Development of a Panel of Genome-Wide Ancestry Informative Markers to Study Admixture Throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region

Implementation and Validation of an LTE D2D Model for ns-3

International audienceThe ability to perform device-to-device (D2D) communication in Long Term Evolution (LTE)-based cellular networks became possible with the introduction of Proximity Services (ProSe) functionalities in the 3rd Generation Partnership Program (3GPP) specifications. In this paper, we provide a description of the ProSe implementation that extends the LTE model already available in ns-3. Our model contains key features defined in LTE Release 12 and further enhanced in LTE Release 13 related to synchronization, discovery, and communication. We also provide validation of each feature by comparing simulation results with analytical models developed as part of our work on D2D communication

A Long Term Evolution (LTE) Device-to-Device module for ns-3

International audienceIn this paper, we provide an overview of our ongoing implementation of a 3 rd Generation Partnership Program (3GPP) Proximity Services (ProSe) module in ns-3 to enable the performance evaluation of device-to-device (D2D) discovery and communication in Long Term Evolution (LTE) networks

Hopping sensor relocation in rugged terrains

Hopping sensors are a type of low cost mobile sensors that are small in size, have limited capability and imprecise movement. However, their unique method of movement makes them suitable for rugged terrains. Sensors may fail when deployed in a rugged terrain or in an obstacle-abundant environment. Therefore, redundant sensors may be identified and relocated to the sensor holes. This paper addresses the problem of relocating such capability- constrained sensors in an obstructive environment. We propose an enhanced Quorum-Grid solution with Binary Splitting Message Forwarding (BSMF), which is decentralized and can detect both existing and newly appearing obstructions in the supplier and consumer cells matching process. Furthermore, a grid-based movement model is introduced for the hopping sensors. Simulation shows that our scheme significantly reduces the communication overhead and achieves relatively constant total energy consumption with varying amount of obstructions. © 2009 IEEE.Link_to_subscribed_fulltex

Leveraging height in a jumping sensor network to extend network coverage

With respect to ground level, wireless communication signal strength increases with the elevation of communicating wireless sensor network devices, within practical bounds. Jumping sensors are mobile sensors that provide relocation capabilities and a temporary increase in elevation can be utilized for improving communication. This paper provides a comprehensive multidimensional analysis for jumping sensors. It studies the main factors that impact the Received Signal Strength (RSS) in sensor communication, and performs a comparative analysis between theoretical and experimental results. Sensor elevation from ground level is a key factor, which is often neglected, and plays an important role for successful wireless communication. The impact of jump height manipulation on a jumping sensor to the packet transmission goodput is presented. An airborne two-way communication scheme is defined and studied with experiments. The results indicate the effectiveness of utilizing the change in elevation of a jumping sensor to increase communication range. Since energy is at premium in sensor nodes, the operational energy cost of a jumping sensor prototype is studied in detail. A jumping sensor network is simulated with the parameters learned from the experimental results and the jumping sensor prototype analysis. Simulation results show the enhancement in connectivity and the feasibility of a jumping sensor network. © 2002-2012 IEEE.Link_to_subscribed_fulltex

Public Safety Communications: How to Maintain Connectivity and Improve Resiliency?

International audienceEmergency personnel operating in highly stressed environments may find themselves unable to connect to traditional network access points such as cell towers. In such a situation, the ability to maintain communication services when outside of network coverage and in the event of widespread network failures is essential. The Public Safety Communication Research (PSCR) program has been developing modeling and simulation tools to evaluate different functionalities such as the use of high power transmission and device-to-device (D2D) communications. This talk presents key findings associated D2D communications in a public safety context. In addition, we will show strategies to maintain network coverage in the case of equipment failures or infrastructure loss and what traffic can be sustained in this case

Genome-wide association study and admixture mapping identify different asthma-associated loci in Latinos: the Genes-environments & Admixture in Latino Americans study.

BackgroundAsthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations, and replication of positive associations has been inconsistent.ObjectiveWe sought to identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping.MethodsLatino children with asthma (n = 1893) and healthy control subjects (n = 1881) were recruited from 5 sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci.ResultsWe identified a significant association between ancestry and asthma at 6p21 (lowest P value: rs2523924, P < 5 × 10(-6)). This association replicates in a meta-analysis of the EVE Asthma Consortium (P = .01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between SNPs in the 17q21 region and asthma in Latinos (IKZF3, lowest P value: rs90792, odds ratio, 0.67; 95% CI, 0.61-0.75; P = 6 × 10(-13)) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies.ConclusionsAdmixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, whereas genome-wide association confirms the previously identified locus on 17q21

Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R² > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region

A Coffee Berry Borer (Coleoptera: Curculionidae: Scolytinae) Bibliography

Native to Africa, the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae: Scolytinae), has gradually invaded most coffee-growing areas worldwide. Adult females colonize the coffee berry and oviposit within galleries in the coffee seeds. Larvae and adults consume the seeds, resulting in drastic reductions in yields and quality, negatively affecting the income of approximately 20 million coffee-growing families (~100 million people) in ~80 countries, with losses surpassing more than $500 million annually (Vega et al. 2015). It has become evident that the coffee berry borer scientific community could greatly benefit from having access to a bibliography of the literature related to the insect. Such an information source would allow scientists to find out what research areas have been explored throughout the many coffee berry borer-infested countries after more than 100 years of research on the topic. It could also help to direct lead future research efforts into novel areas, and away from topics and ideas that have been thoroughly investigated in the past