gebhart/patrepeval huggingface dataset:
Micropatterning of Aptamer Beacons to Create Cytokine-Sensing Surfaces (2010)

Aptamer beacons are DNA or RNA probes that bind proteins or small molecules of interest and emit signal directly upon interaction with the target analyte. This paper describes micropatterning of aptamer beacons for detection of IFN-γ-an important inflammatory cytokine. The beacon consisted of a fluorophore-labeled aptamer strand hybridized with a shorter, quencher-carrying complementary strand. Cytokine molecules were expected to displace quenching strands of the beacon, disrupting FRET effect and resulting in fluorescence signal. The glass substrate was first micropatterned with poly(ethylene glycol) (PEG) hydrogel microwells (35 μm diameter individual wells) so as to define sites for attachment of beacon molecules. PEG microwell arrays were then incubated with avidin followed by biotin-aptamer-fluorophore constructs. Subsequent incubation with quencher-carrying complementary strands resulted in formation of DNA duplex and caused quenching of fluorescence due to FRET effect. When exposed to IFN-γ, microwells changed fluorescence from low (quencher hybridized with fluorophore-carrying strand) to high (quenching strand displaced by cytokine molecules). The fluorescence signal was confined to microwells, was changing in real-time and was dependent on the concentration of IFN-γ. In the future, we plan to co-localize aptamer beacons and cells on micropatterned surfaces in order to monitor in real-time cytokine secretion from immune cells in microwells.
Holographic interference electron microscopy for determining specimen magnetic structure and thickness distribution (1986)

A new holographic method utilizing the time-reversal operation of an electron beam has been de- vised to observe separately electric and magnetic phase distributions as interference electron micrographs, which had been unavailable using conventional methods. By this technique, both the magnetization and thickness distributions of three-dimensional cobalt particles have been determined.
Evolution of Genome Size in Drosophila. Is the Invader's Genome Being Invaded by Transposable Elements? (2002)

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.
Thin Films Deposited by Bias Sputtering (1965)

The application of a suitable negative bias to a film that is being deposited by dc sputtering produces a film of substantially lower resistivity (than without bias). The action of the bias is shown to result from positive ion bombardment of the film during deposition, leading to the selective removal of adsorbed impurities. An analytical expression describing the process is derived and found to give good agreement for tantalum films sputtered in argon containing oxygen as a contaminant. The effect of bias on contaminants originating both at the cathode and in the gas is compared. Comparison of bias sputtering and asymmetric ac sputtering in terms of an ion bombardment model shows that bias sputtering leads to purer films because ion clean-up is in operation during the entire deposition time only for the case of bias sputtering. Good adhesion of bias-sputtered Ta films to glass substrates is obtained by initially applying a small positive bias to the substrate.
An automatic test case generator derived from state-based testing (2002)

This paper describes an automated approach to generating test cases for an object-oriented class. The approach is derived from state-based testing methods and refers to a state machine from which a threaded multi-way tree (duplicating the behaviour of the state machine) is produced. All possible sequential test cases can then be automatically created, when the test case generator parses the tree.
Resonance and scattering in microstructured optical fibers (2002)

We present an investigation into the mechanism for guidance of microstructured optical fibers consisting of high-refractive-index cylinders embedded in a low-index background. A new guidance regime is identified in which the fibers' confinement losses depend strongly on wavelength and the positions of the loss minima and maxima depend on the scattering properties of individual cylinders and only weakly on their position and number. We point out similarities between these results and those reported recently for two-dimensional antiresonant reflecting waveguides.
Ten years of bacterial genome sequencing: comparative-genomics-based discoveries (2006)

It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity--even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information.
Comprehensive analysis of the extracellular proteins from <b><i>Xanthomonas campestris</i></b> pv. <b><i>campestris</i></b> B100 (2005)

The extracellular proteome of Xanthomonas campestris pv. campestris (Xcc) cultivated in minimal medium was isolated from the cell-free culture supernatant and separated by two-dimensional gel electrophoresis. This technique resolved 97 clearly visible protein spots, which were excised, digested with trypsin and identified on the basis of their peptide mass fingerprints generated by matrix assisted laser desorption/ionisation-time of flight-mass spectrometry. Using this approach 87 different proteins could be distinguished. The Signal P software predicted putative signal peptides for 53% of the extracellular proteins. These proteins are probably transported over the inner membrane and are localized in the periplasm, the outer membrane or secreted into the extracellular space. Among the secreted proteins are 11 degradative enzymes, which are involved in pathogenesis of Xcc. The proteins without obvious secretion signals are known to serve functions in the cytosol. How the cytosolic proteins are delivered to the extracellular space remains unclear.
MO‐A‐L100E‐01: Parallel Imaging: Techniques, Quality Control, and Applications (Preview of TG118 Repo (2007)

Task Group ♯118 of the AAPM was established to describe the basis of parallel magnetic resonance imaging (pMRI) and its applications to the Medical Physics community. This presentation reviews the aspects of parallel imaging methods that have led to this technology becoming important clinically. The signature enhancement attributable to pMRI is faster MR image acquisition which leads to decreased motion artifact, reduced breath‐hold time, shorter durations of exams or more series acquired per exam. Increased flexibility is also achieved since parallel imaging has distinct advantages for limiting specific absorption rate (SAR) at higher magnetic field strengths. There are currently two general approaches to pMRI; one based on image‐space reconstruction and the other on k‐space based methods. Details of the design of RF coils, or the entire RF systems, for improving imaging performance in pMRI will be surveyed. Additional benefits may be derived from the use of pMRI in balanced gradient echo imaging, fast spin echo imaging, dynamic MRI, BOLD contrast MRI and diffusion MRI. In addition, the image quality trade‐offs in pMRI will be considered with particular focus on the different ways that signal and noise are handled in pMRI image reconstruction. Finally advanced results, which will likely lead to continuing improvements in pMRI technology, will be discussed. In summary, this presentation will provide practical guidance and assistance for the practicing medical physicist so that pMRI may be more readily applied and understood within the clinical environment. By the end of this presentation the attendee should: 1. understand the basic concept of parallel imaging and how it can be used to reduce the acquisition time of MR images. 2. recognize in which clinical protocols the use of parallel imaging methods is most advantageous and what benefits are bestowed on each. 3. be aware of the image quality trade‐offs involved in implementing pMRI and 4. understand the new image artifacts inherent with this approach.
Using conjoint analysis to elicit preferences for health care (2000)

Traditionally the extent of patients' involvement in medical decision making has been minimal. This has been true at both the micro level of the patient consultation with a doctor and the macro level of planning and developing healthcare services. Since 1989, however, greater involvement of patients and the community in these processes has been advocated.1–5 In principle, the elicitation of patients' and the community's values represents a big step forward in terms of enhancing the benefits from the provision of health care. For the exercise to be worth while, however, the information obtained must be useful and scientifically defensible.6 During the 1990s, conjoint analysis was developed to elicit patients' and the community's views on health care.

#### Summary points

Conjoint analysis is a rigorous method of eliciting preferences

It allows estimation of the relative importance of different aspects of care, the trade-offs between these aspects, and the total satisfaction or utility that respondents derive from healthcare services

The technique can help with decision making for some of the issues facing the NHS

Though further applications of conjoint analysis are encouraged, methodological issues need further consideration

This paper explains conjoint analysis, provides examples of applications in health care which were obtained from a systematic review of databases between 1989 and 1999 (Medline, Embase, HealthSTAR, PsychLIT, EconLIT), and uses a study in orthodontic care to show the uses and pitfalls of the technique.

The survey method of data collection and analysis known as conjoint analysis was developed in mathematical psychology and has a strong theoretical basis.7–9 It has been successfully used in market research,10 transport economics,11 and environmental economics 12 13 and was recommended to the UK Treasury for valuing quality in the provision of public services.14 Within these areas it has been well received …
Interactive Aerospace Engineering and Design (2001)

Index p.333-356.
Bibliography p.325-329.Intended for Introduction to Aerospace Engineering or Introduction to Flight courses,
Interactive Aerospace Engineering and Design is the first work to provide integrated
multimedia and a strong balance of conceptual foundations in design, aircraft, and space flight
engineering. The CD-ROM bound with the book contains the entire text in electronic format
and provides extensive animations, interactive simulations, multimedia design curriculum, and
QuickTimeâ„¢ movies to motivate readers. A student design project is also included to convey
the importance of team-oriented design in an accessible manner. Its active, visual approach and
inclusion of modern aerospace engineering topics make it ideal for the changing needs of the
Aerospace Engineering field.
Features:
With a growing trend toward inclusion of basic design topics in engineering courses,
Newman's book includes a hands-on, comprehensive design project for students, as well as
topical coverage of design issues where appropriate.
Includes coverage of concepts relating to conventional aircraft, satellites and spacecraft.
The book comes with a free CD-ROM (for both IBM PC and Macintosh computers), in a
browser-based format, with a complete electronic version of the book in PDF form, active
animations, simulations, and QuickTimeâ„¢ movies.
The combination of the book and CD provide a highly motivational approach for learning
the basics of aerospace engineering.
A website containing instructor and student online resources can be found at
www.mhhe.com/engcs/aero/newman/A link to the author's website will also
be provided.
Pulse splitting during self-focusing in normally dispersive media (1992)

The self-focusing of femtosecond optical pulses in a normally dispersive medium is studied numerically. This situation represents a general problem that may be modeled by a 3 + 1-dimensional nonlinear Schrödinger equation, where two dimensions are self-focusing and the third is self-defocusing. The numerical simulations show that the dispersion causes the splitting of a pulse before it self-focuses into two temporally separated pulses, which then continue to self-focus and compress rapidly. The calculated behavior results in periodic modulation of the generated continuum spectrum, as was recently observed in continuum generation by focused femtosecond pulses in gases.
Evaluating Opportunity and Effectiveness of Cache Resizing in Reducing Energy Dissipation (2001)

Cache memories are accounting for an increasing fraction of a chip’s transistors and overall energy dissipation. Recent research advocates using “resizable” caches to exploit cache size variability in applications to reduce cache size and eliminate energy dissipation in the cache’s unused sections with minimal impact on performance. Current proposals for resizable caches fundamentally vary in two design aspects: (1) cache organization, where one organization, referred to as selective-ways, varies the cache’s set-associativity, while the other, referred to as selective-sets, varies the number of cache sets, and (2) resizing strategy, where one proposal statically sets the cache size prior to an application’s execution, while the other allows for dynamic resizing both across and within applications. While the various design choices in these proposals vastly differ in how they exploit opportunity for cache resizing and their effectiveness in reducing energy, these choices have never been compared against each other. In this paper, we evaluate the opportunity for and effectiveness of cache resizing in reducing energy dissipation. Rather than evaluating an exhaustive set of design choices, we select a key set of questions to understand the underlying application/system characteristics affecting design choices. We also propose and evaluate a hybrid resizable cache exploiting the advantages of both previous organizations. Using cycle-accurate performance and circuit simulation tools, we show that: (1) selective-ways and selective-sets perform comparably for i-caches, but selective-sets outperforms selective-ways for d-caches because selective-sets maintains setassociativity while reducing size benefitting applications with a high degree of conflict misses, (2) there is only a moderate degree of opportunity for dynamic resizing within applications, (3) a miss-ratio based dynamic resizing framework is more effective in capturing the opportunity for resizing within applications in i-caches than d-caches, because in d-caches misses are often overlapped making performance less sensitive to miss ratio, and (4) a hybrid organization of selective-ways-and-sets offers a richer spectrum of sizes than either individual organization, reducing the energy-delay by 36% and 32% in i- and d-caches as compared to selective-sets.
Loop Plant Electronics: Analog Loop Carrier Systems (1978)

Analog loop carrier systems have several distinct advantages which allow these systems to be economical even for as few as one to eight channels per cable pair. These advantages arise from their insensitivity to near-end and far-end crosstalk between cable pairs and the lack of complex common equipment at the terminals. Until recently, the analog systems have not benefited from the low hardware costs possible with the use of custom linear integrated circuits which can make the cost of companding, modulation, and demodulation inexpensive compared to the costs of powering and interface circuitry. Once this has been achieved as in the SLC™-1 and SLC™-8 systems, the choice between digital and analog systems can no longer be based on hardware costs alone at full fill, but must also be based on such other differences as engineering and installation costs, flexibility, maintainability, and range of application.
Accuracy of the 2500 Meter Isobath from Satellite Bathymetry (2006)

The location of the 2500 m isobath is a key element in seabed territorial claims under the Law of the Sea. We examined the accuracy of the 2500 m isobath as shown in the Bathymetry from Space Version 8.2 product of Smith and Sandwell. This dataset is a two-arc-minute Mercator grid that combines ship soundings where available with topography interpolated from satellite gravity where there are gaps. We find the 2500 m isobath from the Smith and Sandwell satellite bathymetry grid meets International Hydrographic Organization (IHO) S-44 vertical (depth) accuracy standards 90% of the time in areas of smooth topography where good survey control data are available, but only 31% of the time in a rugged and poorly controlled area. A horizontal displacement of the satellite isobath with respect to the National Geophysical Data Center (NGDC) Coastal Relief Model offshore of New Jersey, USA, is due to the underlying depths being uncorrected for the velocity of sound in seawater in the Model and corrected in the satellite bathymetry data.
A robust phase detection structure for M-PSK: theoretical derivations, simulation results, and system identification analysis (2006)

In this paper we shall present a new non data aided (NDA) adaptive phase detection structure for carrier synchronization phase locked loops (PLLs) in M-ary phase shift keying (M-PSK) receivers. The structure's principal novelty is in the fact that it dynamically adapts the phase detector's S-curve to allow the PLL to perform optimally at virtually any input signal-to-noise ratio (SNR) at which it can sustain lock. Investigation of the detector will commence with theoretical derivations of its S-curve, self-noise, and phase-error variance performance. These theoretical predictions will then be verified by computer simulations. As a third method of analysis, simulated PLLs employing the new detector will be investigated using the Steiglitz-McBride system identification algorithm, which will prove that those PLLs indeed perform optimally at every SNR. The theoretical, simulation, and system identification investigations of the proposed structure will be contrasted with results obtained using other NDA and decision directed (DD) phase detectors. As those comparisons will show, the proposed detection scheme offers greatly improved phase-error variance performance as well as superior resistance to fading and to automatic gain control (AGC) imperfections. Moreover, the new detector has a very compact hardware implementation
Preparation and Single-Crystal Characterization of <i><sup>i</sup></i>Pr<sub>2</sub>P(S)NHP(S)<i><sup>i</sup></i>Pr<sub>2</sub> and Homoleptic [<i><sup>i</sup></i>Pr<sub>2</sub>P(S)NP(S)<i><sup>i</sup></i>Pr<sub>2</sub>]<sup>-</sup> Complexes of Zinc, Cadmium, and Nickel (1996)

The X-ray structure of iPr2P(S)NHP(S)iPr2 reveals that the sulfur atoms adopt a gauche conformation. The tetrahedral complexes of Zn, Cd, and Ni contain puckered boatlike MS2P2N rings with enlarged P−N−P angles compared to the starting material.
Relevance of Ground-based Electron Induced Electrostatic Discharge Measurements to Space Plasma Environments (2009)

Electron-induced electrostatic discharge (ESD) can lead to severe spacecraft anomalies. It is crucial to the success of space missions that the likelihood of ESD occurrence is understood and mitigated. To aid in predicting ESD occurrence, a model for electric fields above and below the charge layer inside an electronirradiated dielectric material was developed. An instrumentation system was also designed to induce and detect ESD events. Because ESD events with a wide range of maximum current values can occur over a range of time intervals, multiple simultaneous detection methods were employed as charge was accumulated on a sample surface; these included monitoring of sample current and optical emissions from the sample surface. Data from ESD experimentation for James Webb Space Telescope (JWST) materials was used to verify that the instrumentation system was effective in inducing and observing ESD. Two types of discharge events were observed during JWST testing: a sudden-onset, decaying current accompanied by luminescence in the optical data, and an arc or flash in optical data. JWST test results were applied to the electric field models developed to determine the threshold electric field for luminescence onset. The models were also applied to the JWST materials in five different space plasma environments to determine the accumulated electric field as a function of time, and to thereby predict the likelihood of sample luminescence in each location.