gebhart/patrepeval huggingface dataset:
Measurement of Ga and Al in a molecular-beam epitaxy chamber by atomic absorption spectrometry (AAS) (1975)

The feasibility of using atomic absorption spectrometry (AAS) to monitor aluminum and gallium atoms in a molecular beam of a system designed for growing epitaxial layers of GaAs and AlxGa1−xAs was investigated. Results are reported to demonstrate the effectiveness of the method for monitoring the flux emitted from source ovens during molecular-beam epitaxial deposition. Absorption by atoms was found to be directly correlated with the temperature of the oven and vapor pressure of the metal. No chemical interaction of atomic vapors of Ga, Al, and As was detected in the molecular beam. Atomic absorption spectrometry compared favorably with mass spectrometry for monitoring Ga.
Discovery of Specific Flavodoxin Inhibitors as Potential Therapeutic Agents against <i>Helicobacter pylori</i> Infection (2009)

Helicobacter pylori establishes life-long infections in the gastric mucosa of over 1 billion people worldwide. In many cases, without specific antimicrobial intervention, H. pylori infected individuals will develop type B gastritis, chronic peptic ulcers and, more rarely, gastric neoplasias. Conventional antimicrobial therapy has been complicated by dramatic increases in resistance to macrolides, metronidazole and fluoroquinolones. Here, we report the development of novel therapeutics that specifically target the unique flavodoxin component of an essential metabolic pathway of H. pylori. With the use of high-throughput screening methodology, we have tested 10,000 chemicals and have identified 29 compounds that bind flavodoxin, four of which interrupted in vitro electron transfer to flavodoxin physiological partners. Three of these compounds are bactericidal and promisingly selective for H. pylori. The minimal inhibitory concentrations of two of them are 10 times lower than their minimal cytotoxic concentrations for HeLa cells. Importantly, neither of the four inhibitors is toxic for mice after administration of 1-10 mg kg(-1) doses twice a day for 5 days. Enzymatic, thermodynamic and structural characterization of the inhibitor-flavodoxin complexes suggests these compounds could act by modifying the redox potentials of flavodoxin. These newly discovered inhibitors represent promising selective leads against the different diseases associated to H. pylori infection.
Documenting Wind Speed and Power Deficits behind a Utility-Scale Wind Turbine (2012)

Abstract High-spatial-and-temporal-resolution radial velocity measurements surrounding a single utility-scale wind turbine were collected using the Texas Tech University Ka-band mobile research radars. The measurements were synthesized to construct the first known dual-Doppler analyses of the mean structure and variability of a single turbine wake. The observations revealed a wake length that subjectively exceeded 20 rotor diameters, which far exceeds the typically employed turbine spacing of 7–10 rotor diameters. The mean horizontal wind speed deficits found within the turbine wake region relative to the free streamflow were related to potential reductions in the available power for a downwind turbine. Mean wind speed reductions of 17.4% (14.8%) were found at 7 (10) rotor diameters downwind, corresponding to a potential power output reduction of 43.6% (38.2%). The wind speed deficits found within the wake also exhibit large variability over short time intervals; this variability would have an appreciable impact on the inflow of a downstream turbine. The full understanding and application of these newly collected data have the potential to alter current wind-farm design and layout practices and to affect the cost of energy.
A 96-well culture platform enables longitudinal analyses of engineered human skeletal muscle microtissue strength (2019)

ABSTRACT Three-dimensional (3D) in vitro models of human skeletal muscle mimic aspects of native tissue structure and function, thereby providing a promising system for disease modeling, drug discovery or pre-clinical validation, and toxicity testing. Widespread adoption of this research approach is hindered by the lack of an easy-to-use platform that is simple to fabricate and yields arrays of human skeletal muscle micro-tissues (hMMTs) in culture with reproducible physiological responses that can be assayed non-invasively. Here, we describe a design and methods to generate a reusable mold to fabricate a 96-well platform, referred to as MyoTACTIC, that enables bulk production of 3D hMMTs. All 96-wells and all well features are cast in a single step from the reusable mold. Non-invasive calcium transient and contractile force measurements are performed on hMMTs directly in MyoTACTIC, and unbiased force analysis occurs by a custom automated algorithm, allowing for longitudinal studies of function. Characterizations of MyoTACTIC and resulting hMMTs confirms the reproducibility of device fabrication and biological responses. We show that hMMT contractile force mirrors expected responses to compounds shown by others to decrease (dexamethasone, cerivistatin) or increase (IGF-1) skeletal muscle strength. Since MyoTACTIC supports hMMT long-term culture, we evaluated direct influences of pancreatic cancer chemotherapeutics agents on contraction competent human skeletal muscle fibers. A single application of a clinically relevant dose of Irinotecan decreased hMMT contractile force generation, while clear effects on fiber atrophy were observed histologically only at a higher dose. This suggests an off-target effect that may contribute to cancer associated muscle wasting, and highlights the value of the MyoTACTIC platform to non-invasively predict modulators of human skeletal muscle function.
Multidimensional maximum-likelihood processing of a large aperture seismic array (1967)

The experimental Large Aperture Seismic Array (LASA) represents an attempt to improve the capability to monitor underground nuclear weapons tests and small earthquakes by making a large extrapolation in the existing art of building arrays of spaced and interconnected seismic transducers. The LASA is roughly equivalent to 21 separate subarrays, each consisting of 25 sensors, spread over an aperture of 200 km. The present work considers the problem of designing a linear filter which combines the outputs of the 25 sensors in a subarray so as to suppress the noise without distorting the signal, or event. This filter provides a minimum-variance unbiased estimate of the signal which is the same as the maximum-likelihood estimate of the signal if the noise is a multidimensional Gaussian process. An extensive discussion of the theory of multidimensional maximum-likelihood processing is given. A computer program implementation of the maximum-likelihood filter is presented which employs the cross-correlation matrix of noise measured just prior to the arrival of the event. This time-domain synthesis procedure requires relatively large amounts of computer time to synthesize the filter, and is quite sensitive to the assumption of noise stationarity. The asymptotic theory of maximum-likelihood filtering is also given. An asymptotically optimum frequency-domain synthesis technique is given for two-sided multidimensional filters. This procedure is well suited to machine computation and has the advantage with respect to the time-domain procedure of requiring about 10 times less computation time. A description of a computer program implementation of the frequency-domain synthesis method is given which employs the spectral matrix of the noise estimated just before the arrival of the event. The experimental results obtained by processing several events recorded at the LASA are presented, as well as a comparison of the performance of the frequency-domain method relative to the time-domain synthesis technique. It is found that the signal-to-noise improvement given by the frequency-domain procedure is within 2 dB of the gain obtained with the time-domain procedure, and that the frequency-domain method is relatively insensitive to the assumption of noise stationarity.
Post-layout timing simulation of CMOS circuits (1993)

As a necessary aid to system integration, the authors present the implementation and performance of a pattern-dependent timing simulator, PATH-RUNNER. Organized around an explicit formulation of delays, this is an event-driven simulator which processes only transitions with gates controlled by events. Extraction of conduction paths from a general decomposition of data paths in unidirectional blocks allows general conflictual situations to be solved. Configuration problems detected during the evaluation, such as pulse rejection and strength conflicts, are illustrated, and effective solutions of conflictual configurations are given. It is shown that the implementation of a two-pass algorithm results in a significant improvement of speed. Execution times have been found to be nearly linear with the node numbers. Comparison of simulation times obtained from other timing simulators is given. SPICE compatibilities of PATH-RUNNER allow automatic real characterization of data paths from post-layout extracted net lists, with SPICE-like accuracy for evaluation of delays on real structures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Universal Compression of a Mixture of Parametric Sources with Side Information (2014)

This paper investigates the benefits of the side information on the universal compression of sequences from a mixture of $K$ parametric sources. The output sequence of the mixture source is chosen from the source $i \in \{1,\ldots ,K\}$ with a $d_i$-dimensional parameter vector at random according to probability vector $\mathbf{w} = (w_1,\ldots,w_K)$. The average minimax redundancy of the universal compression of a new random sequence of length $n$ is derived when the encoder and the decoder have a common side information of $T$ sequences generated independently by the mixture source. Necessary and sufficient conditions on the distribution $\mathbf{w}$ and the mixture parameter dimensions $\mathbf{d} = (d_1,\ldots,d_K)$ are determined such that the side information provided by the previous sequences results in a reduction in the first-order term of the average codeword length compared with the universal compression without side information. Further, it is proved that the optimal compression with side information corresponds to the clustering of the side information sequences from the mixture source. Then, a clustering technique is presented to better utilize the side information by classifying the data sequences from a mixture source. Finally, the performance of the clustering on the universal compression with side information is validated using computer simulations on real network data traces.
<title>Quantitative thermal imaging of aircraft structures</title> (1995)

Aircraft structural integrity is a major concern for airlines and airframe manufacturers. To remain economically competitive, airlines are looking at ways to retire older aircraft, not when some fixed number of flight hours or cycles has been reached, but when true structural need dictates. This philosophy is known as `retirement for cause.' The need to extend the life of commercial aircraft has increased the desire to develop nondestructive evaluation (NDE) techniques capable of detecting critical flaws such as disbonding and corrosion. These subsurface flaws are of major concern in bonded lap joints. Disbonding in such a joint can provide an avenue for moisture to enter the structure leading to corrosion. Significant material loss due to corrosion can substantially reduce the structural strength, load bearing capacity and ultimately reduce the life of the structure. The National Aeronautics and Space Administration's Langley Research Center has developed a thermal NDE system designed for application to disbonding and corrosion detection in aircraft skins. By injecting a small amount of heat into the front surface of an aircraft skin, and recording the time history of the resulting surface temperature variations using an infrared camera, quantitative images of both bond integrity and material loss due to corrosion can be produced. This paper presents a discussion of the development of the thermal imaging system as well as the techniques used to analyze the resulting thermal images. The analysis techniques presented represent a significant improvement in the information available over conventional thermal imaging due to the inclusion of data from both the heating and cooling portion of the thermal cycle. Results of laboratory experiments on fabricated disbond and material loss samples are presented to determine the limitations of the system. Additionally, the results of actual aircraft inspections are shown, which help to establish the field applicability for this technique. A recent application of this technology to aircraft repairs using boron/epoxy patches is shown illustrating the flexibility of the technology.
BERT has a Mouth, and It Must Speak: BERT as a Markov Random Field Language Model (2019)

We show that BERT (Devlin et al., 2018) is a Markov random field language model. This formulation gives way to a natural procedure to sample sentences from BERT. We generate from BERT and find that it can produce high-quality, fluent generations. Compared to the generations of a traditional left-to-right language model, BERT generates sentences that are more diverse but of slightly worse quality.
Iodinated cyanine dyes: a new class of sensitisers for use in NIR activated photodynamic therapy (PDT) (2017)

A new class of iodinated cyanine dyes have been prepared for use in NIR excited photodynamic therapy (PDT) and demonstrated improved efficacy in two pancreatic cell lines as well as excellent tumour control in a murine model of the disease.
Characterization and Evaluation of the <i>Moraxella catarrhalis</i> Oligopeptide Permease A as a Mucosal Vaccine Antigen (2010)

Moraxella catarrhalis is a common cause of otitis media in children and of lower respiratory tract infections in adults with chronic obstructive pulmonary disease; therefore, these two groups would benefit from a vaccine to prevent M. catarrhalis infections. A genome mining approach for vaccine antigens identified oligopeptide permease protein A (OppA), an oligopeptide binding protein of an apparent oligopeptide transport system. Analysis of the oppA gene by PCR and sequence analysis revealed that OppA is highly conserved among clinical isolates of M. catarrhalis. Recombinant OppA was expressed as a lipoprotein and purified, and an oppA knockout mutant was constructed. Antiserum raised to recombinant purified OppA recognized epitopes on the bacterial surface of the wild type but not the OppA knockout mutant. Antibodies raised to purified recombinant OppA recognized native OppA in multiple strains. Intranasal immunization of mice induced systemic and mucosal antibodies to OppA and resulted in enhanced clearance of M. catarrhalis in a mouse pulmonary clearance model. OppA is a highly conserved, immunogenic protein that expresses epitopes on the bacterial surface and that induces potentially protective immune responses in a mouse model. OppA should be evaluated further as a vaccine antigen for M. catarrhalis.
Levetiracetam-induced interstitial lung disease in a patient with advanced lung cancer (2020)

An 85-year-old woman with antibiotics-resistant pneumonia after surgery for metastatic brain tumor from lung cancer was consulted to our department. Chest CT showed diffuse GGO bilaterally. BALF showed elevated ratios of lymphocytes and CD4/CD8. Tests for bacteria, mycobacteria, and fungi were negative. She improved following levetiracetam discontinuance and systemic corticosteroid administration, and we diagnosed levetiracetam-induced lung injury. Although levetiracetam is widely used, few reports of levetiracetam-induced pneumonia exist. Changes in chest images may occur after levetiracetam administration if patients have multiple risk factors for development of drug-induced interstitial lung disease. Bronchoscopy is useful for differential diagnosis if new lung lesions appear after starting levetiracetam.
Chemical Attenuation of <i>Plasmodium berghei</i> Sporozoites Induces Sterile Immunity in Mice (2008)

Radiation and genetic attenuation of Plasmodium sporozoites are two approaches for whole-organism vaccines that protect against malaria. We evaluated chemical attenuation of sporozoites as an alternative vaccine strategy. Sporozoites were treated with the DNA sequence-specific alkylating agent centanamycin, a compound that significantly affects blood stage parasitemia and transmission of murine malaria and also inhibits Plasmodium falciparum growth in vitro. Here we show that treatment of Plasmodium berghei sporozoites with centanamycin impaired parasite function both in vitro and in vivo. The infection of hepatocytes by sporozoites in vitro was significantly reduced, and treated parasites showed arrested liver stage development. Inoculation of mice with sporozoites that were treated in vitro with centanamycin failed to produce blood stage infections. Furthermore, BALB/c and C57BL/6 mice vaccinated with treated sporozoites were protected against subsequent challenge with wild-type sporozoites. Our findings demonstrate that chemically attenuated sporozoites could be a viable alternative for the production of an effective liver stage vaccine for malaria.
The use of synthetic linear tetrapyrroles to probe the verdin sites of human biliverdin‐IXα reductase and human biliverdin‐IXβ reductase (2009)

Many vertebrate species express two enzymes that are capable of catalysing the reduction of various isomers of biliverdin. Biliverdin-IXalpha reductase (BVR-A) is most active with its physiological substrate biliverdin-IXalpha, but can also reduce the three other biliverdin isomers IXbeta, IXdelta and IXgamma. Biliverdin-IXbeta reductase (BVR-B) catalyses the reduction of only the IXbeta, IXdelta and IXgamma isomers of biliverdin. Therefore, the activity of BVR-A can be measured using biliverdin-IXalpha as a specific substrate. We now show that the dimethyl esters of biliverdin-IXbeta and biliverdin-IXdelta are substrates for BVR-B, but not for BVR-A. This provides a useful method for specifically assaying the activity of both BVR-A and BVR-B in crude mixtures, using biliverdin-IXalpha for BVR-A and the dimethyl ester of either biliverdin-IXbeta or biliverdin-IXdelta for BVR-B. Human BVR-A has been suggested as a pharmacological target for neonatal jaundice. Because of the absence of a crystal structure with biliverdin bound to BVR-A, we have investigated indirect ways of examining tetrapyrrole binding. In the present study, we report that a number of sterically locked conformers of 18-ethylbiliverdin-IXalpha are substrates for human BVR-A, and discuss the implications for the biliverdin binding site. The oxidation of bilirubin-IXalpha ditaurate to biliverdin-IXalpha ditaurate is also described. We show that biliverdin-IXalpha ditaurate is a substrate for human BVR-A and discuss the possibility of using a competing substrate, which is reduced to a water soluble and excretable rubin, as a prototypic inhibitor of BVR-A.
Model-Based Estimation of Collision Risks of Predatory Birds with Wind Turbines (2012)

Eichhorn, M., K. Johst, R. Seppelt, and M. Drechsler. 2012. Model-based estimation of collision risks of predatory birds with wind turbines. Ecology and Society 17(2): 1. https://doi.org/10.5751/ES-04594-170201
Hardware support for thread-level speculation (2003)

Novel architectures that support multithreading, for example chip multiprocessors, have become increasingly commonplace over the past decade: examples include the Sun MAJC, IBM Power4, Alpha 21464, and Intel Xeon, HP PA-8800. However, only workloads composed of independent threads can take advantage of these processors---to improve the performance of a single application, that application must be transformed into a parallel version. Unfortunately the process of parallelization is extremely difficult: the compiler must prove that potential threads are independent, which is not possible for many general-purpose programs (e.g., spreadsheets, web software, graphics codes, etc.) due to their abundant use of pointers, complex control flow, and complex data structures. This dissertation investigates hardware support for Thread-Level Speculation (TLS), a technique which empowers the compiler to optimistically create parallel threads despite uncertainty as to whether those threads are actually independent. The basic
Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels (2004)

Image registration describes the process of manipulating a distorted version of an image such that its pixels overlay the equivalent pixels in a clean, master or reference image. The need for it has assumed particular prominence in the analysis of images of electrophoretic gels used in the analysis of protein expression levels in living cells, but also has fundamental applications in most other areas of image analysis. Much of the positional information of a data feature is carried in the phase of a complex transform, so a complex transform allows explicit specification of the phase, and hence of the position of features in the image. Registration of a test gel to a reference gel is achieved by using a multiresolution movement map derived from the phase of a complex wavelet transform (the Q-shift wavelet transform) to dictate the warping directly via movement of the nodes of a Delaunay-triangulated mesh of points. This warping map is then applied to the original untransformed image such that the absolute magnitude of the spots remains unchanged. The technique is general to any type of image. Results are presented for a simple computer simulated gel, a simple real gel registration between similar "clean" gels with local warping vectors distributed about one main direction, a hard problem between a reference gel and a "dirty" test gel with multi-directional warping vectors and many artifacts, and some typical gels of present interest in post-genomic biology. The method compares favourably with others, since it is computationally rapid, effective and entirely automatic.