gebhart/patrepeval huggingface dataset:
Collaborative Research: Microbal Reductive Dechlorination of Polychlorinated Biphenyls (PCBs) in Estuarine and Marine Coastal Sediments (2002)

Abstract : For many years researchers have tried to identify and monitor PCB dechlorinating bacteria. Strains o-17 and DF-1 are the first PCB dechlorinating bacteria to be identified. These organisms have proven to be very difficult to grow in pure culture thus far. However, for the first time molecular approaches (165 rDNA analysis) has ben combined with enrichment culture technique to identify these organisms. This is a significant breakthrough that will advance the application of bioremediation and it proves that such an approach can be used to identify difficult to culture environmental microorganisms, which is to say most microorganisms. Now for the first time these organisms can be monitored in order to better understand their physiology and to track the organisms in situ, before, during and after active and passive remediation attempts.
At-wavelength characterization of the extreme ultraviolet Engineering Test Stand Set-2 optic (2001)

At-wavelength interferometric characterization of a new 4×-reduction lithographic-quality extreme ultraviolet (EUV) optical system is described. This state-of-the-art projection optic was fabricated for installation in the EUV lithography Engineering Test Stand (ETS) and is referred to as the ETS Set-2 optic. EUV characterization of the Set-2 optic is performed using the EUV phase-shifting point diffraction interferometer (PS/PDI) installed on an undulator beamline at Lawrence Berkeley National Laboratory’s Advanced Light Source. This is the same interferometer previously used for the at-wavelength characterization and alignment of the ETS Set-1 optic. In addition to the PS/PDI-based full-field wave front characterization, we also present wave front measurements performed with lateral shearing interferometry, the chromatic dependence of the wave front error, and the system-level pupil-dependent spectral-bandpass characteristics of the optic; the latter two properties are only measurable using at-wavelength interferometry.
Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions (2014)

The HIV-1 envelope (Env) mediates viral entry into host cells. To enable the direct imaging of conformational dynamics within Env, we introduced fluorophores into variable regions of the glycoprotein gp120 subunit and measured single-molecule fluorescence resonance energy transfer within the context of native trimers on the surface of HIV-1 virions. Our observations revealed unliganded HIV-1 Env to be intrinsically dynamic, transitioning between three distinct prefusion conformations, whose relative occupancies were remodeled by receptor CD4 and antibody binding. The distinct properties of neutralization-sensitive and neutralization-resistant HIV-1 isolates support a dynamics-based mechanism of immune evasion and ligand recognition.
Flip chip interconnection with anisotropic conductive adhesives for RF and high-frequency applications (2005)

Anisotropic conductive adhesives (ACAs) are as promising interconnect materials for flip chip assembly in low cost, high-density, high-speed interconnection packages. We evaluated and compared several flip chip interconnects that use ACAs at the radio frequency (RF) and high-frequency range. The performance of high-speed circuits is limited by the package interconnect discontinuity which is due to large inductance and resistance in the high-frequency range. This discontinuity is determined by the interconnection geometry and materials used. For bumps on the integrated circuit (IC), we used Au studs, Au electroplated and electroless Ni/Au bumps, for the interconnection adhesives, we used two kinds of anisotropic conductive film (ACF) with a different dielectric constant. To evaluate the high frequency model parameters, which we based on an ACF flip chip model and network analysis, we took the high-frequency measurements of test flip chip vehicles that used different bonding materials. Furthermore, to demonstrate real applications for an ACF interconnection at the RF and high-frequency range, we applied ACF flip chip technologies to assemble a passive device that uses an RF integrated passive device. We also applied these technologies to an active device that uses a highly integrated monolithic microwave (IC) device on an RF module. Moreover, we compared the high-frequency characteristics of these devices with those of flip chip assemblies fabricated with conventional methods such as solder ball interconnection.
Synthetic fuels from peat gasification (1979)

US peat resources are estimated to be about 1440 quads. In the contiguous 48 states, peat deposits are generally located in areas with no other significant fossil fuel resources. Therefore, for those areas, peat represents an important source of energy. Since 1976, the Institute of Gas Technology has been working on a peat gasification program jointly funded by the US Department of Energy and the Minnesota Gas Company. Tests in laboratory- and process development unit-scale equipment have proven that conversion of peat to synthetic fuel is technically feasible. Tests have been conducted with peats from Minnesota, North Carolina, and Maine. This paper presents some of the important gasification characteristics of the three peats. A brief description of the IGT PEATGAS Process, and highlights of its economics for converting peat to Substitute Natural Gas (SNG), benzene, and fuel oil are also presented. On the basis of the gasification characteristics, compared to coal, peat is a better raw material from which to make SNG as well as gasoline blending feedstock in that a greater fraction of the energy results in these products and requires milder operating conditions. Also compared to coal, peat gasification permits more flexibility in the relative yields of gas more » and liquid hydrocarbons. The estimates show that the economics of converting peat (containing 50% moisture) to SNG is competitive with those of converting Eastern coal to SNG. « less
OptChain: Optimal Transactions Placement for Scalable Blockchain Sharding (2019)

A major challenge in blockchain sharding protocols is that more than 95% transactions are cross-shard. Not only those cross-shard transactions degrade the system throughput but also double the confirmation time, and exhaust an already scarce network bandwidth. Are cross-shard transactions imminent for sharding schemes? In this paper, we propose a new sharding paradigm, called OptChain, in which cross-shard transactions are minimized, resulting in almost twice faster confirmation time and throughput. By treating transactions as a stream of nodes in an online graph, OptChain utilizes a lightweight and on-the-fly transaction placement method to group both related and soon-related transactions into the same shards. At the same time, OptChain maintains a temporal balance among shards to guarantee the high parallelism. Our comprehensive and large-scale simulation using Oversim P2P library confirms a significant boost in performance with up to 10 folds reduction in cross-shard transactions, more than twice reduction in confirmation time, and 50% increase in throughput. When combined with Omniledger sharding protocol, OptChain delivers a 6000 transactions per second throughput with 10.5s confirmation time.
A Multiple Instance Learning Approach toward Optimal Classification of Pathology Slides (2010)

Pathology slides are diagnosed based on the histological descriptors extracted from regions of interest (ROIs) identified on each slide by the pathologists. A slide usually contains multiple regions of interest and a positive (cancer) diagnosis is confirmed when at least one of the ROIs in the slide is identified as positive. For a negative diagnosis the pathologist has to rule out cancer for each and every ROI available. Our research is motivated toward computer-assisted classification of digitized slides. The objective in this study is to develop a classifier to optimize classification accuracy at the slide level. Traditional supervised training techniques which are trained to optimize classifier performance at the ROI level yield suboptimal performance in this problem. We propose a multiple instance learning approach based on the implementation of the large margin principle with different loss functions defined for positive and negative samples. We consider the classification of intraductal breast lesions as a case study, and perform experimental studies comparing our approach against the state-of-the-art.
A multi-parameter, feedback-based electrical stimulation system for cardiomyocyte cultures (2004)

Cardiac myocytes are cultured to confluency on a 36-element planar microelectrode array. Spontaneously-active cardiomyocyte cultures are electrically stimulated, eliciting action potentials (APs), and the resulting data is amplified, filtered, and stimulation artifacts are removed during data acquisition. Stimulation circuitry allows real-time control of stimulation waveform amplitude, duration, and rate via 10-bit digital-to-analog converters (DACs). By extracting artifacts and processing AP properties in real time, we incorporate these properties into real-time stimulation algorithms, creating a sensitive feedback-regulated myocyte-based transducer of cell electrophysiological properties. Applications of this technology include toxin detection, automated pharmaceutical screening, and basic cardiac electrophysiology.
Novel thermosensitive chitosan hydrogels: <i>In vivo</i> evaluation (2008)

Chitosan is an attractive biopolymer for the preparation of hydrogels. Its unique combination of biocompatibility, biodegradability, bioadhesivity, and tissue-promoting abilities allows pharmaceutical applications. We investigated novel thermosensitive hydrogels based on chitosan homogeneously reacetylated to a deacetylation degree of about 50%, combined with selected polyols or polyoses such as trehalose, a nontoxic polysaccharide. The latter, a gel-inducing and lyoprotective agent enabled the formulation to be lyophilized and rehydrated without affecting the thermosensitive behavior. This made possible long-term storage and promoted its use in a clinical setup. The thermally induced sol-gel transition allowed injectability and in situ setting. Rheological characterization revealed that storage moduli could be increased by one decade by increasing the chitosan concentration from 1.4 to 2.2% (w/w). Evaluation in vivo provided evidence of in situ implant formation in subcutaneous tissue of Sprague-Dawley rats and permanence for up to 3 months. Histopathological analysis demonstrated a mild, chronic, inflammatory reaction that disappeared with the complete absorption of the gel implant over a few months period. Such in situ forming hydrogels could be advantageous for specific applications in drug delivery and tissue engineering.
Characteristics of Internally Buffered N-Methylol Reagents and Their Reactions with Cotton (1974)

Two t-amino-N-methylol reagents, 2(diethylamino)ethyl N,N-di(hydroxymethvl)carl)amate and dimethyloldi ethylaminopropyltriazone, were prepared, and their reactivities in finishing of cotton fabrics were characterized. Auto- catalysis was shown by these reagents when they were applied as hydrochlorides to cotton fabric and given a conventional pad-dry-cure; however, full development of resilience was not realized unless the pH of the reagent solution was lowered to 1.0. The sluggish reactions of the t-amino-N-methylol reagents are discussed; the stronger-than-normal catalysis that was required counterbalanced potential protective effects from the t-amino groups to lessen acid degradation during finishing reactions.
Indolo[3,2-<i>b</i>]carbazole-Based Thin-Film Transistors with High Mobility and Stability (2004)

Proper functionalization of indolo[3,2-b]carbazole led to a new class of high-performance organic semiconductors suitable for organic thin-film transistor (OTFT) applications. While 5,11-diaryl-substituted indolo[3,2-b]carbazoles without long alkyl side chains provided amorphous thin films upon vacuum deposition, those with sufficiently long alkyl side chains such as 5,11-bis(4-octylphenyl)indolo[3,2-b]carbazole self-organized readily into highly crystalline layered structures under similar conditions. OTFTs using channel semiconductors of this nature exhibited excellent field-effect properties, with mobility up to 0.12 cm(2) V(-1) s(-1) and current on/off ratio to 10(7). As this class of organic semiconductors has relatively low HOMO levels and large band gaps, they also displayed good environmental stability even with prolonged exposure to amber light, an appealing characteristic for OTFT applications.
<title>High-performance MEMS microgyroscope</title> (2002)

This paper reports on JPL's on-going research into MEMS gyroscopes. [1-4] This paper will describe the gyroscope's fabrication- methods, a new 8-electrode layout developed to improve performance and performance statistics of a batch of six gyroscopes (of the 8- electrode design) recently rate tested. Previously in our group, T. Tang and R. Gutierrez presented the results of their extensive use of ethylene diamine pyrocatechol (EDP) to deep-etch the inertial- sensitive r4esonators and post-supporting structures in a 4- electrode gyroscope design. Today, JPL is utilizing an in-house STS DRIE, replacing the old wet-etching steps. This has demonstrated superior precision in machining symmetry of the resonators, thus significantly reducing native rocking mode frequency splits. A performance test of six gyros has shown an average, un-tuned, frequency split of 0.4% (11Hz split for rocking modes at 2.7KHz). The new JPL MEMS gyroscope has a unique 8-electrode layout, whose large electrodes can provide significant electrostatic softening of the resonator's springs. This allows matching of the Coriolis sensitive rocking modal frequencies to be improved from the native 0.4% to an average tuned frequency split of 0.02%. In separate tests, electrostatic tuning in the 8-electrode design has demonstrated the ability to match frequency-splits to within 10mHz, thus ensuring full degeneracy in even a very high Q device. In addition, a newly selected ceramic package-substrate has improved the device's dampening loses such that a mean Q of 28,000 was achieved in the six gyroscope tested. These Q's ere measured via the ring-down time method. The improved fabrication development and other modifications described have led to the JPL's MEMS gyroscope achieving an average bias instability (Allan variance 1/f floor estimate) of 11degree/hr with best in the group being 2degree/hr. In an independent test, Honeywell Inc. reported one of our MEMS gyroscopes as achieving 1degree/hr bias instability flicker floor estimate measured at constant temperature.
Antiguided Ribbon Laser Concept (2000)

We propose a new, robustly scalable technique for phase locking multiple gain cores in a fiber structure based on antiguiding or radiative coupling, rather than the more commonly pursued method of evanescent wave phase locking. Our focus is on a ribbon-like geometry in which a waveguide region contains multiple gain cores arranged in a periodic array. The distinguishing feature of such antiguiding structures is that refractive index of the gain cores is lower than or equal to that of the surrounding waveguide regions. This is just the opposite of evanescently phase locked structures in which the gain cores have higher refractive index than the surrounding regions. The critical design considerations in the structures proposed within are: first that they strongly favor oscillation in a single transverse mode, and second that this strongly favored mode exhibits good intensity uniformity across the entire array of gain cores. We require single mode operation so that a static phase corrector placed in the near field of the ribbon laser's output can optimize the phase across the aperture to achieve a high Strehl ratio in the far field. The requirement that the strongly favored mode exhibit good uniformity across the entire array of gain cores is necessary to ensure that the ribbon structure's gain saturates in a uniform manner, so as not to increase the propensity of the device to operate in multiple transverse modes. Taken together, these two design considerations lead to the surprising result that optimized structures have equal refractive indices in their gain cores and the no-gain surrounding waveguide regions.
Implementation of shading effect for reconstruction of smooth layer-based 3D holographic images (2013)

A holographic rendering algorithm using a layer-based structure with angular tiling supports view-dependent shading and accommodation cues. This approach also has the advantages of rapid computation speed and visual reduction of layer gap artefacts compared to other approaches. Holograms rendered with this algorithm are displayed using an SLM to demonstrate view-dependent shading and occlusion.
Wideband Image-Based Transskull Refocusing Using Dual-Mode Ultrasound Arrays (2018)

A new image-based wideband transcranial refocusing algorithm is presented together with ex vivo experimental verification results. A dual-mode ultrasound array (DMUA) prototype and supporting real-time imaging platform are used for the acquisition and processing of refocusing beams through ex vivo skull samples. The algorithm utilizes pre-beamforming DMUA echo data to perform optimal refocusing in multiple frequency bands within the transducer bandwidth based on user selection of the target and any critical points on the skull where the exposure is to be minimized. Hydrophone measurements were performed in water tank with and without the skull in the path of the beam. These measurements clearly demonstrated that the focusing gain has non-monotonic frequency dependence for any target point. Moreover, the focusing gain profiles vary considerably between different target points. In the former case, the measurements were performed with and without refocusing. Additional experimental verification was obtained using ex vivo skull samples embedded in tissue-mimicking phantoms. Transient temperature rises at the target location (thermocouple junction) were recorded with and without optimal refocusing. The results from both setups clearly demonstrate the increase in focusing gain at the target location and its frequency dependence. The results clearly demonstrate that real-time, site-specific refocusing allows for synthesizing refocused tFUS beams with the maximum operating bandwidth allowable by the transmission characteristics of the skull to the target point(s).
Effect of engine noise on aircraft wing laminar boundary-layer stability (1981)

High-intensity acoustical disturbances can cause transition of controlled laminar flow. An investigation was made to determine whether main propulsion engines installed on an aircraft wing would cause excessive transition of laminar to turbulent flow. A method was developed for analyzing the influence of noise on the stability of a controlled laminar boundary layer, based upon the Tollmien–Schlichting traveling wave solution of the Orr–Sommerfeld equation and some wind tunnel experimental data. It is concluded that wing-mounted, high-bypass-ratio engines with sufficient acoustic treatment for controlling turbomachinery noise would not cause excessive loss of wing laminar flow. Additional analytical and experimental work is needed, however, to improve the accuracy of engine nearfield noise prediction, and the need to improve the proposed models to account for the acoustic transfer function for predicting transition.
Spin-orbit torques in perpendicularly magnetized Ir22Mn78/Co20Fe60B20/MgO multilayer (2016)

The current-induced spin-orbit torques (SOTs) in the perpendicularly magnetized Ir22Mn78/Co20Fe60B20/MgO structures are investigated. The damping- and field-like torques are characterized using a harmonic technique. The spin Hall angle of Ir22Mn78 is determined to be θSHE = +0.057 ± 0.002. The SOT-driven magnetization switching is also demonstrated with the assistance of an external in-plane field. Furthermore, the magneto-optical Kerr effect imaging experiments show that the magnetization switching is realized through domain nucleation and domain wall motion. These results may promise potential practical applications in high-performance SOT devices based on the antiferromagnetic materials.
Dual-wavelength laser annealing (1979)

A simple and efficient method of annealing ion-implantation damage in semiconductors is demonstrated which utilizes a relatively weak optical pulse in the visible to initiate surface melting in combination with a more energetic infrared pulse to drive in the melt front to the crystalline substrate. The efficacy of this approach is illustrated by an example in which an arsenic-implanted silicon crystal is simultaneously exposed to 530- and 1060-nm pulses. The results are discussed in relation to theoretical estimates of the melting thresholds at the two wavelengths.
ChemInform Abstract: Ruthenium and Osmium Complexes Containing 2‐(Aminomethyl)pyridine (Ampy)‐Based Ligands in Catalysis (2015)

Abstract Review: 150 refs.
Digital filter based on the Fisher linear discriminant to reduce dead-time paralysis in photon counting (2014)

Photon counting represents the Poisson limit in signal to noise, but can often be complicated in imaging applications by detector paralysis, arising from the finite rise / fall time of the detector upon photon absorption. We present here an approach for reducing dead-time by generating a deconvolution digital filter based on optimizing the Fisher linear discriminant. In brief, two classes are defined, one in which a photon event is initiated at the origin of the digital filter, and one in the photon event is non-coincident with the filter origin. Linear discriminant analysis (LDA) is then performed to optimize the digital filter that best resolves the coincident and non-coincident training set data.1 Once trained, implementation of the filter can be performed quickly, significantly reducing dead-time issues and measurement bias in photon counting applications. Experimental demonstration of the LDA-filter approach was performed in fluorescence microscopy measurements using a highly convolved impulse response with considerable ringing. Analysis of the counts supports the capabilities of the filter in recovering deconvolved impulse responses under the conditions considered in the study. Potential additional applications and possible limitations are also considered.
Constrained De Novo peptide identification via multi-objective optimization (2004)

Summary form only given. Automatic de novo peptide identification from collision-induced dissociation tandem mass spectrometry data is made difficult by large plateaus in the fitness landscapes of scoring functions and the fuzzy nature of the constraints that is due to noise in the data. A framework is presented for combining different peptide identification methods within a parallel genetic algorithm. The distinctive feature of our approach, based on Pareto ranking, is that it can accommodate constraints and possibly conflicting scoring functions. We have also shown how population structure can significantly improve the wall clock time of a parallel peptide identification genetic algorithm while at the same time maintaining some exchange of information across local populations.