gebhart/patrepeval huggingface dataset:
Saccharides cross-reactive with <i>Bacillus anthracis</i> spore glycoprotein as an anthrax vaccine component (2008)

Bacillus anthracis is a spore-forming bacterium that causes anthrax in humans and in other mammals. The glycoprotein BclA (Bacillus collagen-like protein of anthracis) is a major constituent of the exosporium, the outermost surface of B. anthracis spores. The glycosyl part of BclA is an oligosaccharide composed of 2-O-methyl-4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-d-glucose, referred to as anthrose, and three rhamnose residues. A structure similar to anthrose, 4-(3-hydroxy-3-methylbutanamido)-4,6-dideoxy-d-glucose is found in the side chain of the capsular polysaccharide (CPS) of Shewanella spp. MR-4. Under certain growth conditions the bacteria produce a variant CPS lacking one methyl group on the hydroxybutyrate, 4-(3-hydroxybutanamido)-4,6-dideoxy-d-glucose. Contrary to anthrose, neither of the Shewanella CPSs is 2-O methylated. Here, we report that both Shewanella CPS variants react with anti-B. anthracis spore sera. We also found that these antisera reacted with flagellae of Pseudomonas syringae, reported to be glycosylated with a similar terminal saccharide, 4-(3-hydroxybutanamido)-4,6-dideoxy-2-O-methyl-d-glucose. Sera produced by immunization with Shewanella or P. syringae cells bound to B. anthracis spores but not to Bacillus cereus spores in a fluorescent microscopy assay. These experiments show that methylation of the anthrose at the O-2 of the sugar ring and at the C-3 of 3-hydroxybutyrate are not essential for induction of cross-reactive antibodies. We report the preparation, characterization, and antibody responses to protein conjugates of the two variants of Shewanella CPS. Both conjugates induced antibodies that bound to both Shewanella CPS variants by ELISA and to B. anthracis spores, as detected by fluorescent microscopy. We propose the use of Shewanella CPS conjugates as a component of an anthrax vaccine.
Estimation of Nonhomogeneous and Multi-Section Twisted-Pair Transmission-Line Parameters (2015)

In emerging and future copper access networks, the trend goes towards exploiting higher transmission bandwidths on shorter twisted-pair cables. Methods to accurately determine relevant transmission-line parameters are a prerequisite to exploit the potential of these short-to-medium range access lines. In this paper, we propose a model-based space-frequency optimization approach initially developed for microwave applications. By utilizing the concept of capacitive length, two major advances are achieved. First, we overcome the requirement of a priori information of physical line length. Second, the number of parameters is reduced compared to prior art. We introduce two estimators to illustrate the concept. A low-complexity estimator with only two parameters per spatial unit primarily targets higher frequencies. A wideband estimator with three parameters per spatial unit extends to the lower frequencies used by operational digital subscriber line services. Performance and limitations of the approach are illustrated by both computer simulations and measurements.
Wireless Multi-Sensor Integration for ACL Rehabilitation Using Biofeedback Mechanism (2012)

The objective of this study is to propose an integrated motion analysis system for monitoring and assisting the rehabilitation process for athletes based on biofeedback mechanism, particularly for human subjects already undergone Anterior Cruciate Ligament (ACL) injury operations and thus about to start the rehabilitation process. For this purpose, different types of parameters (kinematics and neuromuscular signals) from multi-sensors integration are combined to analyze the motion of affected athletes. Signals acquired from sensors are pre-processed in order to prepare the pattern set for intelligent algorithms to be integrated for possible implementation of effective assistive rehabilitation processing tools for athletes and sports orthopedic surgeons. Based on the characteristics of different signals invoked during the rehabilitation process, two different intelligent approaches (Elman RNN and Fuzzy Logic) have been tested. The newly introduced integrated multi-sensors approach will assist in identifying the clinical stage of the recovery process of athletes after ACL repair and will facilitate clinical decision-making during the rehabilitation process. The use of wearable wireless miniature sensors will provide an un-obstructive assessment of the kinematics and neuromuscular changes occurring after ACL reconstruction in an athlete.
Fluorene Copolymer and Carbon Nanotube Interaction Modulates Network Transistor Performance (2021)

Conjugated polymer extraction (CPE)-enriched high-purity semiconducting (sc) single-walled carbon nanotubes (SWCNTs) have demonstrated significant application potential as emerging electronic materials. In this work, the interaction of three fluorene-based copolymers with sc-SWCNTs in a toluene solution was systematically compared, covering a wide range of concentrations while considering the phase behavior of the polymer itself. 2D photoluminescence excitation studies show that the polymer containing semiconjugated pyridine units had a higher binding affinity to the SWCNTs due to its twistable main chain conformation. The uniform and high-density SWCNT networks deposited on a silicon wafer have been characterized by SEM and spatial Raman spectroscopy, which reveals ultrahigh sc purity with a metallic tube content less than the parts per million level. The performance of thin-film transistors could be correlated with the structure of wrapping polymers. The threshold voltage shifted with the nitrogen content in their repeat units due to electron donation from the nitrogen atoms. The off-current was reduced with the flexible copolymer, which provided better wrapping and thus limited bundling during network formation.
In Vivo MR-Tracking Based on Magnetic Signature Selective Excitation (2008)

A novel magnetic resonance (MR)-tracking method specifically developed to locate the ferromagnetic core of an untethered microdevice, microrobot, or nanorobot for navigation or closed-loop control purpose is described. The tracking method relies on the application of radio-frequency (RF) excitation signals tuned to the equipotential magnetic curves generated by the magnetic signature of the object being tracked. Positive contrast projections are obtained with reference to the position of the magnetic source. A correlation function performed on only one k-space line for each of the three axes and corresponding to three projections, is necessary to obtain a 3-D location of the device. In this study, the effects of the sphere size and the RF frequency offset were investigated in order to find the best contrast noise ratio (CNR) for tracking. Resolution and precision were also investigated by proper measurement of the position of a ferromagnetic sphere by magnetic resonance imaging (MRI) acquisition and by comparing them with the real position. This method is also tested for a moving marker where the positions found by MRI projections were compared with the ones taken with a camera. In vitro and in vivo experiments show the operation of the technique in tortuous phantom and in animal models. Although the method was developed in the prospect of new interventional MR-guided endovascular operations based on miniature untethered devices, it could also be used as a passive tracking method using tools such as catheters or guide wires.
Engineering the Campylobacter jejuni N-glycan to create an effective chicken vaccine (2016)

Campylobacter jejuni is a predominant cause of human gastroenteritis worldwide. Source-attribution studies indicate that chickens are the main reservoir for infection, thus elimination of C. jejuni from poultry would significantly reduce the burden of human disease. We constructed glycoconjugate vaccines combining the conserved C. jejuni N-glycan with a protein carrier, GlycoTag, or fused to the Escherichia coli lipopolysaccharide-core. Vaccination of chickens with the protein-based or E. coli-displayed glycoconjugate showed up to 10-log reduction in C. jejuni colonization and induced N-glycan-specific IgY responses. Moreover, the live E. coli vaccine was cleared prior to C. jejuni challenge and no selection for resistant campylobacter variants was observed. Analyses of the chicken gut communities revealed that the live vaccine did not alter the composition or complexity of the microbiome, thus representing an effective and low-cost strategy to reduce C. jejuni in chickens and its subsequent entry into the food chain.
Abstract PS18-24: Impact of protein corona formation on Fn14-targeted DART nanoparticle selectivity, uptake, and cytotoxicity on TNBC cells (2021)

Abstract Despite dramatic improvements in the treatment of primary breast cancers, there currently are no effective targeted therapeutics for women diagnosed with metastatic triple negative breast cancer (mTNBC), resulting in an overall survival of just ~13 months in these patients. Drug-loaded nanoparticles (NPs) offer the potential to improve the therapeutic efficacy and pharmacokinetic profile of drugs through use of passive and active targeting to metastatic tumors. However, effective and active targeting of nanodrug formulations to tumor cells is complicated by the adsorption of proteins to NP surfaces upon exposure to the systemic circulation. Termed ‘protein coronas’, this protein coat can drastically reduce the blood circulation time and targeting capability of NPs in vivo. We have developed paclitaxel (PTX)-loaded NPs that are engineered for decreased non-specific adhesivity and receptor-targeting (‘DART’) characteristics, which balance minimal recognition by circulating immune cells and low non-specific binding to tumor extracellular matrix proteins with maximal targeting to tumor tissues. These DARTs selectively bind the fibroblast growth factor-inducible 14 (Fn14) cell surface receptor, which is overexpressed in over a dozen solid cancers and their metastases, including mTNBC tumors. We recently demonstrated the enhanced therapeutic efficacy of Fn14-targeted DARTs in comparison to a non-targeted nanoformulation and Abraxane, an FDA-approved nanoformulation for mTNBC, in xenograft models of primary and intracranial TNBC. In addition, we found that these DARTs retain targeting capability and traffic to Fn14+ tumors in the presence of an endogenous protein corona in vitro and in vivo. This encouraged further investigation into the specific mechanisms of DART NP uptake in tumor cells in both the presence and absence of protein coronas using surface plasmon resonance, flow cytometry, total internal reflection fluorescence and confocal microscopy, and cytotoxicity assays. Understanding the role of protein coronas on this drug delivery platform is crucial for its clinical development and these results provide valuable new information pertaining to the optimization of NP surface properties for minimizing the impact of protein coronas and improving mTNBC tumor targeting in vivo. Citation Format: Christine P Carney, Anshika Kapur, Nikhil Pandey, Jimena G Dancy, Aniket S Wadajkar, Graeme F Woodworth, Jeffrey A Winkles, Anthony J Kim. Impact of protein corona formation on Fn14-targeted DART nanoparticle selectivity, uptake, and cytotoxicity on TNBC cells [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-24.
Multiple isoforms of starch branching enzyme-I in wheat: lack of the major SBE-I isoform does not alter starch phenotype (2004)

The role of starch branching enzyme-I (SBE-I) in determining starch structure in the endosperm has been investigated. Null mutations of SBE-I at the A, B and D genomes of wheat were identified in Australian wheat varieties by immunoblotting. By combining individual null mutations at the B and D genomes through hybridisation, a double-null mutant wheat, which lacks the B and D isoforms of SBE-I, was developed. Wheat mutants lacking all the three isoforms of SBE-I were generated from a doubled haploid progeny of a cross between the BD double-null mutant line and a Chinese Spring (CS) deletion line lacking the A genome isoform. Comparison of starch from this mutant wheat to that from wild type revealed no substantial alteration in any of the structural or functional properties analysed. Further analysis of this triple-null mutant line revealed the presence of another residual peak of SBE-I activity, referred to as SBE-I<sup>r</sup>, in wheat endosperm representing < 3% of the activity of SBE-I in wild type endosperm.
A magneto-optic recording system using TbFeCo (1985)

A large capacity magneto-optic recording system has been developed for mass data storage. The recording material is an amorphous magnetic film of TbFeCo, which is magnetizes vertically. The TbFeCo film is deposited onto a plastic substrate by sputtering. It has a Kerr rotation angle of 0.35°, a Curie temperature of 190°C, and an amorphous-crystal transition temperature of 240°C. The 30cm-diameter disk has a double-sided structure and each side consists of a magnetic layer and protective layers. Using mastering and replication techniques, grooves with address headings are produced in the polycarbonate plastic substrate at a track-pitch of 1.6μm. A lightweight, high performance optical pickup is operated at an average seek time of less than 100msec. The raw bit error rate (BER) of the disk is currently of the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> and the system is designed to provide the corrected BER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> using a Cross Interleave Reed-Solomon Code. The system consists of a 1-Gbyte magneto-optical memory disk drive to be used as a code memory for computers, a controller unit capable of being expanded to 4-Gbytes, and an interface module called the Small Computer System Interface (SCSI).
Characterization of a chromosomal gene and the antigen it expresses from the Lyme disease agent, Borrelia burgdorferi (1993)

The sequence and characterization of a chromosomal gene from the Lyme disease agent Borrelia burgdorferi and the antigen it encodes are described. The gene was cloned and expressed in transformed Escherichia coli cells. The gene is composed of 597 bases and expresses a predicted protein of 199 amino acids. Antibodies specific for the recombinant antigen reacted with a single B. burgdorferi protein with a molecular mass of approximately 22 kDa. The protein was not susceptible to proteinase digestion but was extracted by n-butanol phase partitioning, suggesting a periplasmic location of the antigen. Sera from humans and canines seropositive for B. burgdorferi reacted with the recombinant antigen. The antigen characterized in this report appears to be immunologically significant in naturally infected hosts.
Abstract 2632: Calmodulin Kinase Inhibition Prevents the Arrhythmogenesis in Ryr2r4496c+/− Knock in Mice (2009)

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is caused by mutations in the cardiac ryanodine receptor gene (RyR2) leading to life-threatening arrhythmias elicited by sympathetic act...
Direct Generation of Regular-Grid Ground Surface Map from In-Vehicle Stereo Image Sequences (2013)

We propose a direct method for incrementally estimating a regular-grid ground surface map from stereo image sequences captured by nearly front-looking stereo cameras, taking illumination changes on all images into consideration. At each frame, we simultaneously estimate a camera motion and vertex heights of the regular mesh, composed of piecewise triangular patches, drawn on a level plane in the ground coordinate system, by minimizing a cost representing the differences of the photo metrically transformed pixel values in homography-related projective triangular patches over three image pairs in a two-frame stereo image sequence. The data term is formulated by the Inverse Compositional trick for high computational efficiency. The main difficulty of the problem formulation lies in the instability of the height estimation for the vertices distant from the cameras. We first develop a stereo ground surface reconstruction method where the stability is effectively improved by the combinational use of three complementary techniques, the use of a smoothness term, update constraint term, and a hierarchical meshing approach. Then we extend the stereo method for incremental ground surface map generation. The validity of the proposed method is demonstrated through experiments using real images.
Highly porous gallium oxide with a high CO2 affinity for the photocatalytic conversion of carbon dioxide into methane (2012)

Highly porous gallium oxide was synthesized by reconstructing its surface and body with mesopores and macropores. For the first time, the efficient photocatalytic conversion of CO2 into a high energy carrier, CH4, using the porous gallium oxide was realized without any co-particle or sacrificial reagent. The enhanced photocatalytic activity is mainly attributed to the 300% higher CO2 adsorption capacity, as well as the 200% increased surface area, compared to the bulk nanoparticles. Furthermore, we propose the new reaction pathway based on the result that the carbon dioxide was converted directly into methane without going through carbon monoxide intermediates.
MIMO Downlink Weighted Sum Rate Maximization with Power Constraints per Antenna Groups (2007)

We consider a single-cell multiple-input multiple-output (MIMO) downlink channel where linear transmission and reception strategy is employed. The base station (BS) transmitter is equipped with a scheduler using a simple opportunistic beamforming strategy, which associates an intended user for each of the transmitted data streams. For the case when the channel of the scheduled users is available at the BS, we propose a general method for joint design of linear transmit and receive beamformers, according to weighted sum rate maximization criteria. The proposed method can handle multiple antennas at the BS and at the mobile users with an arbitrary number of data streams per scheduled user. It can also handle a fairly general set of practical power constraints for the transmit beamformers, i.e., we can impose sum power constraints for different subsets of the transmit antennas.
Performance of a Generic Approach in Automated Essay Scoring (2010)

A generic approach in automated essay scoring produces scores that have the same meaning across all prompts, existing or new, of a writing assessment. This is accomplished by using a single set of linguistic indicators (or features), a consistent way of combining and weighting these features into essay scores, and a focus on features that are not based on prompt-specific information or vocabulary. This approach has both logistical and validity-related advantages. This paper evaluates the performance of generic scores in the context of the e-rater® automated essay scoring system. Generic scores were compared with prompt-specific scores and scores that included prompt-specific vocabulary features. These comparisons were performed with large samples of essays written to three writing assessments: The GRE General Test argument and issue tasks and the TOEFL independent task. Criteria for evaluation included level of agreement with human scores, discrepancy from human scores across prompts, and correlations with other available scores. Results showed small differences between generic and prompt-specific scores and adequate performance of both types of scores compared to human performance.
Pump-Enhanced Continuous-Wave Magnetometry Using Nitrogen-Vacancy Ensembles (2017)

In this study, nitrogen-vacancy color centers in diamond are employed in a versatile and promising magnetometer, which is useful for sensing fields that are difficult to detect with alternatives. The authors place an untreated, off-the-shelf diamond in a resonant optical cavity with a split-ring microwave resonator to achieve a remarkable magnetic-field sensitivity of approximately 200 pT/$\sqrt{\text{Hz}}$, with room for improvement. These results emphasize enhancing performance through uniformity of spin polarization, rather than focusing solely on optimizing material properties of the diamond sample.
Recovery of waste rare earth fluorescent powders by two steps acid leaching (2013)

Abstract The effects of the acid leaching and alkali fusion on the leaching efficiency of Y, Eu, Ce, and Tb from the waste rare earth fluorescent powders were investigated in this paper. The results show that hydrochloric acid is better than sulfuric acid in the first acid leaching, and NaOH is better than Na 2 CO 3 in the alkali fusion. In the first acid leaching, the W loss is 20.94 % when the waste rare earth fluorescent powders are acid leached in H + concentration 3 mol·L −1 and S/L ratio 1:3 for 4 h due to red powders dissolved. The better results of the alkali fusion can be got at 800 °C for 2 h when the NaOH is used. The blue powders and the green powders can be dissolved into NaAlO 2 and oxides such as rare earth oxide (REO). The REO can be dissolved in H + concentration 5 mol·L −1 , S/L 1:10 for 3 h in the second acid leaching. The leaching rates of the Y, Eu, Ce, and Tb are 99.06 %, 97.38 %, 98.22 %, and 98.15 %, respectively. The leaching rate of the total rare earth is 98.60 %.
Towards a Model Human Cochlea: Sensory substitution for crossmodal audio-tactile displays (2024)

<p>We present a Model Human Cochlea (MHC): a sensory substitution technique for creating a crossmodal audio-touch display. This research is aimed at designing a chair-based interface to support deaf and hard of hearing users in experiencing musical content associated with film, and seeks to develop this multisensory crossmodal display as a framework for supporting research in enhancing sensory entertainment experiences for universal design. The MHC uses audio speakers as vibrotactile devices placed along the body to facilitate the expression of emotional elements that are associated with music. We present the results of our formative study, which compared the MHC to conventional audio speaker displays for communicating basic emotional information through touch. Results suggest that the separation of audio signals onto multiple vibrotactile channels is more effective at expressing emotional content than is possible using a complete audio signal as vibrotactile stimuli.</p>
Page hunt (2009)

There has been a lot of work on evaluating and improving the relevance of web search engines. In this paper, we suggest using human computation games to elicit data from players that can be used to improve search. We describe Page Hunt, a single-player game. The data elicited using Page Hunt has several applications including providing metadata for pages, providing query alterations for use in query refinement, and identifying ranking issues. We describe an experiment with over 340 game players, and highlight some interesting aspects of the data obtained.