Seismic Reflection Studies in Long Valley Caldera, Califomia

This is the published version, also available here: http://dx.doi.org/10.1029/90JB02401.Seismic reflection studies in Long Valley caldera, California, indicate that seismic methods may be successfully employed to image certain types of features in young silicic caldera environments. However, near-surface geological conditions within these environments severely test the seismic reflection method. Data quality are degraded by static, reverberation, and band-limiting problems due to these near-surface conditions. In Long Valley, seismic reflection and refraction methods were used to image both the shallow and deep geothermal aquifers within the area. The deep geothermal aquifer, the welded Bishop Tuff, was imaged as a fairly continuous reflector across the western moat of the caldera. Near-surface refraction information indicates that there may be a buried paleochannel system or horst and graben system that could control the shallow geothermal flow pattern. High-amplitude events observed in a wide-angle survey were originally interpreted as reflections from a contemporary magma body. However, a migration of the events utilizing the new generalized cellular migration algorithm indicates that these events are probably reflections from the faults of the caldera ring fracture system. The reflections may be caused by the high acoustic impedance contrast associated with the juxtaposition of relatively low-velocity, low-density, caldera fill against the granite plutons and metasediments of the Sierran basement along this fault system

Bank Erosion Study

The Bank Erosion Study was designed to evaluate eroding fast land bank shorelines as contributors of sand, silt and clay and total nitrogen and total phosphorous introduced into the Chesapeake Bay estuarine system. In addition, the extent and effectiveness of erosion control measures were evaluated for selected shoreline reaches. Fastland banks are the uplands along the shorelines that are composed of semi-consolidated sediments. This study evaluates about 2000 miles of primary tidal shoreline in the Virginia portion of the Chesapeake Bay estuarine system for areas of fast land bank erosion. Primary tidal shorelines are those along the main stem of the Chesapeake Bay and the major tributary estuaries. Approximately 383 miles of shoreline comprising 208 shore reaches are included in. the final analysis. These reaches are responsible for 61% of the annual historic sediment volume loading from tidal shoreline erosion. Sediments for selected representative shore reaches were sampled and analyzed for sand, silt, and clay. Volumetric rates of sediment loading for the study shorelines were determined from historical data. Also, the condition of the shorelines were evaluated by analyzing oblique aerial imagery for 1985 and 1990. From the imagery analysis the extent of defensive shoreline structures (i.e. bulkheads, seawall and revetments) and whether the bank was stable or not was determined. Sediment volume loading was considered to be halted where defensive shoreline structures were installed. There was an increase in shoreline defenses of 18% by 1990. This resulted in an annual reduction of sediment loading by 5%. Total nitrogen and total phosphorous loading from eroding fast land bank sediments have been determined to be significant. This study utilized the results of Ibison et al., 1990 which provided average nutrient loading rates for total nitrogen and total phosphorous from eroded fastland bank sediments. The consequent estimated annual reduction in nutrient loading by defended shorelines for 1990 is about 5% for total nitrogen and total phosphorous. Nineteen reaches have been identified as significant contributors of eroding bank sediments and will require further assessment as to the impacts of nutrient loading

Phylogenetic and environmental context of a Tournaisian tetrapod fauna

The end-Devonian to mid-Mississippian time interval has long been known for its depauperate palaeontological record, especially for tetrapods. This interval encapsulates the time of increasing terrestriality among tetrapods, but only two Tournaisian localities previously produced tetrapod fossils. Here we describe five new Tournaisian tetrapods ($\textit{Perittodus apsconditus}$, $\textit{Koilops herma}$, $\textit{Ossirarus kierani}$, $\textit{Diploradus austiumensis}$ and $\textit{Aytonerpeton microps}$) from two localities in their environmental context. A phylogenetic analysis retrieved three taxa as stem tetrapods, interspersed among Devonian and Carboniferous forms, and two as stem amphibians, suggesting a deep split among crown tetrapods. We also illustrate new tetrapod specimens from these and additional localities in the Scottish Borders region. The new taxa and specimens suggest that tetrapod diversification was well established by the Tournaisian. Sedimentary evidence indicates that the tetrapod fossils are usually associated with sandy siltstones overlying wetland palaeosols. Tetrapods were probably living on vegetated surfaces that were subsequently flooded. We show that atmospheric oxygen levels were stable across the Devonian/Carboniferous boundary, and did not inhibit the evolution of terrestriality. This wealth of tetrapods from Tournaisian localities highlights the potential for discoveries elsewhere.NERC consortium grants NE/J022713/1 (Cambridge), NE/J020729/1 (Leicester), NE/J021067/1 (BGS), NE/J020621/1 (NMS) and NE/J021091/1 (Southampton

Seismic imaging in Long Valley, California, by surface and borehole techniques: An investigation of active tectonics

The search for silicic magma in the upper crust is converging on the Long Valley Caldera of eastern California, where several lines of geophysical evidence show that an active magma chamber exists at mid‐to lower‐crustal depths. There are also other strong indications that magma may be present at depths no greater than about 5 km below the surface. In this paper, we review the history of the search for magma at Long Valley. We also present the preliminary results from a coordinated suite of seismic experiments, conducted by a consortium of institutions in the summer and fall of 1984, that were designed to refine our knowledge of the upper extent of the magma chamber. Major funding for the experiments was provided by the Geothermal Research Program of the U.S. Geological Survey (USGS) and by the Magma Energy Technology Program of the U.S. Department of Energy (DOE), a program to develop the technology necessary to extract energy directly from crustal magma. Additional funding came from DOE's Office of Basic Energy Sciences and the National Science Foundation (NSF). Also, because extensive use was made of a 0.9‐km‐deep well lent to us by Santa Fe Geothermal, Inc., the project was conducted partly under the auspices of the Continental Scientific Drilling Program (CSDP). As an integrated seismic study of the crust within the caldera that involved the close cooperation of a large number of institutions, the project was moreover viewed as a prototype for future scientific experiments to be conducted under the Program for Array Seismic Studies of the Continental Lithosphere (PASSCAL). The experiment thus represented a unique blend of CSDP and PASSCAL methods, and achieved goals consistent with both programs

Researching underwater: a submerged study

This chapter explores the unknown territory of a lost project: an ethnography of a public swimming pool. The discussion is contextualised within my broader sociological theory of ‘nothing’, as a category of unmarked, negative social phenomena, including no-things, no-bodies, no-wheres, non-events and non-identities. These meaningful symbolic objects are constituted through social interaction, which can take two forms: acts of commission and acts of omission. I tell the story of how this project did not happen, through the things I did not do or that did not materialise, and how I consequently did not become a certain type of researcher. I identify three types of negative phenomena that I did not observe and document – invisible figures, silent voices and empty vessels – and, consequently, the knowledge I did not acquire. However, nothing is also productive, generating new symbolic objects as substitutes, alternatives and replacements: the somethings, somebodies and somewheres that are done or made instead. Thus finally, I reflect on how not doing this project led me to pursue others, cultivating a different research identity that would not otherwise have existed

Seismic imaging in Long Valley, California, by surface and borehole techniques: An investigation of active tectonics

The search for silicic magma in the upper crust is converging on the Long Valley Caldera of eastern California, where several lines of geophysical evidence show that an active magma chamber exists at mid‐to lower‐crustal depths. There are also other strong indications that magma may be present at depths no greater than about 5 km below the surface. In this paper, we review the history of the search for magma at Long Valley. We also present the preliminary results from a coordinated suite of seismic experiments, conducted by a consortium of institutions in the summer and fall of 1984, that were designed to refine our knowledge of the upper extent of the magma chamber. Major funding for the experiments was provided by the Geothermal Research Program of the U.S. Geological Survey (USGS) and by the Magma Energy Technology Program of the U.S. Department of Energy (DOE), a program to develop the technology necessary to extract energy directly from crustal magma. Additional funding came from DOE's Office of Basic Energy Sciences and the National Science Foundation (NSF). Also, because extensive use was made of a 0.9‐km‐deep well lent to us by Santa Fe Geothermal, Inc., the project was conducted partly under the auspices of the Continental Scientific Drilling Program (CSDP). As an integrated seismic study of the crust within the caldera that involved the close cooperation of a large number of institutions, the project was moreover viewed as a prototype for future scientific experiments to be conducted under the Program for Array Seismic Studies of the Continental Lithosphere (PASSCAL). The experiment thus represented a unique blend of CSDP and PASSCAL methods, and achieved goals consistent with both programs

Acceptability of financial incentives and penalties for encouraging uptake of healthy behaviours: focus groups

BACKGROUND: There is evidence that financial incentive interventions, which include both financial rewards and also penalties, are effective in encouraging healthy behaviours. However, concerns about the acceptability of such interventions remain. We report on focus groups with a cross-section of adults from North East England exploring their acceptance of financial incentive interventions for encouraging healthy behaviours amongst adults. Such information should help guide the design and development of acceptable, and effective, financial incentive interventions. METHODS: Eight focus groups with a total of 74 adults were conducted between November 2013 and January 2014 in Newcastle upon Tyne, UK. Focus groups lasted approximately 60 minutes and explored factors that made financial incentives acceptable and unacceptable to participants, together with discussions on preferred formats for financial incentives. Verbatim transcripts were thematically coded and analysed in Nvivo 10. RESULTS: Participants largely distrusted health promoting financial incentives, with a concern that individuals may abuse such schemes. There was, however, evidence that health promoting financial incentives may be more acceptable if they are fair to all recipients and members of the public; if they are closely monitored and evaluated; if they are shown to be effective and cost-effective; and if clear health education is provided alongside health promoting financial incentives. There was also a preference for positive rewards rather than negative penalties, and for shopping vouchers rather than cash incentives. CONCLUSIONS: This qualitative empirical research has highlighted clear suggestions on how to design health promoting financial incentives to maximise acceptability to the general public. It will also be important to determine the acceptability of health promoting financial incentives in a range of stakeholders, and in particular, those who fund such schemes, and policy-makers who are likely to be involved with the design, implementation and evaluation of health promoting financial incentive schemes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12889-015-1409-y) contains supplementary material, which is available to authorized users

Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands

Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability.

To identify genetic causes of intellectual disability (ID), we screened a cohort of 986 individuals with moderate to severe ID for variants in 565 known or candidate ID-associated genes using targeted next-generation sequencing. Likely pathogenic rare variants were found in ∼11% of the cases (113 variants in 107/986 individuals: ∼8% of the individuals had a likely pathogenic loss-of-function [LoF] variant, whereas ∼3% had a known pathogenic missense variant). Variants in SETD5, ATRX, CUL4B, MECP2, and ARID1B were the most common causes of ID. This study assessed the value of sequencing a cohort of probands to provide a molecular diagnosis of ID, without the availability of DNA from both parents for de novo sequence analysis. This modeling is clinically relevant as 28% of all UK families with dependent children are single parent households. In conclusion, to diagnose patients with ID in the absence of parental DNA, we recommend investigation of all LoF variants in known genes that cause ID and assessment of a limited list of proven pathogenic missense variants in these genes. This will provide 11% additional diagnostic yield beyond the 10%-15% yield from array CGH alone.Action Medical Research (SP4640); the Birth Defect Foundation (RG45448); the Cambridge National Institute for Health Research Biomedical Research Centre (RG64219); the NIHR Rare Diseases BioResource (RBAG163); Wellcome Trust award WT091310; The Cell lines and DNA bank of Rett Syndrome, X-linked mental retardation and other genetic diseases (member of the Telethon Network of Genetic Biobanks (project no. GTB12001); the Genetic Origins of Congenital Heart Disease Study (GO-CHD)- funded by British Heart Foundation (BHF)This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/humu.2290

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease