DRASTIC—INSIGHTS:querying information in a plant gene expression database

DRASTIC––Database Resource for the Analysis of Signal Transduction In Cells (http://www.drastic.org.uk/) has been created as a first step towards a data-based approach for constructing signal transduction pathways. DRASTIC is a relational database of plant expressed sequence tags and genes up- or down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature. More than 17700 records have been obtained from 306 treatments affecting 73 plant species from 512 peer-reviewed publications with most emphasis being placed on data from Arabidopsis thaliana. DRASTIC has been developed by the Scottish Crop Research Institute and the Abertay University and allows rapid identification of plant genes that are up- or down-regulated by multiple treatments and those that are regulated by a very limited (or perhaps a single) treatment. The INSIGHTS (INference of cell SIGnaling HypoTheseS) suite of web-based tools allows intelligent data mining and extraction of information from the DRASTIC database. Potential response pathways can be visualized and comparisons made between gene expression patterns in response to various treatments. The knowledge gained informs plant signalling pathways and systems biology investigations

Applied economic strategies to evaluate policies and environmental outcomes: case studies from immigration and ecosystem services

My dissertation title is, “Applied economic strategies to evaluate policies and environmental outcomes: case studies from immigration and ecosystem services.” The first two chapters of this dissertation concern the relationship between local immigration policies and societal welfare. The third chapter examines the impact of human activity on the environment and the valuation of ecosystem services. The first two chapters examine the outcomes accompanying the institutional adoption of inclusive and exclusive immigration policies. I am studying sanctuary cities as an example of inclusive institutions, where I seek to understand the benefits that inclusivity confers on cities, as well as the costs of exclusive approaches to immigration. In these studies, I test whether economic outcomes vary according to a county's openness to immigrants and determine whether these economic indicators drive the choice of immigration policy. To the extent that sanctuary cities exemplify inclusivity, sanctuary cities' economic characteristics may inform the transition of other institutions to greater inclusivity. The third chapter documents the economic consequences of eutrophication in one of North America's Great Lakes. It also seeks to quantify the broader value of the ecosystem services the lake provides using revealed preference methods. This strategy may, in turn, influence decision-making and incentivize conservation. The first manuscript exploits quasi-experimental variation in the time and space of policy implementation to isolate the effects of local immigration policies on U.S. counties. To assess the impact of a county's openness to immigrants on the local economy, I use county-level data from the American Community Survey on economic indicators and Immigration and Customs Enforcement (ICE) data detailing policy intensity. These policies range from areas where immigrants are strictly regulated via collaboration with ICE compared to those that provide protections. The study finds evidence that providing protections to immigrants increases overall per capita income, wages, GDP, and total employment, while unemployment experienced a decline. Meanwhile, the data show that punitive measures have no statistically significant effect on income and unemployment but adverse effects overall on GDP, total employment, and the proportion of the foreign-born population. These results support a model of immigration policy as an institution that can either support or suppress productivity. They confirm that immigrant labor is a positive driver of economic well-being at the local and regional levels. The second manuscript builds upon the first study data to determine whether the selection of pro- or anti-immigrant policies is consistent with the narrative that economic conditions drive the choice of immigration policy. While also exploiting the variation in economic indicators across time and space to isolate the effects of these indicators on immigration policy choice by counties, this study finds no correlations between included economic variables and selecting immigrant-friendly policies. When using cross-sectional variation, the probability of choosing anti-immigrant policies increases with unemployment, non-citizen population, voting for a Republican president, and wages decline. All correlations between economic variables and policy outcomes disappear once fixed effects at the county level are included. This suggests that policy choice has a stronger relationship with longer-term trends and unobservables. Hence, the policy choice is not driven by short-term fluctuations in per capita income, unemployment, wages, and immigrant presence. In the third manuscript, I examine the economic consequences of eutrophication in one of North America's Great Lakes by measuring whether property values decline due to harmful algal blooms in the urban and suburban areas of the city of Toledo, Ohio. I quantify the broader value of the ecosystem services that the lake provides. With housing sales from around the city of Cleveland, Ohio as a control group, I apply a difference-in-difference model to pre-matched data on housing prices, control for census tract as well as time fixed effects, and in one of the specifications, limit the data to houses sold repeatedly over the study period. Pre-trend tests suggest valid counterfactuals. Estimates show a decline in house prices of 13 and 25 percent in 2008 and 2011, respectively, and comparisons between locations near and far from HABs in Toledo show 9 and 24 percent declines in 2008 and 2011. Results imply an overall loss due to HABs, totaling close to 3 billion dollars during the study period

Magnetometer-only attitude and rate determination for a gyro-less spacecraft

Attitude determination algorithms that requires only the earth's magnetic field will be useful for contingency conditions. One way to determine attitude is to use the time derivative of the magnetic field as the second vector in the attitude determination process. When no gyros are available, however, attitude determination becomes difficult because the rates must be propagated via integration of Euler's equation, which in turn requires knowledge of the initial rates. The spacecraft state to be determined must then include not only the attitude but also rates. This paper describes a magnetometer-only attitude determination scheme with no a priori knowledge of the spacecraft state, which uses a deterministic algorithm to initialize an extended Kalman filter. The deterministic algorithm uses Euler's equation to relate the time derivatives of the magnetic field in the reference and body frames and solves the resultant transcendental equations for the coarse attitude and rates. An important feature of the filter is that its state vector also includes corrections to the propagated rates, thus enabling it to generate highly accurate solutions. The method was tested using in-flight data from the Solar, Anomalous, and Magnetospheric Particles Explorer (SAMPEX), a Small Explorer spacecraft. SAMPEX data using several eclipse periods were used to simulate conditions that may exist during the failure of the on-board digital sun sensor. The combined algorithm has been found effective, yielding accuracies of 1.5 deg in attitude (within even nominal mission requirements) and 0.01 degree per second (deg/sec) in the rates

Advantages of estimating rate corrections during dynamic propagation of spacecraft rates: Applications to real-time attitude determination of SAMPEX

This paper describes real-time attitude determination results for the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX), a gyroless spacecraft, using a Kalman filter/Euler equation approach denoted the real-time sequential filter (RTSF). The RTSF is an extended Kalman filter whose state vector includes the attitude quaternion and corrections to the rates, which are modeled as Markov processes with small time constants. The rate corrections impart a significant robustness to the RTSF against errors in modeling the environmental and control torques, as well as errors in the initial attitude and rates, while maintaining a small state vector. SAMPLEX flight data from various mission phases are used to demonstrate the robustness of the RTSF against a priori attitude and rate errors of up to 90 deg and 0.5 deg/sec, respectively, as well as a sensitivity of 0.0003 deg/sec in estimating rate corrections in torque computations. In contrast, it is shown that the RTSF attitude estimates without the rate corrections can degrade rapidly. RTSF advantages over single-frame attitude determination algorithms are also demonstrated through (1) substantial improvements in attitude solutions during sun-magnetic field coalignment and (2) magnetic-field-only attitude and rate estimation during the spacecraft's sun-acquisition mode. A robust magnetometer-only attitude-and-rate determination method is also developed to provide for the contingency when both sun data as well as a priori knowledge of the spacecraft state are unavailable. This method includes a deterministic algorithm used to initialize the RTSF with coarse estimates of the spacecraft attitude and rates. The combined algorithm has been found effective, yielding accuracies of 1.5 deg in attitude and 0.01 deg/sec in the rates and convergence times as little as 400 sec

Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Skomal, G., Marshall, H., Galuardi, B., Natanson, L., Braun, C. D., & Bernal, D. Horizontal and vertical movement patterns and habitat use of juvenile porbeagles (Lamna nasus) in the Western North Atlantic. Frontiers in Marine Science, 8,(2021): 624158, https://doi.org/10.3389/fmars.2021.624158.The porbeagle (Lamna nasus) is a large, highly migratory endothermic shark broadly distributed in the higher latitudes of the Atlantic, South Pacific, and Indian Oceans. In the North Atlantic, the porbeagle has a long history of fisheries exploitation and current assessments indicate that this stock is severely overfished. Although much is known of the life history of this species, there is little fisheries-independent information about habitat preferences and ecology. To examine migratory routes, vertical behavior, and environmental associations in the western North Atlantic, we deployed pop-up satellite archival transmitting tags on 20 porbeagles in late November, 2006. The sharks, ten males and ten females ranging from 128 to 154 cm fork length, were tagged and released from a commercial longline fishing vessel on the northwestern edge of Georges Bank, about 150 km east of Cape Cod, MA. The tags were programmed to release in March (n = 7), July (n = 7), and November (n = 6) of 2007, and 17 (85%) successfully reported. Based on known and derived geopositions, the porbeagles exhibited broad seasonally-dependent horizontal and vertical movements ranging from minimum linear distances of 937 to 3,310 km and from the surface to 1,300 m, respectively. All of the sharks remained in the western North Atlantic from the Gulf of Maine, the Scotian Shelf, on George's Bank, and in the deep, oceanic waters off the continental shelf along the edge of, and within, the Gulf Stream. In general, the population appears to be shelf-oriented during the summer and early fall with more expansive offshore radiation in the winter and spring. Although sharks moved through temperatures ranging from 2 to 26°C, the bulk of their time (97%) was spent in 6-20°C. In the summer months, most of the sharks were associated with the continental shelf moving between the surface and the bottom and remaining < 200 m deep. In the late fall and winter months, the porbeagles moved into pelagic habitat and exhibited two behavioral patterns linked with the thermal features of the Gulf Stream: “non-divers” (n = 7) largely remained at epipelagic depths and “divers” (n = 10) made frequent dives into and remained at mesopelagic depths (200–1000 m). These data demonstrate that juvenile porbeagles are physiologically capable of exploiting the cool temperate waters of the western North Atlantic as well as the mesopelagic depths of the Gulf Stream, possibly allowing exploitation of prey not available to other predators.This research was funded by the Large Pelagics Research Center (Grant 06-125)

Engineering tyrosine-based electron flow pathways in proteins: The case of aplysia myoglobin

Tyrosine residues can act as redox cofactors that provide an electron transfer ("hole-hopping") route that enhances the rate of ferryl heme iron reduction by externally added reductants, for example, ascorbate. Aplysia fasciata myoglobin, having no naturally occurring tyrosines but 15 phenylalanines that can be selectively mutated to tyrosine residues, provides an ideal protein with which to study such through-protein electron transfer pathways and ways to manipulate them. Two surface exposed phenylalanines that are close to the heme have been mutated to tyrosines (F42Y, F98Y). In both of these, the rate of ferryl heme reduction increased by up to 3 orders of magnitude. This result cannot be explained in terms of distance or redox potential change between donor and acceptor but indicates that tyrosines, by virtue of their ability to form radicals, act as redox cofactors in a new pathway. The mechanism is discussed in terms of the Marcus theory and the specific protonation/deprotonation states of the oxoferryl iron and tyrosine. Tyrosine radicals have been observed and quantified by EPR spectroscopy in both mutants, consistent with the proposed mechanism. The location of each radical is unambiguous and allows us to validate theoretical methods that assign radical location on the basis of EPR hyperfine structure. Mutation to tyrosine decreases the lipid peroxidase activity of this myoglobin in the presence of low concentrations of reductant, and the possibility of decreasing the intrinsic toxicity of hemoglobin by introduction of these pathways is discussed. © 2012 American Chemical Society

Global Phylogeography of the Dusky Shark Carcharhinus obscurus: Implications for Fisheries Management and Monitoring the Shark Fin Trade

Genetic stock structure information is needed to delineate management units and monitor trade in sharks, many of which are heavily exploited and declining. The dusky shark Carcharhinus obscurus is a large apex predator that is sought after for its fins and is considered highly susceptible to overexploitation. The International Union for the Conservation of Nature (IUCN) classifies this species as ‘Vulnerable’ globally and ‘Endangered’ in the northwest Atlantic. We make the first assessment of global stock structure of C. obscurus by analyzing part of the mitochondrial control region (mtCR) in 255 individuals sampled from 8 geographically dispersed locations. We found 25 mtCR haplotypes and rejected a null hypothesis of panmixia (analysis of molecular variance, ΦST = 0.55, p \u3c 0.000001), detecting significant differentiation between 3 management units: US Atlantic (USATL), South Africa (SAF), and Australia (AUS). We also found preliminary evidence of population structure between the USATL and southwest Atlantic (Brazil). There were no shared haplotypes between the western Atlantic and Indo-Pacific. These analyses suggest that replenishment of the collapsed USATL management unit via immigration of females from elsewhere is unlikely. Mixed stock analysis (MSA) simulations show that reconstruction of the relative contributions of USATL, SAF, and AUS management units to the Asian fin trade is possible using these mtCR sequences. We suggest avenues for obtaining samples to conduct MSA of the shark fin trade, which could enhance management of dusky sharks and other species that are exploited for their fins

Application of Bomb Radiocarbon Chronologies to Shortfin Mako (Isurus oxyrinchus)

There is an ongoing disagreement regarding the aging of the shortfin mako due to a difference of interpretation in the periodic deposition of vertebral growth band pairs, especially for the larger size classes. Using analysis of length-month information, tagging data, and length-frequency analysis, concluded that two band pairs were formed in the vertebral centrum every year (biannual band-pair interpretation). Cailliet et al. (1983), however, presented growth parameters based on the common assumption that one band pair forms annually (annual band-pair interpretation). Therefore, growth rates obtained by Pratt & Casey (1983) were twice that of Cailliet et al. (1983) and could lead to age discrepancies of about 15 years for maximum estimated ages on the order of 30 from the annual band-pair interpretation. Serious consequences in the population dynamics could occur for this species if inputs are based on an invalid age interpretation. The latest Fishery Management Plan (FMP) for Highly Migratory Species (HMS), for example, adopted the biannual band pair deposition hypothesis because it apparently fit the observed growth patterns best (Pacific Fishery Management Council 2003). However, the ongoing uncertainty about the aging of the shortfin mako was acknowledged and it was recommended that an endeavor to resolve this issue be made. Since 1983, five additional studies on the age and growth of the shortfin mako have been conducted (Chan 2001, Campana et al. 2002, Hsu 2003, Ribot-Carballal et al. 2005, Bishop et al. 2006). Using Marginal Increment Ratio (MIR), Hsu (2003) indicated the formation of annual translucent bands from July to September in western North Pacific Ocean shortfin makos. Using Marginal Increment Analysis (MIA) Ribot-Carballal et al. (2005) supported the annual band-pair interpretation for 109 shortfin makos collected in the eastern Pacific Ocean. Although the study provided support for annual band-pair deposition, no statistical test was performed and the number of samples for MIA analysis was insufficient for some months. Hence, unequivocal validation of shortfin mako age estimates has yet to be accomplished. Atmospheric testing of thermonuclear devices in the 1950s and 1960s effectively doubled the natural atmospheric radiocarbon ({sup 14}C). The elevated {sup 14}C levels were first recorded in 1957-58, with a peak around 1963. As a consequence, {sup 14}C entered the ocean through gas exchange with the atmosphere at the ocean surface and in terrestrial runoff. Despite variable oceanographic conditions, a worldwide rise of the bomb {sup 14}C signal entered the ocean mixed layer as dissolved inorganic carbon (DIC) in 1957-58. The large amounts of {sup 14}C released from the bomb tests produced a signature that can be followed through time, throughout the marine food web, and into deeper waters. The marked increase of radiocarbon levels was first measured in the DIC of seawater and in biogenic marine carbonates of hermatypic corals in Florida. Subsequently, this record was documented in corals from other regions and in the thallus of rhodoliths. The accumulation of radiocarbon in the hard parts of most marine organisms in the mixed layer (such as fish otoliths and bivalves) was synchronous with the coral time-series. This technique has been used to validate age estimates and longevity of numerous bony fishes to date, as well as to establish bomb radiocarbon chronologies from different oceans. In the first application of this technique to lamnoid sharks, validated annual band-pair deposition in vertebral growth bands for the porbeagle (Lamna nasus) aged up to 26 years. Radiocarbon values from samples obtained from 15 porbeagle caught in the western North Atlantic Ocean (some of which were known-age) produced a chronology similar in magnitude to the reference carbonate chronology for that region. The observed phase shift of about 3 years was attributed to different sources of carbon between vertebrae and those for otoliths, bivalves and corals. In the same study by Campana et al. (2002), a single vertebra from a shortfin mako caught in 1977 was aged at 21 and 10 years, using the annual versus the biannual deposition hypotheses, respectively. Vertebral samples were extracted from the first, last, and two intermediate bands and were assayed for radiocarbon. The results indicated the aging interpretation for the vertebra from this fish best fit the timing of the porbeagle time-series by adopting the annual band-pair interpretation. To provide a more comprehensive basis for valid aging criteria and a definitive growth function for the shortfin mako, more radiocarbon assays were required. The goal of our research was to take heed of this suggestion and continue the use of bomb radiocarbon to validate the aging of the shortfin mako, and specifically to resolve the validity of either annual or biannual band-pair age interpretations

Wigner's Dynamical Transition State Theory in Phase Space: Classical and Quantum

A quantum version of transition state theory based on a quantum normal form (QNF) expansion about a saddle-centre-...-centre equilibrium point is presented. A general algorithm is provided which allows one to explictly compute QNF to any desired order. This leads to an efficient procedure to compute quantum reaction rates and the associated Gamov-Siegert resonances. In the classical limit the QNF reduces to the classical normal form which leads to the recently developed phase space realisation of Wigner's transition state theory. It is shown that the phase space structures that govern the classical reaction d ynamicsform a skeleton for the quantum scattering and resonance wavefunctions which can also be computed from the QNF. Several examples are worked out explicitly to illustrate the efficiency of the procedure presented.Comment: 132 pages, 31 figures, corrected version, Nonlinearity, 21 (2008) R1-R11

Septic cardiomyopathy

Depression of left ventricular (LV) intrinsic contractility is constant in patients with septic shock. Because most parameters of cardiac function are strongly dependent on afterload, especially in this context, the cardiac performance evaluated at the bedside reflects intrinsic contractility, but also the degree of vasoplegia. Recent advances in echocardiography have allowed better characterization of septic cardiomyopathy. It is always reversible providing the patient's recovery. Unlike classic cardiomyopathy, it is not associated with high filling pressures, for two reasons: improvement in LV compliance and associated right ventricular dysfunction. Although, it is unclear to which extent it affects prognosis, a hyperkinetic state is indicative of a profound and persistent vasoplegia associated with a high mortality rate. Preliminary data suggest that the hemodynamic response to a dobutamine challenge has a prognostic value, but large studies are required to establish whether inotropic drugs should be used to treat this septic cardiac dysfunction