Data Collection at Fifteen Selected Creeks in Support of Shallow Water Dredging on Virginia’s Middle Peninsula - Methods & Data Report

Federal funding has been historically available for the Army Corps of Engineers for shallow draft navigation projects. However, past and recent subsidies have not provided ample funding at levels to sustain maintenance dredging for the 17 federal navigation channels on the Middle Peninsula. Further, funding for maintenance of non-federal channels has been historically neglected by the Commonwealth of Virginia until the Virginia General Assembly established the Virginia Waterway Maintenance Fund in 2018. For the past decade the Middle Peninsula Chesapeake Bay Public Access Authority, the Middle Peninsula Planning District Commission and its member jurisdictions, and the Virginia Institute of Marine Science Shoreline Studies Program have worked to advance local solutions and alternatives to address dredging needs in the Commonwealth

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group

A Family Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects

We propose a family-based association test, FBAT-PC, for studies with quantitative traits that are measured repeatedly. The traits may be influenced by partially or completely unknown factors that may vary for each measurement. Using generalized principal component analysis, FBAT-PC amplifies the genetic effects of each measurement by constructing an overall phenotype with maximal heritability. Analytically, and in the simulation studies, we compare FBAT-PC with standard methodology and assess both the heritability of the overall phenotype and the power of FBAT-PC. Compared to univariate analysis, FBAT-PC achieves power gains of up to 200%. Applications of FBAT-PC to an osteoporosis study and to an asthma study show the practical relevance of FBAT-PC. FBAT-PC has been implemented in the software package PBAT and is freely available at http://www.biostat.harvard.edu/~clange/default.htm.status: publishe

A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects

We propose a family-based association test, FBAT-PC, for studies with quantitative traits that are measured repeatedly. The traits may be influenced by partially or completely unknown factors that may vary for each measurement. Using generalized principal component analysis, FBAT-PC amplifies the genetic effects of each measurement by constructing an overall phenotype with maximal heritability. Analytically, and in the simulation studies, we compare FBAT-PC with standard methodology and assess both the heritability of the overall phenotype and the power of FBAT-PC. Compared to univariate analysis, FBAT-PC achieves power gains of up to 200%. Applications of FBAT-PC to an osteoporosis study and to an asthma study show the practical relevance of FBAT-PC. FBAT-PC has been implemented in the software package PBAT and is freely available at http://www.biostat.harvard.edu/~clange/default.htm.

2011 HM[subscript 102]: Discovery of a High-Inclination L5 Neptune Trojan in the Search for a Post-Pluto New Horizons Target

Author manuscript February 21, 2013We present the discovery of a long-term stable L5 (trailing) Neptune Trojan in data acquired to search for candidate trans-Neptunian objects for the New Horizons spacecraft to fly by during an extended post-Pluto mission. This Neptune Trojan, 2011 HM[subscript 102], has the highest inclination (29[˚ over .]4) of any known member of this population. It is intrinsically brighter than any single L5 Jupiter Trojan at H[subscript V] ~ 8.18. We have determined its gri colors (a first for any L5 Neptune Trojan), which we find to be similar to the moderately red colors of the L4 Neptune Trojans, suggesting similar surface properties for members of both Trojan clouds. We also present colors derived from archival data for two L4 Neptune Trojans (2006 RJ[subscript 103] and 2007 VL[subscript 305]), better refining the overall color distribution of the population. In this document we describe the discovery circumstances, our physical characterization of 2011 HM[subscript 102], and this object's implications for the Neptune Trojan population overall. Finally, we discuss the prospects for detecting 2011 HM[subscript 102] from the New Horizons spacecraft during its close approach in mid- to late-2013.W. M. Keck Foundatio

Apophis 2029: Decadal Opportunity for the Science of Planetary Defense

International audienceMany advancements in planetary science are achieved by seizing upon the opportunity created by rare natural events (e.g. comet Shoemaker-Levy 9 Jupiter impact; 1994) and by planned physical interactions (e.g. Deep Impact into comet Tempel 1; 2005). A forthcoming opportunity to seize upon a natural physical “experiment” occurs on April 13, 2029 with the unprecedentedly close Earth encounter by the large 340m asteroid (99942) Apophis. On that date, nature is performing the “experiment” of subjecting the physical body of Apophis to Earth’s tidal torques as it approaches to within 31,000 km of Earth’s surface, a distance that is closer than orbiting geosynchronous satellites.A potentially hazardous asteroid (PHA) as large as Apophis encountering Earth this closely (within 0.1 lunar distances) is, on average, a once-per-thousand year event. (In context, Apophis is 7 times larger and 350 times more massive than the Tunguska 1908 impactor; 5000 times more massive than Chelyabinsk 2013.) Because of this event’s incredible rarity, knowledge gained through measurements and outcomes of the Apophis 2029 “natural experiment” are clearly a decadal, if not millennial, opportunity for planetary science. Most specifically, this knowledge opportunity is for the science supporting planetary defense. Further, on April 13, 2029 all of Earth will be watching: Apophis will be visible to the naked eye speeding across the evening sky for an estimated 2 billion people spanning western Europe and northern Africa.In this White Paper we outline our current best understanding, and uncertainties, for scientific advances in the physical study of potentially hazardous asteroids that may be achievable by measuring physical changes of Apophis’ spin, surface structure, and/or shape configuration inresponse to Earth’s tidal torques. If tidal torques themselves, or surface configuration changes induce any measurable seismic vibration signal inside Apophis, a new field of asteroid seismology has the potential to be born. Over six decades of planetary science, seismology has been achieved beyond Earth for only two planetary worlds: Moon and Mars.With this White Paper, we take no position on how to implement specific investigations capable of achieving the science advances offered by the Apophis 2029 opportunity. Instead we advocate that competitive selection of investigations, be they theoretical or observational (ground-based, space-based, or in situ), be executed under the direction of NASA’s Planetary Defense Coordination Office, with a projected and perhaps necessarily augmented budget capable of supporting them. International collaboration is strongly encouraged.Thus, summarizing in four specific points, we urge the framers of the Decadal Survey to:• Recognize the decadal, if not millennial, opportunity for the science of planetary defense presented by the Apophis 2029 once-per-thousand-year “natural experiment.”• Prioritize as a top-level planetary defense science goal modeling and measuring the physical outcome on Apophis exerted by Earth’s tidal torques so as to achieve the greatest possible new insights into the physical nature, including the internal structure, of PHAs.• Recognize that time is of the essence for defining and implementing investigations of physical effects on Apophis, particularly if in situ measurements are to be considered. An Apophis 2029 Science Definition Team may be prescribed.• Recognize that the achievable knowledge of PHAs presented by the Apophis 2029 opportunity could have immeasurable benefits to the future of humanity, in the highly unlikely, but not impossible necessity to mitigate a future impact threa

Determinants of mosaic chromosomal alteration fitness.

Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT