gebhart/patrepeval huggingface dataset:
Wireless Chalcogenide Nanoionic-Based Radio-Frequency Switch (2013)

A new nonvolatile nanoionic switch is powered and controlled through wireless radio-frequency (RF) transmission. A thin layer of chalcogenide glass doped with a metal ion, such as silver, comprises the operational portion of the switch. For the switch to function, an oxidizable electrode is made positive (anode) with respect to an opposing electrode (cathode) when sufficient bias, typically on the order of a few tenths of a volt or more, is applied. This action causes the metal ions to flow toward the cathode through a coordinated hopping mechanism. At the cathode, a reduction reaction occurs to form a metal deposit. This metal deposit creates a conductive path that bridges the gap between electrodes to turn the switch on. Once this conductive path is formed, no further power is required to maintain it. To reverse this process, the metal deposit is made positive with respect to the original oxidizable electrode, causing the dissolution of the metal bridge thereby turning the switch off. Once the metal deposit has been completely dissolved, the process self-terminates. This switching process features the following attributes. It requires very little to change states (i.e., on and off). Furthermore, no power is required to maintain the states; hence, the state of the switch is nonvolatile. Because of these attributes the integration of a rectenna to provide the necessary power and control is unique to this embodiment. A rectenna, or rectifying antenna, generates DC power from an incident RF signal. The low voltages and power required for the nanoionic switch control are easily generated from this system and provide the switch with a novel capability to be operated and powered from an external wireless device. In one realization, an RF signal of a specific frequency can be used to set the switch into an off state, while another frequency can be used to set the switch to an on state. The wireless, miniaturized, and nomoving- part features of this switch make it suitable for applications such as integration into garments, RFID (radio-frequency identification) tags, and conformal structures (e.g., aircraft wings, sounding rockets contours, etc). In the case of RFID tags the innovation will provide countermeasures to attempts for identity theft and other uninvited attempts for retrieval of information. It could also be applicable to the automotive industry as well as the aerospace industry for collision avoidance and phased array radar systems, respectively
An alignment method for nucleic acid sequences against annotated genomes (2017)

Abstract Motivation Biological sequence alignment is fundamental to their further interpretation. Current alignment algorithms typically align either nucleic acid or amino acid sequences. Using only nucleic acid sequence similarity, divergent sequences cannot be aligned reliably because of the limited alphabet and genetic saturation. To align divergent coding nucleic acid sequences, one can align using the translated amino acid sequences. This requires the detection of the correct open reading frame, is prone to eventual frame shift errors, and typically requires the treatment of genes separately. It was our motivation to design a nucleic acid sequence alignment algorithm to align a nucleic acid sequence against a (reference) genome sequence, that works equally well for similar and divergent sequences, and produces an optimal alignment considering simultaneously the alignment of all annotated coding sequences. Results We define a genome alignment score for evaluating the quality of an alignment of a nucleic acid query sequence against a reference genome sequence, for which coding sequence features have been annotated (for example in a GenBank record). The genome alignment score combines the a ne gap score for the nucleic acid sequence with an a ne gap score for all amino acid alignments resulting from coding sequences in open reading frames contained within the query sequence. We present a Dynamic Programming algorithm to compute the optimal global or local alignment using this genomic alignment score and provide a formal proof of correctness. This algorithm allows the alignment of nucleic acid sequences from closely related and highly divergent sequences within the same software and using the same parameters, automatically correcting any eventual frame shift errors and produces at the same time the aligned translated amino acid sequences of all relevant coding sequence features. Availability The software is available as a web application at http://www.genomedetective.com/app/aga and as command-line application at https://github.com/emweb/aga
Alternating direction method of multipliers for strictly convex quadratic programs: Optimal parameter selection (2014)

We consider an approach for solving strictly convex quadratic programs (QPs) with general linear inequalities by the alternating direction method of multipliers (ADMM). In particular, we focus on the application of ADMM to the QPs of constrained Model Predictive Control (MPC). After introducing our ADMM iteration, we provide a proof of convergence closely related to the theory of maximal monotone operators. The proof relies on a general measure to monitor the rate of convergence and hence to characterize the optimal step size for the iterations. We show that the identified measure converges at a Q-linear rate while the iterates converge at a 2-step Q-linear rate. This result allows us to relax some of the existing assumptions in optimal step size selection, that currently limit the applicability to the QPs of MPC. The results are validated through a large public benchmark set of QPs of MPC for controlling a four tank process.
Jun activation domain-binding protein 1 expression in breast cancer inversely correlates with the cell cycle inhibitor p27(Kip1). (2003)

The Jun activation domain-binding protein 1 (JAB1), aside from being an activator protein 1 coactivator, is involved in degradation of the cyclin-dependent kinase inhibitor p27. We examined JAB1 and p27 protein expression in invasive breast carcinoma specimens and the association of this expression with clinical outcome. JAB1 was detected immunohistochemically in 43 of 53 (81%) tumors; 32 (60%) breast carcinomas showed high JAB1 expression (>50% of cells positive) and reduced or absent p27 levels (P = 0.02, Mann-Whitney U test). Tumors with high p27 expression were rarely positive for JAB1. All eight patients with JAB1-negative tumors had no evidence of relapse or disease progression at a median follow-up of 70 months. Immunoblotting showed strong JAB1 expression in breast carcinoma samples but not in paired normal breast epithelial samples. Targeted overexpression of JAB1 by regulated adenovirus in breast cancer cell lines also reduced p27 levels by accelerating degradation of p27. Thus, the JAB1:p27 ratio may be a novel indicator of aggressive, high-grade tumor behavior, and control of JAB1 could be a novel target for experimental therapies.
Recombinant Modified Vaccinia Virus Ankara Generating Ebola Virus-Like Particles (2017)

There are currently no approved therapeutics or vaccines to treat or protect against the severe hemorrhagic fever and death caused by Ebola virus (EBOV). Ebola virus-like particles (EBOV VLPs) consisting of the matrix protein VP40, the glycoprotein (GP), and the nucleoprotein (NP) are highly immunogenic and protective in nonhuman primates against Ebola virus disease (EVD). We have constructed a modified vaccinia virus Ankara-Bavarian Nordic (MVA-BN) recombinant coexpressing VP40 and GP of EBOV Mayinga and the NP of Taï Forest virus (TAFV) (MVA-BN-EBOV-VLP) to launch noninfectious EBOV VLPs as a second vaccine modality in the MVA-BN-EBOV-VLP-vaccinated organism. Human cells infected with either MVA-BN-EBOV-VLP or MVA-BN-EBOV-GP showed comparable GP expression levels and transport of complex N-glycosylated GP to the cell surface. Human cells infected with MVA-BN-EBOV-VLP produced large amounts of EBOV VLPs that were decorated with GP spikes but excluded the poxviral membrane protein B5, thus resembling authentic EBOV particles. The heterologous TAFV NP enhanced EBOV VP40-driven VLP formation with efficiency similar to that of the homologous EBOV NP in a transient-expression assay, and both NPs were incorporated into EBOV VLPs. EBOV GP-specific CD8 T cell responses were comparable between MVA-BN-EBOV-VLP- and MVA-BN-EBOV-GP-immunized mice. The levels of EBOV GP-specific neutralizing and binding antibodies, as well as GP-specific IgG1/IgG2a ratios induced by the two constructs, in mice were also similar, raising the question whether the quality rather than the quantity of the GP-specific antibody response might be altered by an EBOV VLP-generating MVA recombinant.<b>IMPORTANCE</b> The recent outbreak of Ebola virus (EBOV), claiming more than 11,000 lives, has underscored the need to advance the development of safe and effective filovirus vaccines. Virus-like particles (VLPs), as well as recombinant viral vectors, have proved to be promising vaccine candidates. Modified vaccinia virus Ankara-Bavarian Nordic (MVA-BN) is a safe and immunogenic vaccine vector with a large capacity to accommodate multiple foreign genes. In this study, we combined the advantages of VLPs and the MVA platform by generating a recombinant MVA-BN-EBOV-VLP that would produce noninfectious EBOV VLPs in the vaccinated individual. Our results show that human cells infected with MVA-BN-EBOV-VLP indeed formed and released EBOV VLPs, thus producing a highly authentic immunogen. MVA-BN-EBOV-VLP efficiently induced EBOV-specific humoral and cellular immune responses in vaccinated mice. These results are the basis for future advancements, e.g., by including antigens from various filoviral species to develop multivalent VLP-producing MVA-based filovirus vaccines.
A Systematic Approach to Sensor Selection for Aircraft Engine Health Estimation (2013)

A systematic approach for selecting an optimal suite of sensors for on-board aircraft gas turbine engine health estimation is presented. The methodology optimally chooses the engine sensor suite and the model tuning parameter vector to minimize the Kalman filter mean squared estimation error in the engine s health parameters or other unmeasured engine outputs. This technique specifically addresses the underdetermined estimation problem where there are more unknown system health parameters representing degradation than available sensor measurements. This paper presents the theoretical estimation error equations, and describes the optimization approach that is applied to select the sensors and model tuning parameters to minimize these errors. Two different model tuning parameter vector selection approaches are evaluated: the conventional approach of selecting a subset of health parameters to serve as the tuning parameters, and an alternative approach that selects tuning parameters as a linear combination of all health parameters. Results from the application of the technique to an aircraft engine simulation are presented, and compared to those from an alternative sensor selection strategy.
Inhibition of Marek's Disease Virus DNA Transfection by a Sequence Containing an Alphaherpesvirus Origin of Replication and Flanking Transcriptional Regulatory Elements (1991)

Robin W. Morgan, John L. Cantello, Johnny A. J. Claessens, Paul Sondermeyer, Inhibition of Marek's Disease Virus DNA Transfection by a Sequence Containing an Alphaherpesvirus Origin of Replication and Flanking Transcriptional Regulatory Elements, Avian Diseases, Vol. 35, No. 1 (Jan. - Mar., 1991), pp. 70-81
Desulfurizing Coal By Chlorinolysis and Hydrogenation (1983)

The central motor conduction was studied in 30 normal volunteers using a recently developed magneto-electrical stimulation technique (MES). The results were compared with those obtained by percutaneous electrical stimulation technique (PES) described previously. We made a magnetic stimulator similar to that of Barker et al. To stimulate the motor cortex, the magnetic coil was placed over the head. It was placed over the seventh cervical spinous process (C7) for cervical stimulation, and the first lumbar spinous process (L1) for lumbar stimulation. Cortical stimulation was performed when the subjects were at rest, and also at during weak voluntary contraction in some of them. Recordings were made from the deltoid (Del), biceps brachii (Bi), extensor carpi radialis (ECR), thenar, quadriceps femoris (Quad), tibialis anterior (TA) and flexor hallucis brevis (FHB) muscles with a pair of surface electrodes. The cortical and spinal latent periods (Lcor and Lsp, respectively) were measured. The central conduction time (CCT) was obtained by subtracting Lsp from Lcor for each muscle. In all subjects, responses were readily obtained by cortical, cervical and lumbar stimulations without discomfort in all the muscles examined. The cortical responses with amplitudes of more than 1mV could be recorded even in the lower limb muscles. There were no significant differences in Lsp and CCT between MES and PES, in all the upper limb muscles examined. The Lcors of the lower limb muscles obtained by MES were not different from those obtained by PES. However, the Lsps obtained by MES were significantly shorter than those by PES in the Quad and TA muscles.(ABSTRACT TRUNCATED AT 250 WORDS)
Elk-L3, a novel transmembrane ligand for the Eph family of receptor tyrosine kinases, expressed in embryonic floor plate, roof plate and hindbrain segments. (1996)

The Eph family of receptor tyrosine kinases has 13 distinct members and seven ligands for these receptors have been described to date. These receptors and their ligands have been implicated in regulating neuronal axon guidance and in patterning of the developing nervous system and may also serve a patterning and compartmentalization role outside of the nervous system as well. The ligands are all membrane-attached, and this attachment appears to be crucial for their normal function; five of the known ligands are linked to the membrane via a glycosyl phosphotidylinositol (GPI) linkage, while two of the ligands are transmembrane proteins. Despite the large number of Eph family receptors and ligands, they can be divided into just two major subclasses based on their binding specificities. All the GPI-anchored ligands bind and activate one subclass of the Eph receptors (that represented by Eck) while the two transmembrane ligands bind and activate the other major subclass of receptors (represented by Elk). Here we report the identification and characterization of the third, and most divergent, member of the transmembrane group of Eph ligands, which we term Elk-L3 (Elk-related receptor ligand number 3). Elk-L3 is notable for its remarkably restricted and prominent expression in the floor plate and roof plate of the developing neural tube and its rhombomere-specific expression in the developing hindbrain. The Elk-L3 gene has been localized to mouse chromosome 11 and human chromosome 17.
ORNL biometric eye model for iris recognition (2012)

Iris recognition has been proven to be an accurate and reliable biometric. However, the recognition of non-ideal iris images such as off angle images is still an unsolved problem. We propose a new biometric targeted eye model and a method to reconstruct the off-axis eye to its frontal view allowing for recognition using existing methods and algorithms. This allows for existing enterprise level algorithms and approaches to be largely unmodified by using our work as a pre-processor to improve performance. In addition, we describe the `Limbus effect' and its importance for an accurate segmentation of off-axis irides. Our method uses an anatomically accurate human eye model and ray-tracing techniques to compute a transformation function, which reconstructs the iris to its frontal, non-refracted state. Then, the same eye model is used to render a frontal view of the reconstructed iris. The proposed method is fully described and results from synthetic data are shown to establish an upper limit on performance improvement and establish the importance of the proposed approach over traditional linear elliptical unwrapping methods. Our results with synthetic data demonstrate the ability to perform an accurate iris recognition with an image taken as much as 70 degrees off-axis.
Novel Neighbor Selection Method to Improve Data Sparsity Problem in Collaborative Filtering (2013)

Memory-based collaborative filtering selects the top- k neighbors with high rank similarity in order to predict a rating for an item that the target user has not yet experienced. The most common traditional neighbor selection method for memory-based collaborative filtering is priority similarity. In this paper, we analyze various problems with the traditional neighbor selection method and propose a novel method to improve upon them. The proposed method minimizes the similarity evaluation errors with the existing neighbor selection method by considering the number of common items between two objects. The method is effective for the practical application of collaborative filtering. For validation, we analyze and compare experimental results between an existing method and the proposed method. We were able to confirm that the proposed method can improve the prediction accuracy of memory-based collaborative filtering by neighbor selection that prioritizes the number of common items.
Low-complexity transform and quantization in H.264/AVC (2003)

This paper presents an overview of the transform and quantization designs in H.264. Unlike the popular 8/spl times/8 discrete cosine transform used in previous standards, the 4/spl times/4 transforms in H.264 can be computed exactly in integer arithmetic, thus avoiding inverse transform mismatch problems. The new transforms can also be computed without multiplications, just additions and shifts, in 16-bit arithmetic, thus minimizing computational complexity, especially for low-end processors. By using short tables, the new quantization formulas use multiplications but avoid divisions.
Dominating sets of agents in visibility graphs: distributed algorithms for art gallery problems (2010)

The Art Gallery Problem asks to find a minimum subset of vertices in a polygon that are sufficient to observe the interior. This problem arises in a variety of multiagent systems, including robotics, sensor networks, wireless networking, and surveillance. Despite the fact that the centralized version of the problem has been extensively studied for the past thirty years, there is relatively little in the literature describing distributed solutions to the problem that have desirable guarantees in both runtime and optimality. We propose and analyze a new distributed algorithm for approximating a solution to this problem and a number of its variants that runs in a linear number of communication rounds with respect to the number of nodes (independent of the topology of the network), and, under assumptions on the embedding of the edge weights, will run in a logarithmic number of communication rounds producing solutions within a constant factor of optimal.
Synthesis of Fluorine Analogs of Hematoporphyrin (1993)

With the aim of obtaining a porphyrin derivative useful for diagnosis and therapy of cancer, fluorine analogs of hematoporphyrin, which had trifluorohydroxyethyl group(s) in the place of hydroxyethyl groups, were synthesized by the reaction of deuteroporphyrin dimethyl ester with trifluoroacetaldehyde in the presence of aluminum chloride. Preliminary results of biological tests of the products showed that the hexafluoro analog of hematoporphyrin accumulates to Human liver cancer cells more selectively than other fluorine analogs
Feasibility of RACT for 3D dose measurement and range verification in a water phantom (2015)

This study demonstrates that computed tomographic scanner based on ionizing radiation-induced acoustics can be used to verify dose distribution and proton range with centi-Gray sensitivity. Realizing this technology into the clinic has the potential to significantly impact beam commissioning, treatment verification during particle beam therapy and image guided techniques.
Ultra Wide Swath Imaging With Multi-Channel SAR Systems (2008)

Multi-channel radar systems allow for overcoming the inherent limitation of conventional synthetic aperture radar (SAR). An example is the combination of digital beamforming on receive in elevation with multi-aperture SAR signal reconstruction in azimuth which enables high-resolution wide-swath. As a next step, focus is turned to advanced concepts for the imaging of even wider swaths with high azimuth resolution. In this regard, the paper investigates the operation of multi-channel SAR systems in burst modes like ScanSAR or TOPS-SAR and analyses aspects of applying the multi-aperture reconstruction algorithm in combination with burst mode operation. The impact of the digital processing network on the SNR and the azimuth ambiguity-to-signal-ratio in multi-channel burst mode systems are considered and embedded in the design example of a ScanSAR system that enables the imaging of a 400 km wide swath with a geometric resolution of 5 m
Rational Design and Characterization of the Novel, Broad and Potent Bispecific HIV-1 Neutralizing Antibody iMabm36 (2014)

The interdependency of this dual mechanism of action enables iMabm36 to potently inhibit HIV-1 entry. These results demonstrate that mechanistic-based design of bibNAbs can generate potential preventive and therapeutic candidates for HIV/AIDS.
Tokamak plasma heating with intense pulsed ion beams. Memorandum report (1976)

The recent availability of intense, space-charge-neutralized, energetic ion beams has led one to explore the possibility of using them for heating tokamak plasmas. The following key problems for this application are investigated: (i) beam injection perpendicular to B, (ii) beam propagation across B in vacuum, and (iii) cross-field beam propagation and energy deposition in plasma. It appears possible that, for proper values of the beam energy, radius and current, an intense ion beam can penetrate to the interior of a tokamak plasma and deposit its energy there. (Author)
Fragile watermarking of three-dimensional objects (2002)

There have been many works on watermarking of 2D images and video. However, watermarking of three-dimensional (3D) objects has received little attentions. We introduce and investigate the watermarking of three-dimensional (3D) objects as compared to 2D images, study the watermarking of objects represented by polygonal models, and propose a new fragile watermarking technique that enables the verification of 3D polygonal models for detecting unauthorized alterations. Our proposed technique consists of a watermark encoding process which embeds a sequence of data bits by perturbing coordinates of the vertices in a 3D model, and a watermark decoding process which extracts bit information from 3D geometry, using secure verification keys. Fast 2D visualization of unauthorized modification to 3D objects is also proposed.
Radiation dose reduction in medical x‐ray CT via Fourier‐based iterative reconstruction (2013)

A Fourier-based iterative method has been applied to the reconstruction of fan-bean CT data with reduced x-ray fluence. This method incorporates advantageous features in both real and Fourier space iterative schemes: using a fast and algebraically exact method to calculate forward projection, enforcing the measured data in Fourier space, and applying physical constraints and flexible regularization in real space. Our results suggest that EST can be utilized for radiation dose reduction in x-ray CT via the readily implementable technique of lowering mAs settings. Numerical experiments further indicate that EST requires less computation time than several other iterative algorithms and can, in principle, be extended to helical cone-beam geometry in combination with the ASSR method.