Natural selection favoring more transmissible HIV detected in United States molecular transmission network.

HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven by host risk behavior; however, the effect of viral traits on variable transmission rates is poorly understood. Viral load, the concentration of HIV in blood, is a heritable viral trait that influences HIV infectiousness and disease progression. Here, we reconstruct HIV genetic transmission clusters using data from the United States National HIV Surveillance System and report that viruses in clusters, inferred to be frequently transmitted, have higher viral loads at diagnosis. Further, viral load is higher in people in larger clusters and with increased network connectivity, suggesting that HIV in the United States is experiencing natural selection to be more infectious and virulent. We also observe a concurrent increase in viral load at diagnosis over the last decade. This evolutionary trajectory may be slowed by prevention strategies prioritized toward rapidly growing transmission clusters

Digital Epidemiology

Mobile, social, real-time: the ongoing revolution in the way people communicate has given rise to a new kind of epidemiology. Digital data sources, when harnessed appropriately, can provide local and timely information about disease and health dynamics in populations around the world. The rapid, unprecedented increase in the availability of relevant data from various digital sources creates considerable technical and computational challenges

Principal component analysis identifies patterns of cytokine expression in non-small cell lung cancer patients undergoing definitive radiation therapy

Radiation treatment (RT) stimulates the release of many immunohumoral factors, complicating the identification of clinically significant cytokine expression patterns. This study used principal component analysis (PCA) to analyze cytokines in non-small cell lung cancer (NSCLC) patients undergoing RT and explore differences in changes after hypofractionated stereotactic body radiation therapy (SBRT) and conventionally fractionated RT (CFRT) without or with chemotherapy

Characterizing the Vertical Profile of Aerosol Particle Extinction and Linear Depolarization over Southeast Asia and the Maritime Continent: The 2007-2009 View from CALIOP

Vertical profiles of 0.532 m aerosol particle extinction coefficient and linear volume depolarization ratio are described for Southeast Asia and the Maritime Continent. Quality-screened and cloud-cleared Version 3.01 Level 2 NASA Cloud Aerosol Lidar with Orthogonal Polarization (CALIOP) 5-km Aerosol Profile datasets are analyzed from 2007 to 2009. Numerical simulations from the U.S. Naval Aerosol Analysis and Predictive System (NAAPS), featuring two-dimensional variational assimilation of NASA Moderate Resolution Imaging Spectroradiometer and Multi-angle Imaging Spectro- Radiometer quality-assured datasets, combined with regional ground-based lidar measurements, are considered for assessing CALIOP retrieval performance, identifying bias, and evaluating regional representativeness. CALIOP retrievals of aerosol particle extinction coefficient and aerosol optical depth (AOD) are high over land and low over open waters relative to NAAPS (0.412/0.312 over land for all data points inclusive, 0.310/0.235 when the per bin average is used and each is treated as single data points; 0.102/0.151 and 0.086/0.124, respectively, over ocean). Regional means, however, are very similar (0.180/0.193 for all data points and 0.155/0.159 when averaged per normalized bin), as the two factors offset one another. The land/ocean offset is investigated, and discrepancies attributed to interpretation of particle composition and a-priori assignment of the extinction-to-backscatter ratio ("lidar ratio") necessary for retrieving the extinction coefficient from CALIOP signals. Over land, NAAPS indicates more dust present than CALIOP algorithms are identifying, indicating a likely assignment of a higher lidar ratio representative of more absorptive particles. NAAPS resolvesmore smoke overwater than identified with CALIOP, indicating likely usage of a lidar ratio characteristic of less absorptive particles to be applied that biases low AOD there. Over open waters except within the Bay of Bengal, aerosol particle scattering is largely capped below 1.5 km MSL, though ground-based lidar measurements at Singapore differ slightly from this finding. Significant aerosol particle presence over land is similarly capped near 3.0 km MSL over most regions. Particle presence at low levels regionally, except over India, is dominated by relatively non-depolarizing particles. Industrial haze, sea salt droplets and fresh smoke are thus most likely present

Digital epidemiology

Mobile, social, real-time: the ongoing revolution in the way people communicate has given rise to a new kind of epidemiology. Digital data sources, when harnessed appropriately, can provide local and timely information about disease and health dynamics in populations around the world. The rapid, unprecedented increase in the availability of relevant data from various digital sources creates considerable technical and computational challenges

Modelling the limits on the response of net carbon exchange to fertilization in a south-eastern pine forest

Using a combination of model simulations and detailed measurements at a hierarchy of scales conducted at a sandhills forest site, the effect of fertilization on net ecosystem exchange ( NEE ) and its components in 6-year-old Pinus taeda stands was quantified. The detailed measurements, collected over a 20-d period in September and October, included gas exchange and eddy covariance fluxes, sampled for a 10-d period each at the fertilized stand and at the control stand. Respiration from the forest floor and above-ground biomass was measured using chambers during the experiment. Fertilization doubled leaf area index (LAI) and increased leaf carboxylation capacity by 20%. However, this increase in total LAI translated into an increase of only 25% in modelled sunlit LAI and in canopy photosynthesis. It is shown that the same climatic and environmental conditions that enhance photosynthesis in the September and October periods also cause an increase in respiration The increases in respiration counterbalanced photosynthesis and resulted in negligible NEE differences between fertilized and control stands. The fact that total biomass of the fertilized stand exceeded 2·5 times that of the control, suggests that the counteracting effects cannot persist throughout the year. In fact, modelled annual carbon balance showed that gross primary productivity ( GPP ) increased by about 50% and that the largest enhancement in NEE occurred in the spring and autumn, during which cooler temperatures reduced respiration more than photosynthesis. The modelled difference in annual NEE between fertilized  and  control  stands  (approximately  200 1;g 2;C 3;m −2 y −1 )  suggest that the effect of fertilization was sufficiently large to transform the stand from a net terrestrial carbon source to a net sink.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73712/1/j.1365-3040.2002.00896.x.pd

Effects of Soil Water and Nitrogen on Growth and Photosynthetic Response of Manchurian Ash (Fraxinus mandshurica) Seedlings in Northeastern China

Soil water and nitrogen (N) are considered to be the main environmental factors limiting plant growth and photosynthetic capacity. However, less is known about the interactive effects of soil water and N on tree growth and photosynthetic response in the temperate ecosystem. seedlings. The seedlings were exposed to three water regimes including natural precipitation (CK), higher precipitation (HW) (CK +30%) and lower precipitation (LW) (CK −30%), and both with and without N addition for two growing seasons. We demonstrated that water and N supply led to a significant increase in the growth and biomass production of the seedlings. LW treatment significantly decreased biomass production and leaf N content, but they showed marked increases in N addition. N addition could enhance the photosynthetic capability under HW and CK conditions. Leaf chlorophyll content and the initial activity of Rubisco were dramatically increased by N addition regardless of soil water condition. The positive relationships were found between photosynthetic capacity, leaf N content, and SLA in response to water and N supply in the seedling. Rubisco expression was up-regulated by N addition with decreasing soil water content. Immunofluorescent staining showed that the labeling for Rubisco was relatively low in leaves of the seedlings under LW condition. The accumulation of Rubisco was increased in leaf tissues of LW by N addition. seedlings, which may provide novel insights on the potential responses of the forest ecosystem to climate change associated with increasing N deposition

Managing resistance in the ICU : an evolutionary approach to rational antibiotic deployment

Nosocomial infections account for 5 to 10% of all infections in the United States and act as a continuous reservoir for the maintenance of antibiotic resistance. Development, testing, and implementation of broad antimicrobial deployment strategies are crucial in the proper management of resistance over the long term. We present a population-based model which describes the spread of variably-resistant nosocomial pathogens amongst patients in an intensive care unit of a hospital. Our purpose is to identify treatment strategies which maximize the number of uninfected individuals while maintaining low rates of multi-resistant infections. This was accomplished via the expansion of a previously published model by introducing pharmacodynamics, pharmacokinetics, and cross- resistance tradeoffs. Most importantly, we depart from this model's predecessors by treating the minimization of resistant-infected individuals as secondary to maximizing uninfected. We confirm that the benefit of a random mixing regimen over periodic cycling is minimal, while a hybrid of the two is slightly more effective. Finally, we show that time- and probability-based strategies are inferior to Multi-Drug cocktails in their ability to exploit resistance-associated fitness tradeoffs; thereby selectively favoring susceptible genotypes. These results provide an impetus to identify Multi-Drug cocktails which serve to minimize the incidence of multi-resistance while still maintaining curing efficac

A Population Model Evaluating the Consequences of the Evolution of Double-Resistance and Tradeoffs on the Benefits of Two-Drug Antibiotic Treatments

<div><p>The evolution of antibiotic resistance in microbes poses one of the greatest challenges to the management of human health. Because addressing the problem experimentally has been difficult, research on strategies to slow the evolution of resistance through the rational use of antibiotics has resorted to mathematical and computational models. However, despite many advances, several questions remain unsettled. Here we present a population model for rational antibiotic usage by adding three key features that have been overlooked: 1) the maximization of the frequency of uninfected patients in the human population rather than the minimization of antibiotic resistance in the bacterial population, 2) the use of cocktails containing antibiotic pairs, and 3) the imposition of tradeoff constraints on bacterial resistance to multiple drugs. Because of tradeoffs, bacterial resistance does not evolve directionally and the system reaches an equilibrium state. When considering the equilibrium frequency of uninfected patients, both cycling and mixing improve upon single-drug treatment strategies. Mixing outperforms optimal cycling regimens. Cocktails further improve upon aforementioned strategies. Moreover, conditions that increase the population frequency of uninfected patients also increase the recovery rate of infected individual patients. Thus, a rational strategy does not necessarily result in a tragedy of the commons because benefits to the individual patient and general public are not in conflict. Our identification of cocktails as the best strategy when tradeoffs between multiple-resistance are operating could also be extended to other host-pathogen systems. Cocktails or other multiple-drug treatments are additionally attractive because they allow re-using antibiotics whose utility has been negated by the evolution of single resistance.</p></div