gebhart/patrepeval huggingface dataset:
Transgenic pyrimethamine resistant <i>Plasmodium berghei</i> as a model for <i>in vivo</i> anti-DHFR drug testing (2020)

Abstract Inhibitors for Plasmodium falciparum dihydrofolate reductase (DHFR) form an important class of antimalarial drugs widely used for malaria treatment, but have been compromised by development of resistance to the drugs. Mutations in DHFR are the main contributing factors to the resistance. Although new, rationally designed antifolates active against resistant P. falciparum , such as P218, have been developed, the activity against the quadruple mutant P. falciparum (V1/S) has only been demonstrated in vitro , and in vivo activity has only been shown in SCID mice. A convenient in vivo model for antifolate testing is desirable. In this study, the endogenous P. berghei dihydrofolate reductase-thymidylate synthase ( Pbdhfr -ts) gene was successfully replaced by quadruple dhfr-ts mutant gene from P. falciparum (N51I+C59R+S108N+I164L). The transgenic parasite gained resistance to pyrimethamine but not to other class of antimalarial drugs. While 30 mg/kg of pyrimethamine could not inhibit the transgenic parasite, P218 could inhibit the transgenic parasite with the ED 50 of 0.11±0.02 mg/kg, a level similar to the P. falciparum in SCID mice model. These results demonstrated the validity of our model and showed that P218 was very potent against quadruple Pfdhfr-ts mutant parasite, in vivo .
Learning a Probabilistic Model for Diffeomorphic Registration (2019)

We propose to learn a low-dimensional probabilistic deformation model from data which can be used for the registration and the analysis of deformations. The latent variable model maps similar deformations close to each other in an encoding space. It enables to compare deformations, to generate normal or pathological deformations for any new image, or to transport deformations from one image pair to any other image. Our unsupervised method is based on the variational inference. In particular, we use a conditional variational autoencoder network and constrain transformations to be symmetric and diffeomorphic by applying a differentiable exponentiation layer with a symmetric loss function. We also present a formulation that includes spatial regularization such as the diffusion-based filters. In addition, our framework provides multi-scale velocity field estimations. We evaluated our method on 3-D intra-subject registration using 334 cardiac cine-MRIs. On this dataset, our method showed the state-of-the-art performance with a mean DICE score of 81.2% and a mean Hausdorff distance of 7.3 mm using 32 latent dimensions compared to three state-of-the-art methods while also demonstrating more regular deformation fields. The average time per registration was 0.32 s. Besides, we visualized the learned latent space and showed that the encoded deformations can be used to transport deformations and to cluster diseases with a classification accuracy of 83% after applying a linear projection.
Spectrally-Efficient Wireless Relaying Based on Superposition Coding (2007)

The wireless relay systems represent an important segment in the wireless communication systems. In a simple wireless relay scenario, a source node A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> needs to communicate to a destination A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> , with the help of a relay A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> . In this paper we introduce a new two-step relaying scheme based on superposition coding, SC-relaying. In step 1, A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> broadcasts a message, created by superposition coding, to A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> and A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> . After decoding the information from A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">S</sub> , A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> relays a part of this message in step 2, by adapting the transmission rate with respect to the link quality towards A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> . The unique point of the proposed scheme is that the signal format in the two steps is chosen in a way that enables a simple combining at A <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> . The numerical results show that the proposed scheme can bring a notable gain in spectral efficiency over the conventional multi-hop transmission with adaptive modulation, even in the case when the instantaneous SNR about all the links is not fully known at the source. In addition, the proposed scheme performs very closely to the scheme that is optimal in an information-theoretic sense.
Isolation of specific DNA fragments of Mycobacterium avium and their possible use in diagnosis (1993)

We cloned and sequenced two DNA fragments (DT1 and DT6) from Mycobacterium avium serotype 2 for use in the identification of members of the M. avium-M. intracellulare complex (MAC). Reference strains of MAC belonging to serovars 1 to 28 were examined by using these DNA fragments as probes. The study revealed that the DT6 probe hybridized with DNAs from M. avium strains (serovars 1 to 6, 8 to 11, and 21), while the DT1 probe hybridized with DNAs from serovars 2, 3, 7, 12 to 20, and 23 to 25. DT1- and DT6-derived oligonucleotides were selected for use as primers in a polymerase chain reaction test. Amplification of the DT1 and DT6 sequences may provide the basis for a rapid and reliable assay for the detection of mycobacteria belonging to MAC.
Low-latency visual odometry using event-based feature tracks (2016)

New vision sensors, such as the Dynamic and Active-pixel Vision sensor (DAVIS), incorporate a conventional camera and an event-based sensor in the same pixel array. These sensors have great potential for robotics because they allow us to combine the benefits of conventional cameras with those of event-based sensors: low latency, high temporal resolution, and high dynamic range. However, new algorithms are required to exploit the sensor characteristics and cope with its unconventional output, which consists of a stream of asynchronous brightness changes (called “events”) and synchronous grayscale frames. In this paper, we present a low-latency visual odometry algorithm for the DAVIS sensor using event-based feature tracks. Features are first detected in the grayscale frames and then tracked asynchronously using the stream of events. The features are then fed to an event-based visual odometry algorithm that tightly interleaves robust pose optimization and probabilistic mapping. We show that our method successfully tracks the 6-DOF motion of the sensor in natural scenes. This is the first work on event-based visual odometry with the DAVIS sensor using feature tracks.
A Novel Discrete Wavelet Domain Error-Based Image Quality Metric with Enhanced Perceptual Performance (2012)

In this paper, we present an error-based method to compute image quality scores in the discrete wavelet domain using the Haar wavelet. The proposed method does not extract any human visual system parameters, which noticeably reduces its complexity, and relies on computation of the errors (differences) at an appropriate level of wavelet decomposition. We also propose a formula to automatically calculate the required level of wavelet decomposition at a desired viewing distance. To consider the effect of very fine image details in quality assessment, the proposed method defines a multi-level edge map for each image which comprises only the most informative image subbands. We present the mathematical complexity analysis of our method and compare it to the conventional PSNR. We show that when the defined edge map is not taken into account we can calculate the quality score with lower complexity than with the PSNR, and with a prediction accuracy close to that of SSIM. We tested the performance of our method on two different databases: an image database and a video database.
Athermalization in atomic force microscope based force spectroscopy using matched microstructure coupling (2009)

The authors describe a method for athermalization in atomic force microscope (AFM) based force spectroscopy applications using microstructures that thermomechanically match the AFM probes. The method uses a setup where the AFM probe is coupled with the matched structure and the displacements of both structures are read out simultaneously. The matched structure displaces with the AFM probe as temperature changes, thus the force applied to the sample can be kept constant without the need for a separate feedback loop for thermal drift compensation, and the differential signal can be used to cancel the shift in zero-force level of the AFM.
Cyclooctatetrene derivatives as electron transporters and hole blocker in organic LEDs (2001)

In this paper, we report that novel tetraphenyl- tetraalkynyl-COTs and octaaryl-COTs can be used as electron transport and hole blocker layer in organic LEDs. These materials have the similar reduction potentials compared to traditional electron transporters, such as Alq<SUB>3</SUB>. The energy gaps for all of the COT derivatives studied here are very wide (> 3 eV), making it possible to fabricate blue emitting OLEDs with these materials. We have fabricated devices of the structure ITO/NPD400 angstrom/COT-Me 400 angstrom/Mg-Ag. (ITO equals indium-tin-oxide, NPD equals N,N'-diphenyl-N,N'-dinapthylbenzidine). The external quantum yield reaches 0.15% and the emission comes from NPD ((lambda) <SUB>max</SUB> equals 436 nm). When 1% perylene (by weight) is doped into the NPD, the (lambda) <SUB>max</SUB> of emission shifts to the 454 nm with the external QE reaches 0.60%. It indicates the efficient energy transfer from NPD to perylene. Changing the COT layer thickness from 400 Angstrom to 200 Angstrom, the emission is still from the NPD layer, as seen before. However, the I-V curve and turn-on voltage both shift to lower potentials by ca 2 - 3 V with the QE drops to 0.06%. The device QE can be increased by either using thin Alq layer or replacing Mg:Ag with LiF/Al electrode. Finally, the devices using COTs as hole blocker are fabricated and results are discussed.
Highly temperature insensitive, low threshold-current density (λ = 8.7–8.8 <i>μ</i>m) quantum cascade lasers (2015)

By stepwise tapering, both the barrier heights and quantum-well depths in the active regions of 8.7–8.8 μm-emitting quantum-cascade-laser (QCL) structures, virtually complete carrier-leakage suppression is achieved. Such step-taper active-region-type QCLs possess, for 3 mm-long devices with high-reflectivity-coated back facets, threshold-current characteristic temperature coefficients, T0, as high as 283 K and slope-efficiency characteristic temperature coefficients, T1, as high as 561 K, over the 20–60 °C heatsink-temperature range. These high T0 and T1 values reflect at least a factor of four reduction in carrier-leakage current compared to conventional 8–9 μm-emitting QCLs. Room temperature, pulsed, threshold-current densities are 1.58 kA/cm2; values comparable to those for 35-period conventional QCLs of similar injector-region doping level. Superlinear behavior of the light-current curves is shown to be the result of the onset of resonant extraction from the lower laser level at a drive level of ∼1.3× threshold. Maximum room-temperature slope efficiencies are 1.23 W/A; that is, slope efficiency per period values of 35 mW/A, which are 37%–40% higher than for same-geometry conventional 8–9 μm-emitting QCLs. Since the waveguide-loss coefficients are very similar, we estimate that the internal differential efficiency is at least 30% higher than in conventional QCLs. Such high internal differential efficiency values reflect the combined effect of nearly complete carrier-leakage suppression and high differential efficiency of the laser transition (∼90%), due to resonant extraction from the lower laser level.
Laser Weld Penetration Estimation Using Temperature Measurements (1999)

Penetration depth is an important factor critical to the quality of a laser weld. This paper presents a 3D heat conduction model with a moving line source to correlate the temperature measured on the bottom surface of the workpiece to the weld penetration, weld bead width and welding speed. Temperatures on the bottom surface of the workpiece are measured using infrared thermocouples located behind the laser beam. The averaging effect due to the temperature measurement spot size is analyzed. This paper provides a model-based approach for laser weld penetration monitoring instead of a pure empirical correlation between a measured signal (e.g., acoustic, infrared) and the penetration depth. Experiments were conducted to compare the depth estimation based on the model to bead-on-plate welds on low carbon steel plates of varying thickness at different laser power levels and speeds. It is shown that the temperature on the bottom surface is a consistent indicator of penetration depth and that the correlation is also sensitive to the sensor location as well as other process conditions such as weld shape, width, and the plate thickness. The proposed model is computationally efficient and is suitable for on-line process monitoring application.
Characterization of Botulinum Neurotoxin A Subtypes 1 Through 5 by Investigation of Activities in Mice, in Neuronal Cell Cultures, and <i>In Vitro</i> (2013)

Botulinum neurotoxins (BoNTs) are synthesized by Clostridium botulinum and exist as seven immunologically distinct serotypes designated A through G. For most serotypes, several subtypes have now been described based on nominal differences in the amino acid sequences. BoNT/A1 is the most well-characterized subtype of the BoNT/A serotype, and many of its properties, including its potency, its prevalence as a food poison, and its utility as a pharmaceutical, have been thoroughly studied. In contrast, much remains unknown of the other BoNT/A subtypes. In this study, BoNT/A subtype 1 (BoNT/A1) to BoNT/A5 were characterized utilizing a mouse bioassay, an in vitro cleavage assay, and several neuronal cell-based assays. The data indicate that BoNT/A1 to -5 have distinct in vitro and in vivo toxicological properties and that, unlike those for BoNT/A1, the neuronal and mouse results for BoNT/A2 to -5 do not correlate with their enzymatic activity. These results indicate that BoNT/A1 to -5 have distinct characteristics, which are of importance for a greater understanding of botulism and for pharmaceutical applications.
Using Time Domain Seismic Attributes for History Matching (2006)

The goal of reservoir characterization is to enhance the description of oil and gas reservoirs to get a reliable prediction of their dynamic behaviour using numerical simulations. In optimized management, geological models need to be updated with each new available data (well tests, production data, seismic data, ...). The value of each individual data does not lie in its isolated use, but rather in the value it adds when integrated with other data.<br><br>We present an integrated methodology for reservoir characterization, based on a non-linear optimization loop, which uses both production (rather local information) and 4D seismic (spatial information) informations for an improved geological modelling. The main difficulty is to manage the depth/time conversion for the integration of 4D attributes and to keep it consistent with fluid flow simulation results. To do this, we propose a new methodology to match seismic attributes in time by updating the depth/time conversion in the inversion workflow.<br><br>The proposed methodology is based on a simulation workflow integrating geological modelling, upscaling, multi-phase fluid flow simulation coupled with a rock physics modelling, depth/time conversion and frequency filtering. The reliability of the geological model is improved through the minimisation of a weighted, least-squares objective function, which measures the mismatch between the simulated results and the data (both production and 4D seismic).<br><br>The huge number of data brought by the 4D seismic increases the difficulty in solving the numerical problem during optimization process. Thus, we propose an innovative approach to compute gradients of the objective function with respect to optimization parameters. <br><br>Our methodology was successfully applied for a multi-scale reservoir characterization process. The 3D model is constrained by compressional/shear impedances and the two-way travel times for compressional waves at the base seismic survey.
Nanoporous Surfaces as Harvesting Agents for Mass Spectrometric Analysis of Peptides in Human Plasma (2006)

Silica-based nanoporous surfaces have been developed in order to capture low molecular weight peptides from human plasma. Harvested peptides were subjected to mass spectrometric analysis by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a means of detecting and assessing the bound molecules. Peptide profiles consisting of about 70 peaks in the range 800-10,000 m/z were generated. The method could allow detection of small peptides at ng/mL concentration levels, either in standard solutions or in plasma. The same molecular cutoff effect was observed for mixtures of standard proteins and peptides incubated with silicon-based nanoporous surfaces.
Location dependent key management in sensor networks without using deployment knowledge (2007)

In this paper we propose an approach for key management in sensor networks which takes the location of sensor nodes into consideration while deciding the keys to be deployed on each node. As a result, this approach not only reduces the number of keys that have to be stored on each sensor node but also provides for the containment of node compromise. Thus compromise of a node in a location affects the communications only around that location. This approach which we call as location dependent key management does not require any knowledge about the deployment of sensor nodes. The proposed scheme starts off with loading a single key on each sensor node prior to deployment. The actual keys are then derived from this single key once the sensor nodes are deployed. The proposed scheme allows for additions of sensor nodes to the network at any point in time. We study the proposed scheme using both analysis and simulations and point out the advantages.
MOLECULAR MECHANISMS UNDERLYING ORCHID FLORAL MORPHOGENESIS (2010)

Orchids are known for both their floral diversity and ecological strategies. The versatility and specialization in orchid floral morphology, structure and physiological properties have fascinated botanists for centuries. In floral studies, MADS-box genes contributing to the now famous ABC model of floral organ identity control have dominated conceptual thinking. The sophisticated orchid floral organization, such as labellum and gynostemium, offers an opportunity to discover new variant genes and different levels of complexity to the ABC model. In our studies, we suggest that the duplication and differential expression of B and C class genes may contribute to the specificity of orchid floral morphology. We also proposed a molecular model to explain the development of sterile and fertile floral organs in orchids. Knowledge of MADS-box genes encoding ABC functions in orchids will give insights into the highly evolved floral morphogenetic networks and the diversification of orchids.
Multi-mode subtractive interference cancellation for asynchronous multi-path channels (2003)

Much work on multi-user detection has been done to increase the capacity and/or to enhance the performance of DS-CDMA systems. In this paper, we propose a subtractive interference cancellation (IC) called multi-mode interference cancellation (MIC). The proposed scheme overcomes the limitations of the successive (or serial) IC (SIC) and the multistage parallel IC (PIC) schemes, and can change the IC modes according to the processing speed of the hardware, the number of users, and the power spread of received signals. Especially, the structure is designed to work efficiently in the asynchronous multi-path channels. In addition, based on computer simulations over the asynchronous multi-path Rayleigh fading channels, we determine the system parameters and evaluate the performance of subtractive IC schemes.
A comparison of techniques to find mirrored hosts on the WWW (2000)

We compare several algorithms for identifying mirrored hosts on the World Wide Web. The algorithms operate on the basis of URL strings and linkage data: the type of information about Web pages easily available from Web proxies and crawlers. Identification of mirrored hosts can improve Web-based information retrieval in several ways: first, by identifying mirrored hosts, search engines can avoid storing and returning duplicate documents. Second, several new information retrieval techniques for the Web make inferences based on the explicit links among hypertext documents—mirroring perturbs their graph model and degrades performance. Third, mirroring information can be used to redirect users to alternate mirror sites to compensate for various failures, and can thus improve the performance of Web browsers and proxies. We evaluated four classes of “top-down” algorithms for detecting mirrored host pairs (that is, algorithms that are based on page attributes such as URL, IP address, and hyperlinks between pages, and not on the page content) on a collection of 140 million URLs (on 230,000 hosts) and their associated connectivity information. Our best approach is one which combines five algorithms and achieved a precision of 0.57 for a recall of 0.86 considering 100,000 ranked host pairs.
Catalytic effects of selected transition metal ions in the synthesis of lignosulfonic acid doped polyaniline (2005)

Abstract Lignosulfonic acid doped polyaniline (LIGNO‐PANI) is a water‐dispersible conducting polymer. The incorporation of dopants to achieve higher conductivities in addition to lignosulfonates during the polymerization process results in prohibitively long initiation times. A variety of transition metal ions including silver and ferrous ions were studied as potential catalysts for the reaction. Silver nitrate was found to have superior catalytic properties followed closely by ferrous sulfate heptahydrate. The effects of these ions on the synthesis of LIGNO‐PANI with methanesulfonic acid (HMSA) as an additional dopant (MSA‐LP) and on the synthesis of MSA‐PANI were studied via potential profile monitoring. The LIGNO‐PANI derivatives produced by the catalyzed reaction demonstrated no negative effects on the conductivity (10–15 S/cm) or dispersibility. In addition, residual metal analysis indicated that, although not much iron remained (<0.01%) in the product, a large amount of silver was present (1.8%) in the final product. X‐ray diffraction analysis was used to determine the identity of the silver containing moieties in the products. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 98: 29–33, 2005
Polarization optimization for tracking antennas [spacecraft applications] (2004)

Two methods are described to optimize the polarization of tracking antennas to the received signal's polarization. The objectives of the polarization optimization are to maintain the received signal level by reducing the polarization mismatch loss and to avoid the possibility of unstable antenna tracking when cross polarized signals are received and processed by the antenna control system.