Tropospheric Modeling Improvement

The work performed under this contract provides for the improvement of modeling of troposphere propagation delay in VLBI data, defining of required accuracy of ancillary data type(s) to measure tropospheric behavior, and to develop a clear correspondence between tropospheric behavior and the quality of geodetic VLBI measurements

Dynamics of the solid earth

The work performed under this contract provides for the improvement of modeling of troposphere propagation delay in very long base interferometry (VLBI) data, defining of required accuracy of ancillary data type(s) to measure tropospheric behavior and to develop a clear correspondence between tropospheric behavior and the quality of geodetic VLBI measurements

Interferometric tracking system for the tracking and data relay satellite

This report documents construction and testing of the Interferometric Tracking System project developed under the NASA SBIR contract NAS5-30313. Manuals describing the software and hardware, respectively entitled: 'Field Station Guide to Operations' and 'Field Station Hardware Manual' are included as part of this final report. The objective of this contract was to design, build, and operate a system of three ground stations using Very Long Baseline Interferometry techniques to measure the TDRS orbit. The ground stations receive signals from normal satellite traffic, store these signals in co-located computers, and transmit the information via phone lines to a central processing site which correlates the signals to determine relative time delays. Measurements from another satellite besides TDRS are used to determine clock offsets. A series of such measurements will ultimately be employed to derive the orbital parameters, yielding positions accurate to within 50 meters or possibly better

Intracanopy adjustment of leaf-level thermal tolerance is associated with microclimatic variation across the canopy of a desert tree (Acacia papyrocarpa)

© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. Tree crowns are spatially heterogeneous, sometimes resulting in significant variation in microclimate across the canopy, particularly with respect to temperature. Yet it is not known whether such localised temperature variation equates to intracanopy variation in leaf-level physiological thermal tolerance. Here, we studied whether microclimate variation across the canopy of a dominant desert tree equated to localised variation in leaf thermal thresholds (T 50 ) among four canopy positions: upper south, upper north, lower south, lower north. Principal component analysis was used to generate a composite climatic stress variable (C STRESS ) from canopy temperature, vapour pressure deficit, and relative humidity. We also determined the average number of days that maximum temperatures exceeded the air temperature equating to this species’ critical threshold of 49 °C (AT 49 ). To estimate how closely leaf temperatures track ambient temperature, we predicted the thermal time constant (τ) for leaves at each canopy position. We found that C STRESS and AT 49 were significantly greater in lower and north-facing positions in the canopy. Differences in wind speed with height resulted in significantly longer predicted τ for leaves positioned at lower, north-facing positions. Variation in these drivers was correlated with significantly higher T 50 for leaves in these more environmentally stressful canopy positions. Our findings suggest that this species may optimise resources to protect against thermal damage at a whole-plant level. They also indicate that, particularly in desert environments with steep intracanopy microclimatic gradients, whole-plant carbon models could substantially under- or overestimate productivity under heat stress, depending on where in the canopy T 50 is measured

Study of Regions of Extended Homozygosity Provides a Powerful Method to Explore Haplotype Structure of Human Populations

Previous investigations have reported linkage disequilibrium occurring between nearby polymorphisms, a block-like structure for such relationships, some instances where surprisingly few haplotypes are found and regions of extended homozygosity which are especially marked around centromeres and which are especially common on the X chromosome. We investigated the distribution and nature of regions of extended homozygosity in a sample of 1411 subjects included in a genome wide association study. Regions of extended homozygosity over 1Mb are common, with an average of 35.9 occurring per subject, and containing on average 73 homozygous markers. They have a markedly non-random distribution. They are relatively common on the X chromosome and are seen at centromeres but are also concentrated at other chromosomal regions where presumably recombination is rare. They seem to be a consequence of some haplotypes being very common in the population and although sometimes this reflects the effect of a very common haplotype we also note that there are examples of two or three common haplotypes, each very different from each other, underlying this effect. Regions of extended homozygosity are commoner than previously appreciated. They result from the presence of extended haplotypes with high population frequency. Such regions concentrate in particular locations. The haplotypes involved are sometimes markedly disparate from each other. These regions offer a valuable opportunity for further investigation, in particular with regard to their ancestral history

Investigation into the Ability of SNP Chipsets and Microsatellites to Detect Association with a Disease Locus

We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association

Intracanopy adjustment of leaf-level thermal tolerance is associated with microclimatic variation across the canopy of a desert tree (\u3ci\u3eAcacia papyrocarpa\u3c/i\u3e)

Tree crowns are spatially heterogeneous, sometimes resulting in significant variation in microclimate across the canopy, particularly with respect to temperature. Yet it is not known whether such localised temperature variation equates to intracanopy variation in leaf-level physiological thermal tolerance. Here, we studied whether microclimate variation across the canopy of a dominant desert tree equated to localised variation in leaf thermal thresholds (T50) among four canopy positions: upper south, upper north, lower south, lower north. Principal component analysis was used to generate a composite climatic stress variable (CSTRESS) from canopy temperature, vapour pressure deficit, and relative humidity. We also determined the average number of days that maximum temperatures exceeded the air temperature equating to this species’ critical threshold of 49 °C (AT49). To estimate how closely leaf temperatures track ambient temperature, we predicted the thermal time constant (τ) for leaves at each canopy position. We found that CSTRESS and AT49 were significantly greater in lower and north-facing positions in the canopy. Differences in wind speed with height resulted in significantly longer predicted τ for leaves positioned at lower, north-facing positions. Variation in these drivers was correlated with significantly higher T50 for leaves in these more environmentally stressful canopy positions. Our findings suggest that this species may optimise resources to protect against thermal damage at a whole-plant level. They also indicate that, particularly in desert environments with steep intracanopy microclimatic gradients, whole-plant carbon models could substantially under- or overestimate productivity under heat stress, depending on where in the canopy T50 is measured

Advancing the Microbiome Research Community

The human microbiome has become a recognized factor in promoting and maintaining health. We outline opportunities in interdisciplinary research, analytical rigor, standardization, and policy development for this relatively new and rapidly developing field. Advances in these aspects of the research community may in turn advance our understanding of human microbiome biology. It is now widely recognized that disturbances in our normal microbial populations may be linked to acute infections such as Clostridium difficile and to chronic diseases such as heart disease, cancer, obesity, and autoimmune disorders (Clemente et al., 2012). This has prompted substantial interest in the microbiome from both basic and clinical perspectives. Although our genome is relatively static throughout life, each of our microbial communities changes profoundly from infancy through adulthood, continuing to adapt through ongoing exposures to diet, drugs and environment. Understanding the microbiome and its dynamic nature may be critical for diagnostics and, eventually, interventions based on the microbiome itself. However, several important challenges limit the ability of researchers to enter the microbiome field and/or conduct research most effectively

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

The Human Microbiome Project (HMP) [1],[2] is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome" of microbes carried in and on the human body [3],[4]. Microbial ecologists, realizing that >99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ [5], primarily by sequencing the 16S ribosomal RNA gene (16S) as a phylogenetic and taxonomic marker to identify members of microbial communities [6]. The need to develop corresponding new methods for culture-independent studies [7],[8] in turn precipitated a sea change in the study of microbes and human health, inspiring the new term “metagenomics" [9] both to describe a technological approach—sequencing and analysis of the genes from whole communities rather than from individual genomes—and to emphasize that microbes function within communities rather than as individual species. This shift from a focus on individual organisms to microbial interactions [10] culminated in a National Academy of Science report [11], which outlined challenges and promises for metagenomics as a way of understanding the foundational role of microbial communities both in the environment and in human health.National Institutes of Health (U.S.) (grant U54HG004969)National Institutes of Health (U.S.) (grant U54HG004973)National Institutes of Health (U.S.) (grant U54AI084844)National Institutes of Health (U.S.) (grant U01HG004866)National Institutes of Health (U.S.) (grant R01HG005969)National Institutes of Health (U.S.) (grant R01HG004872)United States. Army Research Office (grant W911NF-11-1-0473)National Science Foundation (U.S.) (NSF DBI-1053486)Howard Hughes Medical Institute (Early Career Scientist

Automated construction and testing of multi-locus gene–gene associations

Summary: It has been argued that the missing heritability in common diseases may be in part due to rare variants and gene–gene effects. Haplotype analyses provide more power for rare variants and joint analyses across genes can address multi-gene effects. Currently, methods are lacking to perform joint multi-locus association analyses across more than one gene/region. Here, we present a haplotype-mining gene–gene analysis method, which considers multi-locus data for two genes/regions simultaneously. This approach extends our single region haplotype-mining algorithm, hapConstructor, to two genes/regions. It allows construction of multi-locus SNP sets at both genes and tests joint gene–gene effects and interactions between single variants or haplotype combinations. A Monte Carlo framework is used to provide statistical significance assessment of the joint and interaction statistics, thus the method can also be used with related individuals. This tool provides a flexible data-mining approach to identifying gene–gene effects that otherwise is currently unavailable