONFICTION - Published
- 2019
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112. Late-glacial and Holocene glacier fluctuations and environmental change on South Georgia, Southern Ocean
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Clapperton, Chalmers M., Sugden, David E., Birnie, Jacqueline, and Wilson, Mandy J.
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South Georgia provides a terrestrial record of postglacial environmental change from a largely oceanic zone of the Earth. The record is representative of the southern westerlies and provides a link between Antarctica and the temperate zones of southern South America. Evidence from glacial geomorphology, slope stratigraphy, and analyses of environmental indicators in peat and lake cores is used to interpret this record. Wastage of the full-glacial ice cap was interrupted by a late-glacial stade of the outlet and valley glaciers before ca. 10,000 yr B.P. Plant growth had begun at low altitude (<50 m) on the sheltered (lee side) northeast coast within the late-glacial moraine limits by 9700 yr B.P. Environmental conditions on slopes above 80 m probably were too rigorous for a stable vegetation cover until ca. 6400 yr B.P. This was followed by a period from 5600 to 4800 yr B.P. when conditions were warmer than at present by up to 0.6°C. Periods of climatic cooling occurred at ca. 4800-3800 yr B.P., ca. 3400-1800 yr B.P., and within the last 1400 yr. The most extensive Holocene advance of South Georgia glaciers culminated just before 2200 yr B.P. These Holocene temperature changes of between 0.5 and 1.0°C are comparable in scale and timing to those identified from recent analyses of Vostok ice cores from the Antarctic ice sheet.
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- 1989
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113. Sequence verification of synthetic DNA by assembly of sequencing reads
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Wilson, Mandy L., Cai, Yizhi, Hanlon, Regina, Taylor, Samantha, Chevreux, Bastien, Setubal, João C., Tyler, Brett M., Peccoud, Jean, Wilson, Mandy L., Cai, Yizhi, Hanlon, Regina, Taylor, Samantha, Chevreux, Bastien, Setubal, João C., Tyler, Brett M., and Peccoud, Jean
- Abstract
Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org
114. Combining Participatory Influenza Surveillance with Modeling and Forecasting: Three Alternative Approaches.
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Brownstein, John S, Shuyu Chu, Marathe, Achla, Marathe, Madhav V, Nguyen, Andre T., Paolotti, Daniela, Perra, Nicola, Perrotta, Daniela, Santillana, Mauricio, Swarup, Samarth, Tizzoni, Michele, Vespignani, Alessandro, Vullikanti, Anil Kumar S., Wilson, Mandy L., and Qian Zhang
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INFLUENZA ,EPIDEMICS ,SEASONAL influenza ,PUBLIC health surveillance ,SIMULATION methods & models - Abstract
Background: Influenza outbreaks affect millions of people every year and its surveillance is usually carried out in developed countries through a network of sentinel doctors who report the weekly number of Influenza-like Illness cases observed among the visited patients. Monitoring and forecasting the evolution of these outbreaks supports decision makers in designing effective interventions and allocating resources to mitigate their impact. Objective: Describe the existing participatory surveillance approaches that have been used for modeling and forecasting of the seasonal influenza epidemic, and how they can help strengthen real-time epidemic science and provide a more rigorous understanding of epidemic conditions. Methods: We describe three different participatory surveillance systems, WISDM (Widely Internet Sourced Distributed Monitoring), Influenzanet and Flu Near You (FNY), and show how modeling and simulation can be or has been combined with participatory disease surveillance to: i) measure the non-response bias in a participatory surveillance sample using WISDM; and ii) nowcast and forecast influenza activity in different parts of the world (using Influenzanet and Flu Near You). Results: WISDM-based results measure the participatory and sample bias for three epidemic metrics i.e. attack rate, peak infection rate, and time-to-peak, and find the participatory bias to be the largest component of the total bias. The Influenzanet platform shows that digital participatory surveillance data combined with a realistic data-driven epidemiological model can provide both short-term and long-term forecasts of epidemic intensities, and the ground truth data lie within the 95 percent confidence intervals for most weeks. The statistical accuracy of the ensemble forecasts increase as the season progresses. The Flu Near You platform shows that participatory surveillance data provide accurate short-term flu activity forecasts and influenza activity predictions. The correlation of the HealthMap Flu Trends estimates with the observed CDC ILI rates is 0.99 for 2013-2015. Additional data sources lead to an error reduction of about 40% when compared to the estimates of the model that only incorporates CDC historical information. Conclusions: While the advantages of participatory surveillance, compared to traditional surveillance, include its timeliness, lower costs, and broader reach, it is limited by a lack of control over the characteristics of the population sample. Modeling and simulation can help overcome this limitation as well as provide real-time and long-term forecasting of influenza activity in data-poor parts of the world. [ABSTRACT FROM AUTHOR]
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- 2017
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115. Book Reviews.
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Bankoff, Greg, Brookfield, Harold, Dening, Greg, Glaskin, Katie, Herriman, Nicholas, Huntsman, Judith, Lindstrom, Lamont, Lipset, David, McDougall, Debra, McWilliam, Andrew, Ninetto, Amy, Shimoda, Yukimi, Szarycz, Gregory S., Tomlinson, Matt, Wadley, Reed L., Wilson, Mandy, Yengoyan, Aram A., and Young, Diana
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NONFICTION - Abstract
The article reviews several books including "Colonial Pathologies: American Tropical Medicine, Race, and Hygiene in the Philippines," by Warwick Anderson, "Conservation is Our Government Now: The Politics of Ecology in Papua New Guinea," by Paige West, and "Critical Junctions: Anthropology and History Beyond the Cultural Turn," edited by Don Kalb and Herman Tak.
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- 2008
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116. What's your Story.
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Wilson, Mandy
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CREATIVE writing ,YOUTH ,CHARITIES - Abstract
The article offers information on the What's your Story programme launched by the charity Scottish Book Trust, aiming to increase and develop creative writing opportunities for youth in Scotland.
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- 2017
117. Book Reviews.
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Smith, Moya, Ram, Kalpana, Bacon, Violet, Fuary, Maureen, Herdman, Elizabeth, May, Ron J., Pomponio, Alice, Law, Lisa, Wilson, Mandy, Kenyon, Susan M., Hadas, Miklos, Skrbis, Zlatko, Layton, Robert, and Bowdler, Sandra
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- ANTHROPOLOGY Explored (Book), CULTURAL Dialectics of Knowledge & Desire, The (Book), DEALING With Alcohol: Indigenous Usage in Australia, New Zealand & Canada (Book), MODERN Papua New Guinea (Book)
- Abstract
Reviews several books on anthropology. 'Anthropology Explored: The Best of Smithsonian AnthroNotes,' edited by Ruth Osterweis Selig and Marilyn R. London; 'The Cultural Dialectics of Knowledge and Desire,' by Charles W. Nuckolls; 'Dealing With Alcohol: Indigenous Usage in Australia, New Zealand and Canada,' by Sherry Saggers and Dennis Gray; 'Modern Papua New Guinea,' edited by Laura Zimmer-Tamakoshi.
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- 2001
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118. LABOR OF LOVE.
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WILSON, MANDY
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LESBIANS ,HUMAN rights workers ,LGBTQ+ rights ,BUSINESS insurance ,LGBTQ+ youth - Abstract
The article features lesbian human rights campaigner Pam Sheffer. It highlights Sheffer's campaign for lesbian, gay, bisexual and transgender (LGBT) rights in the Bible Belt region of the U.S. Background is presented on Sheffer's career including how she left her career in corporate insurance to start a campaign for LGBT youth's rights in Nashville, Tennessee.
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- 2013
119. Heart and Soul.
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Wilson, Mandy
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LGBTQ+ communities ,SPIRITUALITY ,HUMAN sexuality ,DISCRIMINATION (Sociology) ,LGBTQ+ people - Abstract
The author presents guidelines for members of the lesbian, gay, bisexual, and transgender (LGBT) community on how to reconcile their spirituality and sexuality. Finding like-minded individuals or a support system to overcome doubt and insecurity is recommended. The author talks about how religious extremists misuse the Scriptures to discriminate against various groups of people. LGBT people are also encouraged to engage in activities that enrich the spirit.
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- 2012
120. Women's experiences with HIV/AIDS (Book).
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Wilson, Mandy
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DISEASES in women , *NONFICTION - Abstract
Reviews the book 'Women's Experiences With HIV/AIDS: An International Perspective,' edited by Lynellyn D. Long and E. Maxine Ankrah.
- Published
- 1999
121. reviews. Mood Swings: Managing anger, anxiety and low mood.
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Wilson, Mandy
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AFFECTIVE disorders - Published
- 2017
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122. The Innovative School Librarian (second edition).
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Wilson, Mandy
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SCHOOL librarians ,AIMS & objectives of school libraries ,NONFICTION - Published
- 2017
123. "They just don't care about us!": Police custody experiences for young men with histories of injecting drug use.
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Walker, Shelley, Higgs, Peter, Stoové, Mark, and Wilson, Mandy
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PRISONERS & drugs , *DETENTION of persons - Abstract
Young men (aged 18–24) represent a quarter of all episodes of police custody detention for adult males in Victoria, Australia. Despite this, little is known about their experience. Using Bacchi's Foucauldian-influenced "What's the problem represented to be?" approach and data from interviews with 28 young men with histories of injecting drug use who were detained in police custody prior to adult prison, we aim to address this gap in the literature. We highlight how dividing practices of discrimination made possible their subjectification as "dangerous violent Others" and how unruly behaviour and self-harm were simultaneous mechanisms for voicing their despair and frustration, for gaining power in a place in which they had very little control and for resisting dominant truths imposed upon them as worthless subjects. It is such positioning we argue, that allowed the forfeiting of their rights to basic health care, fair treatment and respect, and at the same time produced and exacerbated a range of psychological, physical and social harms. Our analysis raises important questions about police custody, notably its role in the production of inequality and further marginalisation of vulnerable groups. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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124. "A spray bottle and a lollipop stick": An examination of policy prohibiting sterile injecting equipment in prison and effects on young men with injecting drug use histories.
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Walker, Shelley, Seear, Kate, Higgs, Peter, Stoové, Mark, and Wilson, Mandy
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INTRAVENOUS drug abuse , *MALE prisoners , *DETENTION of persons , *EPIDEMIOLOGY education , *SYRINGES , *PHARMACEUTICAL policy , *HEALTH policy , *RESEARCH , *CORRECTIONAL institutions , *PRISONERS , *RESEARCH methodology , *MEDICAL cooperation , *EVALUATION research , *COMPARATIVE studies , *DRUGS - Abstract
Background: Australian young male prisoners with histories of injecting drug use are more likely to report injecting in prison, to do so more frequently, and to be involved in more un-safe injecting-related practices than their older counterparts. Despite international evidence that prison needle and syringe programs are both feasible and effective in reducing the harms associated with injecting drug use in prison, these young men do not have access to such equipment.Methods: We critically analyse the interview transcripts of 28 young men with histories of injecting drug use who were recently released from adult prisons in Victoria, Australia, and prison drug policy text. We use Bacchi's 'What's the problem represented to be?' approach to examine how the 'problem' of injecting drug use in prison is represented in prison drug policy, including the assumptions that underpin these problematisations, and the subjectification and lived effects that are produced for the young men in our study.Results: Our analysis reveals how prison drug policy enables the creation and re-use of homemade injecting equipment crafted from unsterile items found in prison, and that in doing so the policy produces a range of stigmatising subjectification effects and other harmful material effects (such as hepatitis C virus transmission and injecting related injury and harms). Findings highlight, how injecting drug use is represented in policy silences other ways of understanding the 'problem' that may have less harmful effects for incarcerated young men who inject drugs.Conclusion: We argue that somewhat paradoxically, the approach of prohibiting access to sterile injecting equipment in prison-which is constituted as a solution for addressing such harms-in fact helps to produce them. [ABSTRACT FROM AUTHOR]- Published
- 2020
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125. Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.
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Bhattacharya P, Machi D, Chen J, Hoops S, Lewis B, Mortveit H, Venkatramanan S, Wilson ML, Marathe A, Porebski P, Klahn B, Outten J, Vullikanti A, Xie D, Adiga A, Brown S, Barrett C, and Marathe M
- Abstract
We present MacKenzie, a HPC-driven multi-cluster workflow system that was used repeatedly to configure and execute fine-grained US national-scale epidemic simulation models during the COVID-19 pandemic. Mackenzie supported federal and Virginia policymakers, in real-time, for a large number of "what-if" scenarios during the COVID-19 pandemic, and continues to be used to answer related questions as COVID-19 transitions to the endemic stage of the disease. MacKenzie is a novel HPC meta-scheduler that can execute US-scale simulation models and associated workflows that typically present significant big data challenges. The meta-scheduler optimizes the total execution time of simulations in the workflow, and helps improve overall human productivity. As an exemplar of the kind of studies that can be conducted using Mackenzie, we present a modeling study to understand the impact of vaccine-acceptance in controlling the spread of COVID-19 in the US. We use a 288 million node synthetic social contact network (digital twin) spanning all 50 US states plus Washington DC, comprised of 3300 counties, with 12 billion daily interactions. The highly-resolved agent-based model used for the epidemic simulations uses realistic information about disease progression, vaccine uptake, production schedules, acceptance trends, prevalence, and social distancing guidelines. Computational experiments show that, for the simulation workload discussed above, MacKenzie is able to scale up well to 10K CPU cores. Our modeling results show that, when compared to faster and accelerating vaccinations, slower vaccination rates due to vaccine hesitancy cause averted infections to drop from 6.7M to 4.5M, and averted total deaths to drop from 39.4K to 28.2K across the US. This occurs despite the fact that the final vaccine coverage is the same in both scenarios. We also find that if vaccine acceptance could be increased by 10% in all states, averted infections could be increased from 4.5M to 4.7M (a 4.4% improvement) and total averted deaths could be increased from 28.2K to 29.9K (a 6% improvement) nationwide., Competing Interests: Parantapa Bhattacharya reports financial support was provided by Centers for Disease Control and Prevention. Parantapa Bhattacharya reports financial support was provided by Virginia Department of Health. Parantapa Bhattacharya reports financial support was provided by National Science Foundation. Parantapa Bhattacharya reports financial support was provided by National Institutes of Health.
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- 2024
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126. Exposure to Childhood Adversity and Intimate Partner Violence in a Sample of Incarcerated Women in Australia.
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Fischer L, Wilson M, Schofield PW, Jones J, Kariminia A, Barrett E, Dean K, Sullivan E, Covington S, and Butler T
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Women who use violence represent one of the fastest growing groups within the Australian prisoner population, including Aboriginal women who are more likely to be incarcerated than non-Aboriginal women for violent crimes. Many incarcerated women report histories of adverse childhood experiences (ACEs) and intimate partner violence. This exploratory study examines baseline data from a sample of 167 women in 3 Western Australia women's prisons enrolled in a gender-specific violent behavior program. It describes their exposure to intimate partner violence, head injury, and childhood adversities. Overall, 94% of women had experienced at least one childhood adversity (median 6), and 94% reported being a victim of physical violence by a current or former intimate partner. Aboriginal women were more likely than non-Aboriginal women to report that a family member was incarcerated as a child ( p = .001). There was an association between an increased number of ACEs and head injury with a loss of consciousness ( p = .008). Overall, these results present a harrowing picture of childhood exposure to adversity and violence in adulthood. Successful rehabilitation of women incarcerated for violent crimes should be cognizant of the histories of extreme violence endured by most of these women., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
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- 2024
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127. Factors associated with unintended pregnancy and contraceptive practices in justice-involved adolescent girls in Australia.
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Smith H, Wilson M, Donovan B, Jones J, Butler T, Nathan S, and Simpson P
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- Adolescent, Female, Humans, Pregnancy, Pregnancy in Adolescence statistics & numerical data, Australia epidemiology, Risk Factors, Pregnancy, Unplanned, Contraception Behavior statistics & numerical data
- Abstract
Introduction: Despite a decline in unintended teenage pregnancy in Australia, rates remain higher amongst justice-involved adolescent girls, who are more likely to be from disadvantaged socio-economic backgrounds, have histories of abuse, substance use and/or mental health issues. Furthermore, exposure to the criminal justice system may alter access to education and employment and opportunities, potentially resulting in distinct risk-factor profiles. We examine factors associated with unintended pregnancy, non-contraceptive use and Long-Acting Reversible Contraception (LARC) in a sample of sexually active, justice-involved adolescent girls from Western Australia and Queensland., Methods: Data from the Mental Health, Sexual Health and Reproductive Health of Young People in Contact with the Criminal Justice System (MeH-JOSH) Study was analysed on 118 sexually active adolescent girls. Participants were aged between 14 and 17 years, purposefully sampled based on justice-system involvement and completed an anonymous telephone survey. We constructed two multivariate models taking reproductive outcomes as the dependent variables., Results: Over one quarter (26%, 30/118) reported a past unintended pregnancy, 54 did not use any contraception at their last sexual encounter, and 17 reported LARC use. Following adjustments in the multivariate analysis, lifetime ecstasy use was associated with both unintended pregnancy (aOR 3.795, p = 0.022) and non-contraception use (aOR 4.562, p = 0.004). A history of physical abuse was also associated with both any contraception (aOR 3.024, p = 0.041) and LARC use (aOR 4.892, p = 0.050). Identifying as Aboriginal & Torres Strait Islander, education/employment status and geographic location appeared to have no association., Conclusion: Our findings suggest that justice-involved adolescent girls have distinct risk factors associated with unplanned pregnancy and contraception use compared to the general population, but more research is required to understand the mechanisms and contexts underlying these risk factors. How exposure to physical violence may encourage contraception and LARC use, in particular, warrants further attention as does the association with ecstasy use., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Smith et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2024
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128. Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections.
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Porebski P, Venkatramanan S, Adiga A, Klahn B, Hurt B, Wilson ML, Chen J, Vullikanti A, Marathe M, and Lewis B
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- Humans, United States epidemiology, Pandemics prevention & control, COVID-19 Vaccines immunology, Virginia epidemiology, Epidemiological Models, Forecasting, COVID-19 transmission, COVID-19 epidemiology, COVID-19 prevention & control, COVID-19 immunology, SARS-CoV-2 immunology
- Abstract
Scenario-based modeling frameworks have been widely used to support policy-making at state and federal levels in the United States during the COVID-19 response. While custom-built models can be used to support one-off studies, sustained updates to projections under changing pandemic conditions requires a robust, integrated, and adaptive framework. In this paper, we describe one such framework, UVA-adaptive, that was built to support the CDC-aligned Scenario Modeling Hub (SMH) across multiple rounds, as well as weekly/biweekly projections to Virginia Department of Health (VDH) and US Department of Defense during the COVID-19 response. Building upon an existing metapopulation framework, PatchSim, UVA-adaptive uses a calibration mechanism relying on adjustable effective transmissibility as a basis for scenario definition while also incorporating real-time datasets on case incidence, seroprevalence, variant characteristics, and vaccine uptake. Through the pandemic, our framework evolved by incorporating available data sources and was extended to capture complexities of multiple strains and heterogeneous immunity of the population. Here we present the version of the model that was used for the recent projections for SMH and VDH, describe the calibration and projection framework, and demonstrate that the calibrated transmissibility correlates with the evolution of the pathogen as well as associated societal dynamics., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
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- 2024
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129. Police custody in Australia: A call for transparency and accountability.
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Walker S, Wilson M, Seear K, Doyle M, Saich F, Stoové M, and Winter R
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- Humans, Cause of Death, Australia, Social Responsibility, Police, Prisoners
- Abstract
Competing Interests: Conflicts of interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
- Published
- 2023
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130. Scalable Epidemiological Workflows to Support COVID-19 Planning and Response.
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Machi D, Bhattacharya P, Hoops S, Chen J, Mortveit H, Venkatramanan S, Lewis B, Wilson M, Fadikar A, Maiden T, Barrett CL, and Marathe MV
- Abstract
The COVID-19 global outbreak represents the most significant epidemic event since the 1918 influenza pandemic. Simulations have played a crucial role in supporting COVID-19 planning and response efforts. Developing scalable workflows to provide policymakers quick responses to important questions pertaining to logistics, resource allocation, epidemic forecasts and intervention analysis remains a challenging computational problem. In this work, we present scalable high performance computing-enabled workflows for COVID-19 pandemic planning and response. The scalability of our methodology allows us to run fine-grained simulations daily, and to generate county-level forecasts and other counter-factual analysis for each of the 50 states (and DC), 3140 counties across the USA. Our workflows use a hybrid cloud/cluster system utilizing a combination of local and remote cluster computing facilities, and using over 20,000 CPU cores running for 6-9 hours every day to meet this objective. Our state (Virginia), state hospital network, our university, the DOD and the CDC use our models to guide their COVID-19 planning and response efforts. We began executing these pipelines March 25, 2020, and have delivered and briefed weekly updates to these stakeholders for over 30 weeks without interruption.
- Published
- 2021
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131. Prioritizing allocation of COVID-19 vaccines based on social contacts increases vaccination effectiveness.
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Chen J, Hoops S, Marathe A, Mortveit H, Lewis B, Venkatramanan S, Haddadan A, Bhattacharya P, Adiga A, Vullikanti A, Srinivasan A, Wilson M, Ehrlich G, Fenster M, Eubank S, Barrett C, and Marathe M
- Abstract
We study allocation of COVID-19 vaccines to individuals based on the structural properties of their underlying social contact network. Even optimistic estimates suggest that most countries will likely take 6 to 24 months to vaccinate their citizens. These time estimates and the emergence of new viral strains urge us to find quick and effective ways to allocate the vaccines and contain the pandemic. While current approaches use combinations of age-based and occupation-based prioritizations, our strategy marks a departure from such largely aggregate vaccine allocation strategies. We propose a novel approach motivated by recent advances in (i) science of real-world networks that point to efficacy of certain vaccination strategies and (ii) digital technologies that improve our ability to estimate some of these structural properties. Using a realistic representation of a social contact network for the Commonwealth of Virginia, combined with accurate surveillance data on spatiotemporal cases and currently accepted models of within- and between-host disease dynamics, we study how a limited number of vaccine doses can be strategically distributed to individuals to reduce the overall burden of the pandemic. We show that allocation of vaccines based on individuals' degree (number of social contacts) and total social proximity time is significantly more effective than the currently used age-based allocation strategy in terms of number of infections, hospitalizations and deaths. Our results suggest that in just two months, by March 31, 2021, compared to age-based allocation, the proposed degree-based strategy can result in reducing an additional 56-110k infections, 3.2- 5.4k hospitalizations, and 700-900 deaths just in the Commonwealth of Virginia. Extrapolating these results for the entire US, this strategy can lead to 3-6 million fewer infections, 181-306k fewer hospitalizations, and 51-62k fewer deaths compared to age-based allocation. The overall strategy is robust even: (i) if the social contacts are not estimated correctly; (ii) if the vaccine efficacy is lower than expected or only a single dose is given; (iii) if there is a delay in vaccine production and deployment; and (iv) whether or not non-pharmaceutical interventions continue as vaccines are deployed. For reasons of implementability, we have used degree, which is a simple structural measure and can be easily estimated using several methods, including the digital technology available today. These results are significant, especially for resource-poor countries, where vaccines are less available, have lower efficacy, and are more slowly distributed.
- Published
- 2021
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132. From 5Vs to 6Cs: Operationalizing Epidemic Data Management with COVID-19 Surveillance.
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Peddireddy AS, Xie D, Patil P, Wilson ML, Machi D, Venkatramanan S, Klahn B, Porebski P, Bhattacharya P, Dumbre S, Raymond E, and Marathe M
- Abstract
The COVID-19 pandemic brought to the forefront an unprecedented need for experts, as well as citizens, to visualize spatio-temporal disease surveillance data. Web application dashboards were quickly developed to fill this gap, including those built by JHU, WHO, and CDC, but all of these dashboards supported a particular niche view of the pandemic (ie, current status or specific regions). In this paper, we describe our work developing our own COVID-19 Surveillance Dashboard, available at https://nssac.bii.virginia.edu/covid-19/dashboard/, which offers a universal view of the pandemic while also allowing users to focus on the details that interest them. From the beginning, our goal was to provide a simple visual way to compare, organize, and track near-real-time surveillance data as the pandemic progresses. Our dashboard includes a number of advanced features for zooming, filtering, categorizing and visualizing multiple time series on a single canvas. In developing this dashboard, we have also identified 6 key metrics we call the 6Cs standard which we propose as a standard for the design and evaluation of real-time epidemic science dashboards. Our dashboard was one of the first released to the public, and remains one of the most visited and highly used. Our group uses it to support federal, state and local public health authorities, and it is used by people worldwide to track the pandemic evolution, build their own dashboards, and support their organizations as they plan their responses to the pandemic. We illustrate the utility of our dashboard by describing how it can be used to support data story-telling - an important emerging area in data science.
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- 2020
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133. Evaluating the impact of international airline suspensions on the early global spread of COVID-19.
- Author
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Adiga A, Venkatramanan S, Schlitt J, Peddireddy A, Dickerman A, Bura A, Warren A, Klahn BD, Mao C, Xie D, Machi D, Raymond E, Meng F, Barrow G, Mortveit H, Chen J, Walke J, Goldstein J, Wilson ML, Orr M, Porebski P, Telionis PA, Beckman R, Hoops S, Eubank S, Baek YY, Lewis B, Marathe M, and Barrett C
- Abstract
Global airline networks play a key role in the global importation of emerging infectious diseases. Detailed information on air traffic between international airports has been demonstrated to be useful in retrospectively validating and prospectively predicting case emergence in other countries. In this paper, we use a well-established metric known as effective distance on the global air traffic data from IATA to quantify risk of emergence for different countries as a consequence of direct importation from China, and compare it against arrival times for the first 24 countries. Using this model trained on official first reports from WHO, we estimate time of arrival (ToA) for all other countries. We then incorporate data on airline suspensions to recompute the effective distance and assess the effect of such cancellations in delaying the estimated arrival time for all other countries. Finally we use the infectious disease vulnerability indices to explain some of the estimated reporting delays.
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- 2020
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134. Aboriginal mothers in prison in Australia: a study of social, emotional and physical wellbeing.
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Sullivan EA, Kendall S, Chang S, Baldry E, Zeki R, Gilles M, Wilson M, Butler T, Levy M, Wayland S, Cullen P, Jones J, and Sherwood J
- Subjects
- Adult, Australia epidemiology, Cross-Sectional Studies, Delivery of Health Care, Female, Humans, Mental Disorders epidemiology, Mothers, Native Hawaiian or Other Pacific Islander statistics & numerical data, Substance-Related Disorders epidemiology, Emotions, Health Status, Mental Health statistics & numerical data, Native Hawaiian or Other Pacific Islander psychology, Prisoners psychology
- Abstract
Objective: To describe the social, emotional and physical wellbeing of Aboriginal mothers in prison., Methods: Cross-sectional survey, including a Short Form Health Survey (SF-12) and Kessler Psychological Distress Scale (5-item version) administered to Aboriginal women who self-identified as mothers., Results: Seventy-seven Aboriginal mothers in New South Wales (NSW) and 84 in Western Australia (WA) participated in the study. Eighty-three per cent (n=59) of mothers in NSW were in prison for drug-related offences, 64.8% (n=46) of mothers in WA were in prison for offences committed under the influence of alcohol. Sixty-eight per cent (n=52) of mothers in NSW and 35% (n=28) of mothers in WA reported mental health problems. Physical (PCS) and Mental (MCS) component scores of SF-12 varied for mothers in NSW and WA. Mothers in NSW experienced poorer health and functioning than mothers in WA (NSW: PCS 49.5, MCS 40.6; WA: PCS 54.4, MCS 48.3) and high levels of psychological distress (NSW: 13.1; WA 10.1)., Conclusions: Aboriginal mothers in prison have significant health needs associated with physical and mental health, and psychological distress. Implications for public health: Adoption of social and emotional wellbeing as an explanatory framework for culturally secure healthcare in prison is essential to improving health outcomes of Aboriginal mothers in prison in Australia., (© 2019 The Authors.)
- Published
- 2019
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135. Australian Aboriginal women prisoners' experiences of being a mother: a review.
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Jones J, Wilson M, Sullivan E, Atkinson L, Gilles M, Simpson PL, Baldry E, and Butler T
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- Adolescent, Adult, Australia, Female, Humans, Young Adult, Mothers, Native Hawaiian or Other Pacific Islander, Prisoners
- Abstract
Purpose: The rise in the incarceration of Aboriginal and Torres Strait Islander mothers is a major public health issue with multiple sequelae for Aboriginal children and the cohesiveness of Aboriginal communities. The purpose of this paper is to review the available literature relating to Australian Aboriginal women prisoners' experiences of being a mother., Design/methodology/approach: The literature search covered bibliographic databases from criminology, sociology and anthropology, and Australian history. The authors review the literature on: traditional and contemporary Aboriginal mothering roles, values and practices; historical accounts of the impacts of white settlement of Australia and subsequent Aboriginal affairs policies and practices; and women's and mothers' experiences of imprisonment., Findings: The review found that the cultural experiences of mothering are unique to Aboriginal mothers and contrasted to non-Aboriginal concepts. The ways that incarceration of Aboriginal mothers disrupts child rearing practices within the cultural kinship system are identified., Practical Implications: Aboriginal women have unique circumstances relevant to the concept of motherhood that need to be understood to develop culturally relevant policy and programs. The burden of disease and cycle of incarceration within Aboriginal families can be addressed by improving health outcomes for incarcerated Aboriginal mothers and female carers., Originality/value: To the authors' knowledge, this is the first literature review on Australian Aboriginal women prisoners' experiences of being a mother.
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- 2018
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136. EpiViewer: an epidemiological application for exploring time series data.
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Thorve S, Wilson ML, Lewis BL, Swarup S, Vullikanti AKS, and Marathe MV
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- Humans, Information Dissemination methods, Software trends
- Abstract
Background: Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers identify anomalies and unexpected trends that could be overlooked if the data were reviewed in tabular form; these details can influence a researcher's recommended course of action or choice of simulation models. However, there are challenges in reviewing data sets from multiple data sources - data can be aggregated in different ways (e.g., incidence vs. cumulative), measure different criteria (e.g., infection counts, hospitalizations, and deaths), or represent different geographical scales (e.g., nation, HHS Regions, or states), which can make a direct comparison between time series difficult. In the face of an emerging epidemic, the ability to visualize time series from various sources and organizations and to reconcile these datasets based on different criteria could be key in developing accurate forecasts and identifying effective interventions. Many tools have been developed for visualizing temporal data; however, none yet supports all the functionality needed for easy collaborative visualization and analysis of epidemic data., Results: In this paper, we present EpiViewer, a time series exploration dashboard where users can upload epidemiological time series data from a variety of sources and compare, organize, and track how data evolves as an epidemic progresses. EpiViewer provides an easy-to-use web interface for visualizing temporal datasets either as line charts or bar charts. The application provides enhanced features for visual analysis, such as hierarchical categorization, zooming, and filtering, to enable detailed inspection and comparison of multiple time series on a single canvas. Finally, EpiViewer provides several built-in statistical Epi-features to help users interpret the epidemiological curves., Conclusion: EpiViewer is a single page web application that provides a framework for exploring, comparing, and organizing temporal datasets. It offers a variety of features for convenient filtering and analysis of epicurves based on meta-attribute tagging. EpiViewer also provides a platform for sharing data between groups for better comparison and analysis. Our user study demonstrated that EpiViewer is easy to use and fills a particular niche in the toolspace for visualization and exploration of epidemiological data.
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- 2018
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137. GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis.
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Coll A, Wilson ML, Gruden K, and Peccoud J
- Subjects
- Gene Expression Regulation, Plant genetics, Genetic Vectors, Plants genetics, Genetic Engineering methods, Promoter Regions, Genetic, Software, Synthetic Biology methods
- Abstract
With the rapid advances in prediction tools for discovery of new promoters and their cis-elements, there is a need to improve plant expression methodologies in order to facilitate a high-throughput functional validation of these promoters in planta. The promoter-reporter analysis is an indispensible approach for characterization of plant promoters. It requires the design of complex plant expression vectors, which can be challenging. Here, we describe the use of a plant grammar implemented in GenoCAD that will allow the users to quickly design constructs for promoter analysis experiments but also for other in planta functional studies. The GenoCAD plant grammar includes a library of plant biological parts organized in structural categories to facilitate their use and management and a set of rules that guides the process of assembling these biological parts into large constructs.
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- 2016
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138. EpiCaster: An Integrated Web Application For Situation Assessment and Forecasting of Global Epidemics.
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Deodhar S, Bisset K, Chen J, Barrett C, Wilson M, and Marathe M
- Abstract
Public health decision makers need access to high resolution situation assessment tools for understanding the extent of various epidemics in different regions of the world. In addition, they need insights into the future course of epidemics by way of forecasts. Such forecasts are essential for planning the allocation of limited resources and for implementing several policy-level and behavioral intervention strategies. The need for such forecasting systems became evident in the wake of the recent Ebola outbreak in West Africa. We have developed EpiCaster, an integrated Web application for situation assessment and forecasting of various epidemics, such as Flu and Ebola, that are prevalent in different regions of the world. Using EpiCaster, users can assess the magnitude and severity of different epidemics at highly resolved spatio-temporal levels. EpiCaster provides time-varying heat maps and graphical plots to view trends in the disease dynamics. EpiCaster also allows users to visualize data gathered through surveillance mechanisms, such as Google Flu Trends (GFT) and the World Health Organization (WHO). The forecasts provided by EpiCaster are generated using different epidemiological models, and the users can select the models through the interface to filter the corresponding forecasts. EpiCaster also allows the users to study epidemic propagation in the presence of a number of intervention strategies specific to certain diseases. Here we describe the modeling techniques, methodologies and computational infrastructure that EpiCaster relies on to support large-scale predictive analytics for situation assessment and forecasting of global epidemics.
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- 2015
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139. A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.
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Wilson ML, Hertzberg R, Adam L, and Peccoud J
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- Algorithms, Gene Library, Internet, Base Sequence, Computer-Aided Design, Genes, Synthetic, Software, User-Computer Interface
- Abstract
GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project. Design strategies include limited sets of user-defined parts and rules indicating how these parts are to be combined in genetic constructs. In addition to reducing design time to minutes, GenoCAD improves the quality and reliability of the finished sequence by ensuring that the designs follow established rules of sequence construction. GenoCAD.org is a publicly available instance of GenoCAD that can be found at www.genocad.org. The source code and latest build are available from SourceForge to allow advanced users to install and customize GenoCAD for their unique needs. This chapter focuses primarily on how the GenoCAD tools can be used to organize genetic parts into customized personal libraries, then how these libraries can be used to design sequences. In addition, GenoCAD's parts management system and search capabilities are described in detail. Instructions are provided for installing a local instance of GenoCAD on a server. Some of the future enhancements of this rapidly evolving suite of applications are briefly described., (Copyright © 2011 Elsevier Inc. All rights reserved.)
- Published
- 2011
- Full Text
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