Visualizing genetic constraints

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, evolutionary biologists gain important insights from these low variation directions. Specifically, they are interested in directions of low genetic variability that are biologically interpretable. These directions are called genetic constraints and indicate directions in which a trait cannot evolve through selection. Here, we propose studying the subspace spanned by low variance principal components by determining vectors in this subspace that are simplest. Our method and accompanying graphical displays enhance the biologist's ability to visualize the subspace and identify interpretable directions of low genetic variability that align with simple directions.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS603 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Swine Influenza A Outbreak, Fort Dix, New Jersey, 1976

Published literature and events surrounding the outbreak are reviewed

DoD-GEIS Rift Valley Fever Monitoring and Prediction System as a Tool for Defense and US Diplomacy

Over the last 10 years the Armed Forces Health Surveillance Center's Global Emerging Infections Surveillance and Response System (GEIS) partnering with NASA'S Goddard Space Flight Center and USDA's USDA-Center for Medical, Agricultural & Veterinary Entomology established and have operated the Rift Valley fever Monitoring and Prediction System to monitor, predict and assess the risk of Rift Valley fever outbreaks and other vector-borne diseases over Africa and the Middle East. This system is built on legacy DoD basic research conducted by Walter Reed Army Institute of Research overseas laboratory (US Army Medical Research Unit-Kenya) and the operational satellite environmental monitoring by NASA GSFC. Over the last 10 years of operation the system has predicted outbreaks of Rift Valley fever in the Horn of Africa, Sudan, South Africa and Mauritania. The ability to predict an outbreak several months before it occurs provides early warning to protect deployed forces, enhance public health in concerned countries and is a valuable tool use.d by the State Department in US Diplomacy. At the international level the system has been used by the Food and Agricultural Organization (FAD) and the World Health Organization (WHO) to support their monitoring, surveillance and response programs in the livestock sector and human health. This project is a successful testament of leveraging resources of different federal agencies to achieve objectives of force health protection, health and diplomacy

Large, persistent epidemic of adenovirus type 4-associated acute respiratory disease in U.S. army trainees.

In May 1997, a large, persistent epidemic of adenovirus type 4-associated acute respiratory disease began at Fort Jackson, South Carolina, the largest army basic training center. The epidemic lasted until December and declined when vaccine administration resumed. More than 1,000 male and female trainees were hospitalized; 66.1% of those hospitalized had an adenovirus type 4 isolate

Evaluation of the Performance of a Point-of-Care Test for Chlamydia and Gonorrhea

Importance: Rates of chlamydial and gonococcal infection continue to increase in the United States, as do the associated costs of untreated infections. Improved diagnostic technologies that support testing and treating in 1 clinical visit are critical to advancing efforts to control the rates of chlamydial and gonococcal infection. Objective: To evaluate the clinical performance of a point-of-care (POC) molecular diagnostic assay for the detection of chlamydia and gonorrhea. Design, setting, and participants: A noninterventional, cross-sectional clinical study was conducted from September 18, 2018, through March 13, 2019, at sexually transmitted infection (STI), HIV, family planning, and obstetrics and gynecology clinics where STI screening is routine, using a convenience sample and comparing commercially available assays with a new 30-minute POC assay. Patients included were those eligible for STI screening or diagnostic testing who had not taken antibiotics effective against chlamydia or gonorrhea within the previous 28 days. Four vaginal swab samples were collected from women and a first-catch urine sample was obtained from men. Main outcomes and measures: A composite infection status was used to classify participants as infected if 2 or more comparator results were positive, as not infected if 2 or more comparator samples were negative, and as unevaluable if 1 result was invalid and the other 2 results did not agree with each other. Results: Swab samples from 1523 women (median age, 27 years [interquartile range, 17-37 years]), 817 (53.6%) of whom presented with symptoms, and 922 men (median age, 29 years [interquartile range, 17-41 years]), 308 (33.4%) of whom were symptomatic, were tested. For chlamydia, sensitivity of the new POC assay was 96.1% (95% CI, 91.2%-98.3%) for women and 92.5% (95% CI, 86.4%-96.0%) for men. For gonorrhea, sensitivity estimates were 100.0% (95% CI, 92.1%-100.0%) for women and 97.3% (95% CI, 90.7%-99.3%) for men. For chlamydia, specificity of the new POC assay was 99.1% (95% CI, 98.4%-99.5%) for women and 99.3% (95% CI, 98.4%-99.7%) for men. For gonorrhea, specificity estimates were 99.9% (95% CI, 99.5%-100%) for women and 100% (95% CI, 95.5%-100%) for men. Non-laboratory-trained personnel performed 94.8% of all tests (2318 of 2445) during the study. Conclusions and relevance: This study suggests that self-obtained vaginal swab samples were associated with performance equivalent to laboratory-based molecular diagnostics, which can support use of this POC assay in many settings. The availability of an easy-to-use, rapid (30-minute) molecular test for accurate detection of chlamydia and gonorrhea has the power to facilitate testing and treatment in a single patient visit for these STIs

The AFHSC-Division of GEIS Operations Predictive Surveillance Program: a multidisciplinary approach for the early detection and response to disease outbreaks

The Armed Forces Health Surveillance Center, Division of Global Emerging Infections Surveillance and Response System Operations (AFHSC-GEIS) initiated a coordinated, multidisciplinary program to link data sets and information derived from eco-climatic remote sensing activities, ecologic niche modeling, arthropod vector, animal disease-host/reservoir, and human disease surveillance for febrile illnesses, into a predictive surveillance program that generates advisories and alerts on emerging infectious disease outbreaks. The program’s ultimate goal is pro-active public health practice through pre-event preparedness, prevention and control, and response decision-making and prioritization. This multidisciplinary program is rooted in over 10 years experience in predictive surveillance for Rift Valley fever outbreaks in Eastern Africa. The AFHSC-GEIS Rift Valley fever project is based on the identification and use of disease-emergence critical detection points as reliable signals for increased outbreak risk. The AFHSC-GEIS predictive surveillance program has formalized the Rift Valley fever project into a structured template for extending predictive surveillance capability to other Department of Defense (DoD)-priority vector- and water-borne, and zoonotic diseases and geographic areas. These include leishmaniasis, malaria, and Crimea-Congo and other viral hemorrhagic fevers in Central Asia and Africa, dengue fever in Asia and the Americas, Japanese encephalitis (JE) and chikungunya fever in Asia, and rickettsial and other tick-borne infections in the U.S., Africa and Asia

Respiratory diseases among U.S. military personnel: countering emerging threats.

Emerging respiratory disease agents, increased antibiotic resistance, and the loss of effective vaccines threaten to increase the incidence of respiratory disease in military personnel. We examine six respiratory pathogens (adenoviruses, influenza viruses, Streptococcus pneumoniae, Streptococcus pyogenes, Mycoplasma pneumoniae, and Bordetella pertussis) and review the impact of the diseases they cause, past efforts to control these diseases in U.S. military personnel, as well as current treatment and surveillance strategies, limitations in diagnostic testing, and vaccine needs