Marrow of Tragedy: The Health Crisis of the American Civil War

The Issue of Public Health in a Time of War At the American Sociological Association’s annual meeting during August, 1986, Maris A. Vinovskis posed a question: “Have social historians lost the Civil War? He stated that indeed the “social historians of the nineteenth century appear to hav...

On a Great Battlefield: The Making, Management, and Memory of Gettysburg National Military Park, 19332012

The Origins and Changing Meaning of Battlefield Preservation Efforts On what is likely the most consecrated 6,000 acres of the United States landscape, is the Gettysburg National Military Park. Timothy B. Smith in The Golden Age of Battlefield Preservation: The Decade of the 1890\u27s and ...

Reflections Of A Civil War Medical Cadet, Burt Green Wilder

February 5 About one o\u27clock Dr. Marsh came to say that in ward 5 Dr. Hartsuff was to amputate the leg of a man who had be shot in the knee; the joint is shattered and discharges profusely.; he is so weak that he will die unless relieved of the drain. All the surgeons and cadets wer...

Nature\u27s Civil War: Common Soldiers and the Environment in 1862 Virginia

Medical Care at the Intersection Between Men and Their Environment Stephen Berry’s 2012 top ten list of “predictions for how broader professional trends will reshape Civil War historiography in the coming decades offers #7: The Blue and Gray Will Go Green. Berry predicts that by 2022 ign...

Lincoln and the Power of the Press: The War for Public Opinion

The Press and the President Lincoln and The Power of the Press: The War for Public Opinion is a detailed story of the process of journalism and the cult of personality of editors and owners. For a politician who declared that public sentiment is everything, Lincoln recognized that, ...

Frequency and implications of HIV superinfection

HIV superinfection occurs when an individual with HIV is infected with a new distinct HIV viral strain. Superinfection has been reported throughout the world, and studies have recorded incidence rates of 0–7·7% per year. Use of next-generation sequencing has improved detection of superinfection, which can be transmitted by injecting drug use and sexual intercourse. Superinfection might have incidence rates comparable to those of initial HIV infection. Clinicians should encourage safe sexual and injecting drug use practices for HIV-infected patients because superinfection has detrimental effects on clinical outcomes and could pose a concern for large-scale antiretroviral treatment plans. The occurrence of superinfection has implications for vaccine research, since it seems initial HIV infection is not fully protective against a subsequent infection. Additional collaborative research could benefit care of patients and inform future vaccine design

An Additive Bivariate Hierarchical Model for Functional Data and Related Computations

The work presented in this dissertation centers on the theme of regression and computation methodology. Functional data is an important class of longitudinal data, and principal component analysis is an important approach to regression with this type of data. Here we present an additive hierarchical bivariate functional data model employing principal components to identify random e ects. This additive model extends the univariate functional principal component model. These models are implemented in the pfda package for R. To t the curves from this class of models orthogonalized spline basis are used to reduce the dimensionality of the t, but retain exibility. Methods for handing spline basis functions in a purely analytical manner, including the orthogonalizing process and computing of penalty matrices used to t the principal component models are presented. The methods are implemented in the R package orthogonalsplinebasis. The projects discussed involve complicated coding for the implementations in R. To facilitate this I created the NppToR utility to add R functionality to the popular windows code editor Notepad . A brief overview of the use of the utility is also included

A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection

Funder: Isaac Newton Trust; funder-id: http://dx.doi.org/10.13039/501100004815Funder: Li Ka Shing Foundation; funder-id: http://dx.doi.org/10.13039/100007421Funder: Division of Intramural Research, National Institute of Allergy and Infectious Diseases; funder-id: http://dx.doi.org/10.13039/100006492Funder: Helsingin Yliopisto; funder-id: http://dx.doi.org/10.13039/100007797In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. We also identified a putative new CTL escape site (residue 286 in gag), and a region of gp41 (including residues 644, 648, 655 in env) likely to be associated with immune escape. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies

Enacting boundaries or building bridges? Language and engagement in food-energy-water systems science

Scientific study of issues at the nexus of food–energy–water systems (FEWS) requires grappling with multifaceted, “wicked” problems. FEWS involve interactions occurring directly and indirectly across complex and overlapping spatial and temporal scales; they are also imbued with diverse and sometimes conflicting meanings for the human and more-than-human beings that live within them. In this paper, we consider the role of language in the dynamics of boundary work, recognizing that the language often used in stakeholder and community engagement intended to address FEWS science and decision-making constructs boundaries and limits diverse and inclusive participation. In contrast, some language systems provide opportunities to build bridges rather than boundaries in engagement. Based on our experiences with engagement in FEWS science and with Indigenous knowledges and languages, we consider examples of the role of language in reflecting worldviews, values, practices, and interactions in FEWS science and engagement. We particularly focus on Indigenous knowledges from Anishinaabe and the language of Anishinaabemowin, contrasting languages of boundaries and bridges through concrete examples. These examples are used to unpack the argument of this work, which is that scientific research aiming to engage FEWS issues in working landscapes requires grappling with embedded, practical understandings. This perspective demonstrates the importance of grappling with the role of language in creating boundaries or bridges, while recognizing that training in engagement may not critically reflect on the role of language in limiting diversity and inclusivity in engagement efforts. Leaving this reflexive consideration of language unexamined may unknowingly perpetuate boundaries rather than building bridges, thus limiting the effectiveness of engagement that is intended to address wicked problems in working landscapes