gebhart/patrepeval huggingface dataset:
Effect of shell thickness and composition on blinking suppression and the blinking mechanism in ‘giant’ CdSe/CdS nanocrystal quantum dots (2010)

We recently developed an inorganic shell approach for suppressing blinking in nanocrystal quantum dots (NQDs) that has the potential to dramatically improve the utility of these fluorophores for single-NQD tracking of individual molecules in cell biology. Here, we consider in detail the effect of shell thickness and composition on blinking suppression, focusing on the CdSe/CdS core/shell system. We also discuss the blinking mechanism as understood through profoundly altered blinking statistics. We clarify the dependence of blinking behavior and photostability on shell thickness, as well as on interrogation times. We show that, while the thickest-shell systems afford the greatest advantages in terms of enhanced optical properties, thinner-shell NQDs may be adequate for certain applications requiring relatively shorter interrogation times. Shell thickness also determines the sensitivity of the NQD optical properties to aqueous-phase transfer, a critical step in rendering NQDs compatible with bioimaging applications. Lastly, we provide a proof-of-concept demonstration of the utility of these unique NQDs for fluorescent particle tracking.
Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain (2008)

Fe65 is a three-domain neuronal adaptor protein involved in brain development and amyloid precursor protein (APP) signalling. The phosphotyrosine-binding domain 1 (PTB1) of human Fe65 has been cloned, overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals belong to the space group R3 and diffract to 2.6 A resolution. This crystal form suffered from high thermal B factors and pseudo-symmetry, resulting in a bisection of the c axis. Co-crystallization with a mercury compound under similar conditions induced an orthorhombic crystal form in the space group P2(1)2(1)2(1) diffracting to 2.2 A resolution. SAD phases have been computed to the diffraction limit at the wavelength of maximum absorption (L(III) edge).
SARLock: SAT attack resistant logic locking (2016)

Logic locking is an Intellectual Property (IP) protection technique that thwarts IP piracy, hardware Trojans, reverse engineering, and IC overproduction. Researchers have taken multiple attempts in breaking logic locking techniques and recovering its secret key. A Boolean Satisfiability (SAT) based attack has been recently presented that breaks all the existing combinational logic locking techniques. In this paper, we develop a lightweight countermeasure against this and other attacks that aim at gradually pruning the key search space. Our proposed logic locking technique, referred to as SARLock, maximizes the required number of distinguishing input patterns to recover the secret key. SARLock thwarts the SAT attack by rendering the attack effort exponential in the number of bits in the secret key, while its overhead grows only linearly.
Getting rid of the wires and connectors in physiological monitoring (2008)

One of the main limitations towards an easy-touse, comfortable, and reliable product for physiological monitoring comes from wires and associated connectors. Wireless solutions for data transmission are more and more common in every domain, but for biopotential and impedance measurements, at least one galvanic line will always be needed. This paper describes a new technology that can make possible the measurement of biopotentials and body impedances with high quality standard using only one wire. As this wire requires neither shield nor isolation, one can imagine a conductive garment that simply connects several sensors distributed over the body. From the user point of view, the product would be 'cableless'.
Detection of Sinkholes or Anomalies Using Full Seismic Wave Fields (2013)

This research presents an application of two-dimensional (2-D) time-domain waveform tomography for detection of embedded sinkholes and anomalies. The measured seismic surface wave fields were inverted using a full waveform inversion (FWI) technique, based on a finite-difference solution of 2_D elastic wave equations and Gauss-Newton inversion method. The key advantage of this approach was the ability to generate all possible wave propagation modes of seismic wave fields (body waves and Rayleigh waves) that were then compared with measured surface data to infer complex subsurface properties. Both the pressure wave (P-wave) and shear wave (S-wave) velocities were inverted independently and simultaneously. The FWI was applied to two synthetic and four real experimental data sets. The synthetic inversion results showed that the inversion was capable of detecting layering (e.g., strong over weak), and anomalies; in addition, the initial input velocity profile for the inversion was straightforward (i.e., linearly increasing with depth). The developed FWI algorithm could run on raw collected data with a minimum manual effort (no picking of first-arrival travel times). The inversion results of real data sets showed that the waveform analysis was able to delineate: (1) an embedded concrete culvert; (2) extent of multiple existing sink holes/chimneys; and (3) a complex profile with an embedded void (unknown at time of data collection) and highly variable bedrock both laterally and vertically. Independent invasive testing (standard penetration test, SPT, and cone penetration testing, CPT) was conducted to verify the seismic test results. Finally, for the cases presented, the 2-D full waveform inversion was found computationally practical, i.e., the results were achieved in 2-4 hours of computer time on a standard laptop computer.
Rapid freeze prototyping technique in bio‐plotters for tissue scaffold fabrication (2008)

Purpose The purpose of this paper is to develop a new bio‐plotter using a rapid freeze prototyping (RFP) technique and to investigate its potential applications in fabricating tissue scaffolds. Design/methodology/approach The development of cryogenic bio‐plotters including design steps of hardware as well as software is addressed. Effects of structural parameters and process parameters on the properties of tissue scaffolds are demonstrated through simulation and experimental results. Findings The paper finds that the RFP method is suitable to fabricate macro‐ and micro‐porous scaffolds, especially for temperature‐sensitive polymers. In addition, through simulation and experiment results, it also shows that macro‐ and micro‐porous properties could be manipulated by structural parameters and process parameters, respectively. Research limitations/implications This paper shows that the chamber temperature is an important process parameter that can provide the means to control the micro‐porous structure of the scaffold. However, if the temperature is set too high, the fiber is frozen so rapidly that it cannot be fused with other fibers of the previous layer. On the other hand, if the temperature is too low, the fiber is not solidified fast enough. So, the chamber temperature, together with extruding pressure and nozzle velocity, must be optimized, which will be further investigated in future work. Originality/value The RFP technique is successfully proposed to construct 3D tissue scaffolds. In addition, a new cryogenic bio‐plotter is designed and developed, in which general algorithms of rapid prototyping method are presented and implemented, facilitating the fabrication of tissue scaffolds with various cross‐hatching patterns in a RFP process.
Auxin-Regulated Genes Encoding Cell Wall-Modifying Proteins Are Expressed during Early Tomato Fruit Growth (2000)

An expansin gene, LeExp2, was isolated from auxin-treated, etiolated tomato (Lycopersicon esculentum cv T5) hypocotyls. LeExp2 mRNA expression was restricted to the growing regions of the tomato hypocotyl and was up-regulated during incubation of hypocotyl segments with auxin. The pattern of expression of LeExp2 was also studied during tomato fruit growth, a developmental process involving rapid cell enlargement. The expression of genes encoding a xyloglucan endotransglycosylase (LeEXT1) and an endo-1, 4-beta-glucanase (Cel7), which, like LeExp2, are auxin-regulated in etiolated hypocotyls (C. Catalá, J.K.C. Rose, A.B. Bennett [1997] Plant J 12: 417-426), was also studied to examine the potential for synergistic action with expansins. LeExp2 and LeEXT1 genes were coordinately regulated, with their mRNA accumulation peaking during the stages of highest growth, while Cel7 mRNA abundance increased and remained constant during later stages of fruit growth. The expression of LeExp2, LeEXT1, and Cel7 was undetectable or negligible at the onset of and during fruit ripening, which is consistent with a specific role of these genes in regulating cell wall loosening during fruit growth, not in ripening-associated cell wall disassembly.
High Nonlinearity Holey Fibers: Design, Fabrication and Applications (2006)

We describe our recent progress in the development of next-generation small-core holey fibers (HFs) with unique dispersive and nonlinear properties. We report the use of Genetic Algorithms to optimize the dispersion characteristics of silica-based HFs, and report progress in soft-glass HF fabrication which has resulted in fibers with record values of nonlinearity.
A new iterative technique to characterize and design transmission fiber Bragg gratings (2006)

The authors present an iterative algorithm to recover the whole complex spectrum of any transmission fiber Bragg grating (FBG) from only the information of either its group-delay spectrum or its magnitude spectrum. Both numerical simulations and experimental results confirm that this simple algorithm is fast and accurate. This technique is especially useful for the practical design and characterization of transmission FBGs with desired spectral features.
GfxDoctor (2017)

Graphics is one of the major energy drain sources in smartphone apps. To optimize the app graphics energy, however, developers face the challenge of highly complex graphics rendering process, which involves multiple system layers including the app, the framework, the GPU, and the asynchronous interactions among them. Current diagnostic tools can profile the resource usage from certain layers, but fall short in stitching together profiling information across all the layers which is needed to provide developers with the visual effect-energy tradeoff at the app source-code level.
SPEED: Precise and Efficient Static Estimation of Program Computational Complexity (Full Version) (2009)

This paper describes an inter-procedural technique for computing symbolic bounds on the number of statements a procedure executes in terms of its scalar inputs and user-defined quantitative functions of input data-structures. Such computational complexity bounds for even simple programs are usually disjunctive, non-linear, and involve numerical properties of heaps. We address the challenges of generating these bounds using two novel ideas. We introduce a proof methodology based on multiple counter instrumentation (each counter can be initialized and incremented at potentially multiple program locations) that allows a given linear invariant generation tool to compute linear bounds individually on these counter variables. The bounds on these counters are then composed together to generate total bounds that are non-linear and disjunctive. We also give an algorithm for automating this proof methodology. Our algorithm generates complexity bounds that are usually precise not only in terms of the computational complexity, but also in terms of the constant factors. Next, we introduce the notion of user-defined quantitative functions that can be associated with abstract data-structures, e.g., length of a list, height of a tree, etc. We show how to compute bounds in terms of these quantitative functions using a linear invariant generation tool that has support for handling uninterpreted functions. We show application of this methodology to commonly used data-structures (namely lists, list of lists, trees, bit-vectors) using examples from Microsoft product code. We observe that a few quantitative functions for each data-structure are usually sufficient to allow generation of symbolic complexity bounds of a variety of loops that iterate over these data-structures, and that it is straightforward to define these quantitative functions. The combination of these techniques enables generation of precise computational complexity bounds for real-world examples (drawn from Microsoft product code and C++ STL library code) for some of which it is non-trivial to even prove termination. Such automatically generated bounds are very useful for early detection of egregious performance problems in large modular codebases that are constantly being changed by multiple developers who make heavy use of code written by others without a good understanding of their implementation complexity. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. POPL’09, January 18–24, 2009, Savannah, Georgia, USA. Copyright c © 2009 ACM 978-1-60558-379-2/09/01. . . $5.00.
Assessment of vascular remodeling under antiangiogenic therapy using DCE‐MRI and vessel size imaging (2009)

DCE-MRI and vessel size imaging provide reliable and supplementing biomarkers of antiangiogenic therapy response. The results of both methods are in excellent agreement with histology. Nevertheless, our results also indicate that vascular remodeling is complex and that a uniform response cannot be expected for different tumors and therapies.
The aerocapacitor: A carbon aerogel based supercapacitor (1992)

During the 1980`s, a wide variety of carbon foams, formed by the pyrolysis of polymeric foams, were developed at several Department of Energy Laboratories. These foams are known for their monolithic structure and the ability to tailor their critical parameters (e.g. porosity, density). Lawrence Livermore National Laboratory (LLNL) exclusively developed a unique type of carbon foam, known as carbon aerogels. Carbon aerogels are a special class of open-cell foams with (1) homogeneous ultrafine particle and pore size, (2) very large useful surface area per unit volume, and (3) monolithic structure, that yields (4) excellent electrical conductivity due to the intimate connection of the particles. We have applied carbon aerogels to make an ``Aerocapacitor``; a high power- and energy-density electrochemical double layer capacitor (EDLC) that uses carbon aerogels as electrodes. Carbon aerogel surface areas range from about 100 to 700 m{sup 2}/cc (as measured by BET analysis), with bulk densities of 0.05 to 1.0 g/cm{sup 3} and their morphology allows stored energy to be released rapidly, resulting in high power-densities.
How to Design a Thermoacoustic System Considering the Relaxation Time τ: Introduction of Parameter ωτ to Determine the Position of Stack (2008)

Experimental investigations were carried out to establish a design method for a thermoacoustic cooling system. When a straight acoustic tube is used, the acoustic power is supplied from the tube end. The ceramic stack, which consists of many narrow channels, is inserted into the tube. By changing the insertion position and the stack channel radius, a temperature decrease at the stack end is observed as the energy conversion parameter. A nondimensional parameter, ωτ, considering the relaxation time τ is determined from resonance frequency and stack channel radius. The temperature decrease is examined using several values of ωτ. Results show that the insertion position for which the maximum temperature decrease is obtained depends on ωτ. Therefore, the best stack insertion position can be designed according to the given frequency and stack channel radius. For that reason, ωτ is an important index for thermoacoustic cooling systems.
A Comparison of Cu-Ceria-SDC and Au-Ceria-SDC Composites for SOFC Anodes (2003)

Solid oxide fuel cells (SOFC) with samaria-doped ceria (SDC) electrolytes were prepared with anodes made from either Cu, ceria, and SDC or Au, ceria, and SDC. These cells were tested in and n-butane fuels at 650°C. The similarity of performance curves and impedance results for cells made with Au and Cu suggests that both metals are simply electronic conductors in the anode and that Cu does not play a catalytic role in direct-oxidation anodes made with Cu. The addition of ceria is shown to play an important role in improving anode performance, either through improved catalytic activity or mixed ion-electronic conductivity. © 2003 The Electrochemical Society. All rights reserved.
The electroreduction of oxygen to hydrogen peroxide on fixed bed cathodes (1976)

Abstract The production of dilute alkaline peroxide bleaching solutions by electro‐reduction of oxygen on fixed beds of graphite particles was investigated. The cell was operated both in the two‐phase mode where oxygen saturated 0.1 M NaOH was passed continuously through the bed, and in the three‐phase mode where oxygen gas and electrolyte flowed co‐currently downward through the cell. Experiments were carried out under oxygen pressures from 1 to 12 atmospheres. The peroxide concentration at the reactor outlet, and the current efficiency dependence on the applied current are reported as functions of electrolyte and oxygen flowrates, oxygen pressure, graphite particle size, fixed bed height and electrolyte pH. Conditions for producing maximum peroxide concentrations are described and possible rate limiting steps in the reaction suggested.
Microstructurally Toughened Articles and Casting Thereof. (1991)

Abstract : The present invention relates in general to articles reinforced with discontinuous composites and the like, and a process of making the same, and in particular, to the use of preforms which can be used to form articles such as microstructurally toughened tubes by casting. Discontinuous metal matrix composites (MMC) have relatively recently been used industrially. The most widely used discontinuous composites are silicon carbide whiskers (SiC) and silicon carbide particles (SiCp) or (SiCw). Discontinuously reinforced aluminum is commonly designated as SiC/Al and SiCp/Al, respectively. Patent applications.
Toward Real-Time Automotive Model Predictive Control: A Perspective from a Diesel Air Path Control Development (2018)

To meet increasingly stringent fuel economy and emissions regulations, automotive powertrain architectures are becoming increasingly sophisticated, e.g., through downsizing and electrification, with increasing numbers of actuators and interacting dynamics. Simultaneously, the corresponding control systems are becoming more complex and the degree of difficulty involved in developing them using traditional methods is increasing. Model Predictive Control (MPC) has long been identified as a promising technique to control complex power-train dynamics under performance, reliability, and regulatory constraints. However, despite an abundance of research in applying MPC to powertrain control, the computational burden of these MPC strategies is still too great for widespread production adoption of MPC on low cost embedded control units (ECU). This paper summarizes our path toward a real-time-on-ECU model predictive controller in the context of a Diesel air path control development and comments on model accuracy, optimal control problem formulation, solver accuracy, performance, robustness, and practicality.
RNA Incorporation Is Critical for Retroviral Particle Integrity after Cell Membrane Assembly of Gag Complexes (2002)

The nucleocapsid (NC) domain of retroviruses plays a critical role in specific viral RNA packaging and virus assembly. RNA is thought to facilitate viral particle assembly, but the results described here with NC mutants indicate that it also plays a critical role in particle integrity. We investigated the assembly and integrity of particles produced by the human immunodeficiency virus type 1 M1-2/BR mutant virus, in which 10 of the 13 positive residues of NC have been replaced with alanines and incorporation of viral genomic RNA is virtually abolished. We found that the mutations in the basic residues of NC did not disrupt Gag assembly at the cell membrane. The mutant Gag protein can assemble efficiently at the cell membrane, and viral proteins are detected outside the cell as efficiently as they are for the wild type. However, only approximately 10% of the Gag molecules present in the supernatant of this mutant sediment at the correct density for a retroviral particle. The reduction of positive charge in the NC basic domain of the M1-2/BR virus adversely affects both the specific and nonspecific RNA binding properties of NC, and thus the assembled Gag polyprotein does not bind significant amounts of viral or cellular RNA. We found a direct correlation between the percentage of Gag associated with sedimented particles and the amount of incorporated RNA. We conclude that RNA binding by Gag, whether the RNA is viral or not, is critical to retroviral particle integrity after cell membrane assembly and is less important for Gag-Gag interactions during particle assembly and release.
SampleRank Training for Phrase-Based Machine Translation (2011)

Statistical machine translation systems are normally optimised for a chosen gain function (metric) by using MERT to find the best model weights. This algorithm suffers from stability problems and cannot scale beyond 20-30 features. We present an alternative algorithm for discriminative training of phrasebased MT systems, SampleRank, which scales to hundreds of features, equals or beats MERT on both small and medium sized systems, and permits the use of sentence or document level features. SampleRank proceeds by repeatedly updating the model weights to ensure that the ranking of output sentences induced by the model is the same as that induced by the gain function. 1
The Ohio State University Seed Vigor Imaging System (SVIS) for Soybean and Corn Seedlings (2005)

An image processing computer application to automatically assess the vigor of three-day-old soybean [Glycine max (L.) Merrill.] and corn (Zea mays L.) seedlings was developed. The software operates on acquired digital images of soybean and corn seed lots placed on a paper towel. Seedlings were digitally extracted away from the paper towel and converted into various dig ital representations. These representations were used to analyze the seedlings and segment them into normal and abnormal categories. The normal seedlings were further processed so that a one-pixel-wide summary structure of the shape of the seedling was produced. From the soybean summary struc ture, the software classified the seedlings into six type categories based on their shape. Each normal seedling was processed to remove the cotyledon portion of the summary structure based on the type category it fell into. The remaining summary structure, with the cotyledon removed, was then used to compute the length of each seedling in pixels. From the corn summary struc ture, the software first identified seeds based on their yellowish-red color, connected nearby multiple roots to the seed, and separated overlapping roots to the correct seed. Once the seedling structures were correctly identified for soybean and corn, seedling length measurements were determined. From these length measurements, speed of growth and uniformity of growth val ues were computed. These two values were normalized and combined into a zero to 1,000 vigor index for the soybean or corn seed lot. Combined with the post-processing corrective features, this computer software was able to achieve highly accurate and standardized measurements of each soybean and corn seedling, providing an alternative to the current method of manually measuring seedlings for speed and uniformity of growth when performing a vigor test.