SAGE 1 data user's guide

A guide for using the data products from the Stratospheric Aerosol and Gas Experiment 1 (SAGE 1) for scientific investigations of stratospheric chemistry related to aerosol, ozone, nitrogen dioxide, dynamics, and climate change is presented. A detailed description of the aerosol profile tape, the ozone profile tape, and the nitrogen dioxide profile tape is included. These tapes are the SAGE 1 data products containing aerosol extinction data and ozone and nitrogen dioxide concentration data for use in the different scientific investigations. Brief descriptions of the instrument operation, data collection, processing, and validation, and some of the scientific analyses that were conducted are also included

Soft-bottom benthic assemblages and levels of contaminants in sediments and biota at Gray's Reef National Marine Sanctuary and nearby shelf waters off the coast of Georgia (2000 and 2001)

A series of studies was initiated to assess the condition of benthic macroinfauna and chemical contaminant levels in sediments and biota of the Gray’s Reef National Marine Sanctuary (GRNMS) and nearby shelf waters off the coast of Georgia. Four key objectives of the research are (1) to document existing environmental conditions within the sanctuary in order to provide a quantitative benchmark for tracking any future changes due to either natural or human disturbances; (2) to examine broader cross-shelf spatial patterns in benthic fauna and sediment contaminant concentrations and to identify potential controlling factors associated with the observed patterns; (3) to assess any between-year temporal variability in benthic fauna; and (4) to evaluate the importance of benthic fauna as prey for higher trophic levels. Such questions are being addressed to help fulfill long-term science and management goals of the GRNMS. However, it is anticipated that the information will be of additional value in broadening our understanding of the surrounding South Atlantic Bight (SAB) ecosystem and in bringing the knowledge to bear on related resourcemanagement issues of the region. We have begun to address the first three of these objectives with data from samples collected in spring 2000 at stations within GRNMS, and in spring 2001 at stations within the sanctuary and along three cross-shelf transects extending from the mouths of Sapelo, Doboy, and Altamaha Sounds out to sanctuary depths (about 17-20 m). This report provides a description of baseline conditions within the sanctuary, based on results of the spring 2000 survey (Section II), and uses data from both 2000 and 2001 to examine overall spatial and temporal patterns in biological and chemical variables within the sanctuary and surrounding inner-shelf environment (Section III). (PDF contains 65 pages

Comparison of Growth Morphology in Ge (001) Homoepitaxy Using Pulsed Laser Deposition and MBE

Differences in the homoepitaxy of Ge(001) are explored using a dual MBE/PLD deposition system. With identical substrate preparation, temperature calibration, background pressure and analysis, the system provides a unique comparison of the processes arising only from kinetic differences in the flux and at the surface. All films show mounded growth. At substrate temperatures below 200ºC, PLD films are smoother than MBE films, whereas they are similar at higher temperatures.Engineering and Applied Science

Comparison of Morphology Evolution of Ge(001) Homoepitaxial Films Grown by Pulsed Laser Deposition and Molecular Beam Epitaxy

Using a dual Molecular Beam Epitaxy (MBE)-Pulsed Laser Deposition (PLD) Ultra-High Vacuum chamber, we have conducted the first experiments under identical thermal, background, and surface preparation conditions to compare Ge(001) homoepitaxial growth morphology in PLD and MBE. We find that in PLD with low kinetic energy and in MBE the film morphology evolves in a similar fashion: initially irregularly shaped mounds form, followed by pyramidal mounds with edges of the square-base along directions; the film roughness and mound separation increase with film thickness. In PLD with high kinetic energy, well-defined pyramidal mounds are not observed and the morphology rather resembles that of an ion-etched Ge(001) surface. The areal feature density is higher for PLD films than for MBE films grown at the same average growth rate and temperature. Furthermore, the dependence upon film thickness of roughness and feature separation differ for PLD and MBE. We attribute these differences to the higher yield of defect generation by energetic species in PLD.Engineering and Applied Science

On the Phase Shift of Reflection High Energy Electron Diffraction Intensity Oscillations during Ge(001) Homoepitaxy by Molecular Beam Epitaxy

We have conducted a systematic investigation of the phase shift of the Reflection High Energy Electron Diffraction (RHEED) intensity oscillations during homoepitaxy of Ge(001) by molecular beam epitaxy for a wide range of diffraction conditions. Our results show that for small incidence angles with a beam azimuth several degrees away from the crystallographic symmetry direction, the phase is independent of incidence angle; however, it starts to shift once the incidence angle is high enough that the (004) Kikuchi line appears in the RHEED pattern. Moreover, under some conditions we observe the oscillations from only the Kikuchi feature and not from the specular spot, and the oscillatory behavior of the Kikuchi feature is almost out of phase with that of the specular spot. We conclude that the phase shift is caused by the overlap of the specular spot and the Kikuchi features, in contrast to models involving dynamical scattering theory for the phase shift. We discuss necessary conditions for avoiding interference.Engineering and Applied Science

Economic and operational appraisal of an allogeneic CAR T-cell bioprocess

Allogeneic CAR T-cell therapies face a variety of challenges from a processing point of view. Pressures to deliver cell therapies at affordable prices demand the development of efficient and cost-effective manufacturing strategies and process technologies for the manufacture of such products. Consideration must be paid to both financial and operational aspects of bioprocess designs from the early stages of product development. This work presents the application of a decisional tool to a case study which describes the manufacture of an allogeneic CAR T-cell therapy. The tool, developed at University College London, is able to quantitatively evaluate bioprocess designs from both a financial and an operational perspective. In this instance the tool has been used to carry out mass balances and equipment sizing calculations in order to compute resource utilisation and cost of goods (COG) for a range of bioprocess designs. Scenario analyses have been used to pinpoint future process improvements that result in feasible manufacturing COG. Furthermore, multi-attribute decision making (MADM) has been employed in order to allow the appraisal of optimal bioprocess designs from both a financial and an operational perspective. The tool outputs provide COG breakdowns for bioprocess designs at a range of annual demands and dose sizes. MADM has been used to provide quantitative output values to key financial and operational performance metrics. Further to this, key process bottlenecks and economic drivers have been identified; these provide a basis for the focus of future process improvements. This work presents a computational technique that can be used to drive effective decision making early on in the development of allogeneic CAR T-cell therapy bioprocesses

Microarray and EST database estimates of mRNA expression levels differ: The protein length versus expression curve for C. elegans

BACKGROUND: Various methods for estimating protein expression levels are known. The level of correlation between these methods is only fair, and systematic biases in each of the methods cannot be ruled out. We here investigate systematic biases in the estimation of gene expression rates from microarray data and from abundance within the Expressed Sequence Tag (EST) database. We suggest that length is a significant factor in biases to measured gene expression rates. As a specific example of the importance of the bias of expression rate with length, we address the following evolutionary question: Does the average C. elegans protein length increase or decrease with expression level? Two different answers to this question have been reported in the literature, one method using expression levels estimated by abundance within the EST database and another using microarrays. We have investigated this issue by constructing the full protein length versus expression curve for C. elegans, using both methods for estimating expression levels. RESULTS: The microarray data show a monotonic decrease of length with expression level, whereas the abundance within the EST database data show a non-monotonic behavior. Furthermore, the ratio of the expression level estimated by the EST database to that measured by microarrays is not constant, but rather systematically biased with gene length. CONCLUSIONS: It is suggested that the length bias may lie primarily in the abundance within the EST database method, being not ameliorated by internal standards as it is in the microarray data, and that this bias should be removed before data interpretation. When this is done, both the microarray and the abundance within the EST database give a monotonic decrease of spliced length with expression level, and the correlation between the EST and microarray data becomes larger. We suggest that standard RNA controls be used to normalize for length bias in any method that measures expression

Boundary Avoidance Tracking for Instigating Pilot Induced Oscillations

In order to advance research in the area of pilot induced oscillations, a reliable method to create PIOs in a simulated environment is necessary. Using a boundary avoidance tracking task, researchers performing an evaluation of control systems were able to create PIO events in 42% of cases using a nominal aircraft, and 91% of cases using an aircraft with reduced actuator rate limits. The simulator evaluation took place in the NASA Ames Vertical Motion Simulator, a high-fidelity motion-based simulation facility

Complete genome sequence of Liberibacter crescens BT-1

Liberibacter crescens BT-1, a Gram-negative, rod-shaped bacterial isolate, was previously recovered from mountain papaya to gain insight on Huanglongbing (HLB) and Zebra Chip (ZC) diseases. The genome of BT-1 was sequenced at the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida. A finished assembly and annotation yielded one chromosome with a length of 1,504,659 bp and a G+C content of 35.4%. Comparison to other species in the Liberibacter genus, L. crescens has many more genes in thiamine and essential amino acid biosynthesis. This likely explains why L. crescens BT-1 is culturable while the known Liberibacter strains have not yet been cultured. Similar to Candidatus L. asiaticus psy62, the L. crescens BT-1 genome contains two prophage regions