Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution

In this paper we determine the extent to which host-mediated mutations and a known sampling bias affect evolutionary studies of human influenza A. Previous phylogenetic reconstruction of influenza A (H3N2) evolution using the hemagglutinin gene revealed an excess of nonsilent substitutions assigned to the terminal branches of the tree. We investigate two hypotheses to explain this observation. The first hypothesis is that the excess reflects mutations that were either not present or were at low frequency in the viral sample isolated from its human host, and that these mutations increased in frequency during passage of the virus in embryonated eggs. A set of 22 codons known to undergo such “host-mediated” mutations showed a significant excess of mutations assigned to branches attaching sequences from egg-cultured (as opposed to cell-cultured) isolates to the tree. Our second hypothesis is that the remaining excess results from sampling bias. Influenza surveillance is purposefully biased toward sequencing antigenically dissimilar strains in an effort to identify new variants that may signal the need to update the vaccine. This bias produces an excess of mutations assigned to terminal branches simply because an isolate with no close relatives is by definition attached to the tree by a relatively long branch. Simulations show that the magnitude of excess mutations we observed in the hemagglutinin tree is consistent with expectations based on our sampling protocol. Sampling bias does not affect inferences about evolution drawn from phylogenetic analyses. However, if possible, the excess caused by host-mediated mutations should be removed from studies of the evolution of influenza viruses as they replicate in their human hosts.

Attentional processes associated with victimization history and posttraumatic symptomatology in women exposed to intimate partner violence

Exposure to intimate partner violence (IPV) puts women at risk for severe and chronic physical and mental health consequences, including elevations in IPV-related psychopathology and increased risk for future victimization. Previous research has examined attention as one of the key information processing mechanisms associated with elevated psychopathology and risk for victimization; however, the nature of attentional processing in response to IPV-related information in women exposed to IPV is poorly understood. Therefore, the current study aimed to further understanding of associations between attentional processing, IPV exposure, and related distress using measures of eye movement and subjective interpretations of IPV-related information. A sample of women exposed to IPV (n = 57) viewed sets of negative, positive, and neutral relationship images for 15 s each while having their eye movements monitored and later provided subjective ratings and interpretations of levels of risk and safety in those images. We examined associations of outcome measures with proximal victimization experiences and IPV-related psychopathology (i.e., depression, posttraumatic stress disorder (PTSD), anxiety, and dissociation). Results indicated a bias to attend to negative relationship images relative to positive and neutral images, though this attention bias fluctuated over time and varied as a function of symptomatology such that depression corresponded with increases in attention to negative images over time and PTSD corresponded with decreases in attention to negative images. The general attention bias for negative images appeared to be explained by rumination on and/or difficulty disengaging from negative images, which was related to general elevations in psychopathology as well as exposure to revictimization by different perpetrators. Subjective interpretations and perception of danger cues were related to victimization history and level and type of IPV-related distress. We replicated these procedures with a sample of undergraduate students without IPV histories or related symptomatology (n = 33) and found that the overall attention bias for negative images was not replicated, despite general similarities in patterns of attention over time. Results therefore indicated associations between attentional processing and IPV exposure and related symptomatology. Implications for models of IPV-related psychopathology and attentional processing as well as directions for future study and interventions are discussed.

Background Checks for Firearms Sales and Loans: Law, History, and Policy

This article examines past and present systems requiring that a person receive permission before buying or borrowing a firearm. The article covers laws from the eighteenth century to the present. Such laws have traditionally been rare in the United States. The major exceptions are antebellum laws of the slaves states, and of those same states immediately after the Civil War, which forbade gun ownership by people of color, unless the individual had been granted government permission. Today “universal background checks” are based on a system created by former New York City Mayor Michael Bloomberg and his “Everytown” lobby. Such laws have been enacted in several states, and also proposed as federal legislation. Besides covering the private sale of firearms, they also cover most loans of firearms and the return of loaned firearms. By requiring that almost all loans and returns may only be processed by a gun store, these laws dangerously constrict responsible firearms activities, such as safety training and safe storage. Massachusetts, Connecticut, and California are among the jurisdictions which have enacted less restrictive, more effective legislation which create controls on private firearms sales, without inflicting so much harm on firearms safety.

An early archaeological example of tattooing from northwestern Alaska / James W. VanStone, Curator, North American Archaeology and Ethnology, Field Museum of Natural History, and Charles V. Lucier, Alaska Dept. of Fish and Game.

v.66:no.1(1974)

The Mammalian faunas of the Washakie Formation, Eocene Age, of Southern Wyoming. Introduction: The geology, history, and setting / William D. Turnbull --.

v.33:no.30(1978)

The brown-tail moth, Euproctis chrysorrhcea (L.). A report on the life history and habits of the imported brown-tail moth, together with a description of the remedies best suited for destroying it. By Charles H. Fernald ... and Archie H. Kirkland ... Pub. under the direction of the State board of agriculture by authority of the legislature.

1903

Catalogue of birds of the Americas and the adjacent islands in Field Museum of Natural History and including all species and subspecies known to occur in North America, Mexico, Central America, South America, the West Indies, and islands of the Caribbean Sea, the Galapagos Archipelago, and other islands which may properly be included on account of their faunal affinities.

v.13:pt.1:no.1(1942)

The brown-tail moth, Euproctis chrysorrhcea (L.). A report on the life history and habits of the imported brown-tail moth, together with a description of the remedies best suited for destroying it. By Charles H. Fernald ... and Archie H. Kirkland ... Pub. under the direction of the State board of agriculture by authority of the legislature.

1903

Mathematical notebook, and commonplace book, circa 1689-1769

Manuscript notebook, possibly kept by Harvard students, containing 17th century English transcriptions of arithmetic and geometry texts, one of which is dated 1689-1690; 18th century transcriptions from John Ward’s “The Young Mathematician’s Guide”; and notes on physics lectures delivered by John Winthrop, the Hollis Professor of Mathematics and Natural Philosophy at Harvard from 1738 to 1779. The notebook also contains 18th century reading notes on Henry VIII, Tudor succession, and English history from Daniel Neal’s “The History of the Puritans” and David Hume’s “History of England,” and notes on Ancient history, taken mainly from Charles Rollin’s “The Ancient History of the Egyptians, Carthaginians, Assyrians, Babylonians, Medes and Persians, Macedonians and Grecians.” Additionally included are an excerpt from Plutarch’s “Lives” and transcriptions of three articles from “The Gentleman’s Magazine, and Historical Chronicle,” published in 1769: “A Critique on the Works of Ovid”; a book review of “A New Voyage to the West-Indies”; and “Genuine Anecdotes of Celebrated Writers, &.” The flyleaf contains the inscription “Semper boni aliquid operis facito ut diabolus te semper inveniat occupatum,” a variation on a quote of Saint Jerome that translates approximately as “Always good to do some work so that the devil may always find you occupied.” In the seventeenth and eighteenth centuries, Harvard College undergraduates often copied academic texts and lecture notes into personal notebooks in place of printed textbooks. Winthrop used Ward’s textbook in his class, while the books of Hume, Neal, and Rollin were used in history courses taught at Harvard in the 18th century.

Ed-Dürer ül-müntehabât ül-mensûre fî ıslâh il-galatat il-meşhûre

[Mehmed Hafid Efendi].

Essays on Firm Heterogeneity with Empirical Applications in Economic History and Agricultural Economics

This thesis uses models of firm-heterogeneity to complete empirical analyses in economic history and agricultural economics. In Chapter 2, a theoretical model of firm heterogeneity is used to derive a statistic that summarizes the welfare gains from the introduction of a new technology. The empirical application considers the use of mechanical steam power in the Canadian manufacturing sector during the late nineteenth century. I exploit exogenous variation in geography to estimate several parameters of the model. My results indicate that the use of steam power resulted in a 15.1 percent increase in firm-level productivity and a 3.0-5.2 percent increase in aggregate welfare. Chapter 3 considers various policy alternatives to price ceiling legislation in the market for production quotas in the dairy farming sector in Quebec. I develop a dynamic model of the demand for quotas with farmers that are heterogeneous in their marginal cost of milk production. The econometric analysis uses farm-level data and estimates a parameter of the theoretical model that is required for the counterfactual experiments. The results indicate that the price of quotas could be reduced to the ceiling price through a 4.16 percent expansion of the aggregate supply of quotas, or through moderate trade liberalization of Canadian dairy products. In Chapter 4, I study the relationship between farm-level productivity and participation in the Commercial Export Milk (CEM) program. I use a difference-in-difference research design with inverse propensity weights to test for causality between participation in the CEM program and total factor productivity (TFP). I find a positive correlation between participation in the CEM program and TFP, however I find no statistically significant evidence that the CEM program affected TFP.