gebhart/patrepeval huggingface dataset:
Identification of the ligand‐binding domain of the surface‐located fibrinogen receptor (clumping factor) of <i>Staphylococcus aureus</i> (1995)

The ability of Staphylococcus aureus to bind to fibrinogen and fibrin is believed to be an important factor in the initiation of foreign-body and wound infections. Recently, we reported the cloning and sequencing of the gene clfA encoding the fibrinogen receptor (clumping factor, ClfA) of S. aureus strain Newman and showed that the gene product was responsible for the clumping of bacteria in soluble fibrinogen and for the adherence of bacteria to solid-phase fibrinogen. This was confirmed here by showing that antibodies raised against purified Region A inhibited both of these properties. Also, immunofluorescent microscopic analysis of wild-type Newman and a clfA::Tn917 mutant of Newman with anti-ClfA Region A sera confirmed that Region A is exposed on the bacterial cell surface. Furthermore, polystyrene beads coated with the Region A protein formed clumps in soluble fibrinogen showing that the ClfA protein alone is sufficient for the clumping phenotype. Western immunoblotting with anti-ClfA Region A antibodies identified the native ClfA receptor as a 185 kDa protein that was released from the cell wall of S. aureus by lysostaphin treatment. A single extensive ligand-binding site was located within Region A of the ClfA protein. Truncated ClfA proteins were expressed in Escherichia coli. Lysates of E. coli and proteins that had been purified by affinity chromatography were tested for (i) their ability to bind fibrinogen in Western ligand blotting experiments, (ii) for their ability to inhibit clumping of bacteria in fibrinogen solution and adherence of bacteria to solid-phase fibrinogen, and (iii) for their ability to neutralize the blocking activity of anti-ClfA Region A antibody. These tests allowed the ligand-binding domain to be localized to a 218-residue segment (residues 332-550) within Region A.
Characteristics of the Plasma Impedance Probe with Applied DC Bias (2005)

Summary form only given. The impedance of a small spherical probe immersed in a uniform plasma is measured by recording the reflection coefficient of an applied signal using a network analyzer. This impedance has a resonance at the plasma frequency where the imaginary part goes to zero, a feature that has made this measurement a good way of determining electron density. When the sphere is biased negatively with respect to the plasma potential a second resonance occurs at omega<omega <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> due to the depleted electron density in the sheath around the probe. A greatly increased power deposition occurs at this lower resonance, whose frequency can be controlled by changing the sheath width using a DC bias. As the bias is increased the value of this frequency becomes smaller until the resonance disappears completely at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">probe</sub> =V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">plasma</sub> . As the bias is further increased past the plasma potential an electron sheath forms with its own resonance which is at a lower frequency than the resonance associated with the ion sheath. The impedance of the electron sheath can be approximated using the Llewellyn-Peterson formulas for a space charge limited diode. As with the ion sheath resonance, the largest energy deposition occurs at the lower of the two frequencies.
Development and Evaluation of Six Gamut-Mapping Algorithms for Pictorial Images (1999)

Six techniques for mapping the colors of an image into the gamut of printable colors were compared. Six pictorial scenes were used in two psychophysical experiments, one to test accurate reproduction and one to test preferred reproduction. A new contrast-enhancing algorithm was found to give more favorable reproductions than several gamut-mapping techniques described in the literature. This algorithm performs luminance compression by applying an inverted power function to images in a linear RGB color space: 1 - (1 - RGB)γ. Remaining out-of-gamut pixels are clipped to the gamut surface in the direction of a central point on the neutral axis.Other algorithms that performed well were those that clip out-of-gamut colors to the surface of the gamut, and do not affect colors within the gamut. These algorithms can sometimes result in undesirable artifacts for certain images, including contouring and loss of shadow detail. However, observers did not object to the loss of shadow detail if the colorfulness of the image was maintained or increased.Also, the results of a matching experiment (original present) and a preference experiment gave quite different results. Clipping algorithms did well in the matching experiments, while contrast boosting algorithms did best in the preference matching. The preferred techniques did well in both experiments.
Spiral planar-waveguide Bragg gratings (2009)

A photonic integrated circuit is designed containing a long grating with spiral geometry. Waveguide width and index modulation are studied as methods to form the grating structure. Both methods require an initial mask step for waveguide formation. In the case of width modulation the grating is formed in the same step as the waveguide, whereas a second mask step is required for index modulation. Thus width modulation removes the alignment tolerances associated with a two step process. The spiral geometry enables a long grating (~1 m) to be realized in a small area (1 cm<sup>2</sup>). The ability to form the grating in such a small area enables the use of current lithography mask / projection equipment. Thus, the requirements for mechanical/optical precision in a customized long fiber Bragg grating fabrication system is transferred to the precision of commercial lithography mask fabrication and projection equipment.
Epitope-specific suppression of antibody response in experimental autoimmune myasthenia gravis by a monomethoxypolyethylene glycol conjugate of a myasthenogenic synthetic peptide. (1992)

A synthetic peptide corresponding to a myasthenogenic region of Torpedo californica acetylcholine (AcCho) receptor (AcChoR) alpha subunit, AcChoR alpha-(125-148), was conjugated to monomethoxypolyethylene glycol (mPEG). Injection of mice with the mPEG-AcChoR alpha-(125-148) conjugate and subsequent immunization with whole Torpedo AcChoR suppressed the development of experimental autoimmune myasthenia gravis (EAMG) by electrophysiological criteria. In anti-AcChoR sera from these animals, the antibody response against unconjugated AcChoR alpha-(125-148) was decreased, while the antibody responses against whole AcChoR and other epitopes were not altered. There were no detectable changes in T-cell proliferation responses to AcChoR alpha-(125-148) or to whole AcChoR in these animals. Prior injections with a "nonsense" peptide-mPEG conjugate had no effect on responses to the subsequent immunization with whole Torpedo AcChoR. The results indicate that the mPEG-AcChoR alpha-(125-148) conjugate has epitope-specific tolerogenicity for antibody responses in EAMG and that the AcChoR alpha-subunit region comprising residues 125-148 plays an important pathophysiological role in EAMG. The epitope-directed tolerogenic conjugates may be useful for future immunotherapies of human myasthenia gravis. The strategy of specific suppression of the antibody response to a predetermined epitope by using a synthetic mPEG-peptide conjugate may prove useful in manipulation and suppression of unwanted immune responses such as autoimmunity and allergy.
A Chemoenzymatic Route to a Class of Sucrose Esters (2017)

Sucrose esters are the most developed carbohydrate esters and are used in the food, cosmetic, and pharmaceutical industries. Herein, we introduce a novel chemoenzymatic pathway for the synthesis of β‐ d ‐fructofuranosyl‐(2,1)‐α‐ d ‐uronic acid derivatives, a new class of sucrose esters.
Natural T-helper immunity against human papillomavirus type 16 (hpv16) e7-derived peptide epitopes in patients with hpv16-positive cervical lesions: Identification of 3 human leukocyte antigen class ii-restricted epitopes (2001)

Tumor-specific T-helper (Th) immunity was found to play a pivotal role in the natural and vaccine-induced immune defense against tumors. Since the majority of cervical cancers express human papillomavirus type 16 (HPV16) E7 oncoprotein, it is important to investigate the Th response against this target antigen in detail. By means of PBMC cultures from HLA-typed healthy donors, we identified the central part of HPV16 E7 (E7(41-72)) as the major immunogenic region within this antigen. Furthermore, we mapped 3 distinct Th epitopes within this region (DR15/E7(50-62), DR3/E7(43-77), DQ2/E7(35-50)). In a parallel approach, employing IFN-gamma ELISPOT analysis, we detected Th immunity against HPV16 E7 in subjects with HPV16+ lesions. Several of these responses matched with the 3 Th epitopes defined in our study. A number of other HPV16+ subjects did not display any E7-specific type 1 cytokine-producing T-cell immunity, indicating failure of the immune response. Our combined data argue for more extensive as well as longitudinal analysis of HPV16-specific T-cell immunity using the ELISPOT assay described, as well as for HPV-specific vaccination of individuals with HPV+ lesions.
Auditory prosthesis, noise suppression apparatus and feedback suppression apparatus having focused adaptive filtering (1995)

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Estimating mutation load at 5% LOD from FFPE samples using a targeted next-generation sequencing assay. (2018)

28 Background: High tumor mutation load is a biomarker which positively correlates with response to immune checkpoint inhibitors. Current methods to estimate tumor mutation load often require large amounts of DNA. Herein, we demonstrate the ability of a targeted panel to estimate mutation load from FFPE samples using low input amount of DNA. Methods: We developed a single-sample analysis workflow to estimate mutation load (somatic mutation count per Megabase (Mb)) from FFPE and fresh frozen tumor research samples. The assay utilizes a PCR-based target enrichment panel that covers ~1.7 Mb. Our workflow requires only 10 ng of input DNA, and enables a 2.5-day turn-around time from sample to the final report. The workflow enables < 60 minutes of hands-on time for automated library preparation and templating on a batch of 8 samples. Sequencing is performed using a high throughput semiconductor sequencing platform to achieve sufficient depth (~500x coverage) and accuracy. Our analysis pipeline calls variants with optimized parameters on the tumor sample only, with no matched normal sample required, and applies filters to remove germ-line. Results: An in-silico analysis using 21,000 exomes from COSMIC demonstrated the panel can achieve high sensitivity (>=93%) and specificity (>99%) necessary to stratify high and low mutation burden samples. Matched tumor-normal analyses on 14 lung and colorectal samples showed that our single tumor analysis workflow detects mutation load with strong correlation (r=0.8699) with tumor-normal analysis. Through dilution experiments on engineered control we learned that the workflow provides accurate estimates of mutation load, predicting ± 7% of expected mutation load on >=20% tumor content. To assess reproducibility, we compared mutation load in library replicates for a cohort of 8 samples (FFPE and fresh frozen tumors, engineered control, and NIST cell-lines) and observed high correlation (r=0.9906) among replicates. Conclusions: We developed a simple workflow on the Ion Torrent sequencing platform to estimate mutation load from FFPE and fresh frozen tumor research samples. This solution will advance research in immuno-oncology.
Direct Imaging of Cerebral Thromboemboli Using Computed Tomography and Fibrin-targeted Gold Nanoparticles (2015)

Computed tomography (CT) is the current standard for time-critical decision-making in stroke patients, informing decisions on thrombolytic therapy with tissue plasminogen activator (tPA), which has a narrow therapeutic index. We aimed to develop a CT-based method to directly visualize cerebrovascular thrombi and guide thrombolytic therapy. Glycol-chitosan-coated gold nanoparticles (GC-AuNPs) were synthesized and conjugated to fibrin-targeting peptides, forming fib-GC-AuNP. This targeted imaging agent and non-targeted control agent were characterized in vitro and in vivo in C57Bl/6 mice (n = 107) with FeCl3-induced carotid thrombosis and/or embolic ischemic stroke. Fibrin-binding capacity was superior with fib-GC-AuNPs compared to GC-AuNPs, with thrombi visualized as high density on microCT (mCT). mCT imaging using fib-GC-AuNP allowed the prompt detection and quantification of cerebral thrombi, and monitoring of tPA-mediated thrombolytic effect, which reflected histological stroke outcome. Furthermore, recurrent thrombosis could be diagnosed by mCT without further nanoparticle administration for up to 3 weeks. fib-GC-AuNP-based direct cerebral thrombus imaging greatly enhance the value and information obtainable by regular CT, has multiple uses in basic / translational vascular research, and will likely allow personalized thrombolytic therapy in clinic by a) optimizing tPA-dosing to match thrombus burden, b) enabling the rational triage of patients to more radical therapies such as endovascular clot-retrieval, and c) potentially serving as a theranostic platform for targeted delivery of concurrent thrombolysis.
ASE reflector-based gain-clamped erbium-doped fiber amplifier using an optical interleaver (2005)

We use a 50-GHz optical interleaver for the reflection of amplified spontaneous emission (ASE) to realize ASE reflector-based gain-clamped erbium-doped fiber amplifiers. The amplifier schemes can secure International Telecommunications Union Telecommunication Standardization Sector grids with 100-GHz channel spacing in the whole conventional band (C-band) for signal amplification gain-clamping characteristics including dynamic ranges lower than -7 dBm are successfully demonstrated.
A quasiexact reconstruction algorithm for helical CT using a 3‐Pi acquisition (2003)

Recently, an exact reconstruction method for helical CT was published by A. Katsevich. The algorithm is of the filtered backprojection type and is, therefore, computationally efficient. Moreover, during backprojection, only data are used which correspond to an illumination interval of 180 degrees as seen from the object-point. We propose a new reconstruction method, which is applicable to data obtained with a 3-Pi acquisition [IEEE Trans. Med. Imaging 19, 848-863 (2000)]. The method uses the same filter types as the Katsevich algorithm, but the directions and the number of the filter lines are chosen differently. For the derivation of the new algorithm, we analyze the relationship of the Katsevich method and radon inversion. A certain radon plane can intersect with the backprojection interval related to a 3-Pi acquisition either once, three, or five times. In analogy to the definition of quasiexactness introduced by Kudo et al. for a 1-Pi acquisition, we use the term quasiexactness for algorithms on a 3-Pi acquisition, if radon planes with one or three intersections within the backprojection interval are treated correctly. Using the results on the relationship with radon inversion, we can prove that our algorithm is quasiexact in this sense. We use simulation results in order to demonstrate that the algorithm yields excellent image quality.
Critical illumination condenser for extreme ultraviolet projection lithography (1995)

A condenser system couples a radiation source to an imaging system. The authors have designed a critical illumination condenser system which meets the technical challenges of extreme ultraviolet projection lithography based on a ring field imaging system and a laser produced plasma source. The optical system, a three spherical mirror optical design, is capable of illuminating the extent of the mask plane by scanning either the primary mirror or the laser plasma source. This type of condenser optical design is sufficiently versatile to be employed with two distinct systems, one from Lawrence Livermore National Laboratory and one from AT and T/Sandia.
Spherical Logarithmic Quantization and its Application for DPCM Dedicated to Prof. Dr. Karlheinz Tron the occasion of his retirement and 65th birthday (2004)

A new method for efcient digitizing analog signals while preserving the original waveform as close as possible with respect to the relative quantization error is presented. Logarithmic quantization is applied to short vectors of samples represented in sphere coordinates. The resulting advantages, i.e. a constant Signal-to-Noise Ratio over a very high dynamic range at a small loss with respect to rate-distortion theory are discussed. In order to increase the Signal-to-Noise Ratio (SNR) by exploitation of correlations within the source signal, a method of combining differential pulse- codemodulation (DPCM) with spherical logarithmic quantization is presented. The resulting technique achieves an efcient digital representation of waveforms with a high longterm as well as segmental SNR at an extrem low delay of the signal.
Effect of Treatment of Cystic Fibrosis Pulmonary Exacerbations on Systemic Inflammation (2015)

Circulating inflammatory proteins demonstrate and predict a response to treatment of CF pulmonary exacerbations. A systemic biomarker panel could speed up drug discovery, leading to a quicker, more efficient drug development process for the CF community.
The preproghrelin gene is required for the normal integration of thermoregulation and sleep in mice (2009)

Peptidergic mechanisms controlling feeding, metabolism, thermoregulation, and sleep overlap in the hypothalamus. Low ambient temperatures and food restriction induce hypothermic (torpor) bouts and characteristic metabolic and sleep changes in mice. We report that mice lacking the preproghrelin gene, but not those lacking the ghrelin receptor, have impaired abilities to manifest and integrate normal sleep and thermoregulatory responses to metabolic challenges. In response to fasting at 17 degrees C (a subthermoneutral ambient temperature), preproghrelin knockout mice enter hypothermic bouts associated with reduced sleep, culminating in a marked drop in body temperature to near-ambient levels. Prior treatment with obestatin, another preproghrelin gene product, attenuates the hypothermic response of preproghrelin knockout mice. Results suggest that obestatin is a component in the coordinated regulation of metabolism and sleep during torpor.
Column Access of a Bubble Lattice: Column Translation and Lattice Translation (1976)

The use of a regular array, or lattice, of magnetic bubbles for the storage of information requires two kinds of functions: the read-write functions involving the generation and discrimination of bubbles with different wall structures, and the access functions involving the insertion and removal of bubbles at selected locations in the lattice. In a column-accessed bubble lattice device, accessing is accomplished by first translating the lattice to position the desired column of bubbles in an input-output access channel and then translating this column along the channel to a detector area outside of the lattice while simultaneously introducing new bubbles from a generator area at the other end of the channel. An analysis of the influence of device design parameters on access rate indicates that the most important parameters are the column translation rate and lattice capacity. A device is described that was designed to study the translation of a lattice of bubbles and of a single column of bubbles within the lattice. Quasistatic operating margins and dynamic measurements of this test device indicate that the column-access configuration provides feasible means for the rapid access of bubbles from a lattice.
AdenoLibrary approach for vector construction and selection of targeted adenoviruses employing novel fiber-fibritin chimeric fibers (2005)

1332 Adenovirus serotype 5 (Ad5) has been widely used as a viral vector for cancer gene therapy applications. However, the paucity of the Ad5 primary receptor (coxsackie and adenovirus receptor, CAR) on target cancer cells of interest has rendered many tissues refractory to Ad-mediated transduction. Additionally, this endogenous tropism may potentially lead to undesired transduction of tissues expressing CAR. In view of this, strategies have been proposed to modify Ad5 to achieve targeted gene delivery by ablating native tropism while redirecting Ad to target cell markers of interest. Such strategies involve modification of the trimeric capsid fiber protein, whose C-terminal knob domain has been shown to dictate the native tropism associated with Ad5. While approaches employing genetic fusion of simple targeting ligands to the fiber have shown promise in retargeting, in many cases, the incorporated ligands tend to lose specificity and/or affect virion integrity. As an alternative, several so-called knob-less fiber platforms have been utilized. These modifications are based on the concept of replacing the native fiber with an alternative protein capable of providing the trimerization functions that the knob usually confers. Such a strategy would accrue the additional benefit of an expanded repertoire of incorporable ligands, based on removal of the structural constraints imposed by the fiber knob. Previously, our group has utilized the bacteriophage T4 fibritin protein for fiber replacement, with subsequent display of complex targeting ligands providing for expanded tropism. However, vectors employing these knob-less fiber platforms often exhibit poor capsid incorporation of the alternate fibers in comparison to that of wild-type Ad5 fiber, which consequently leads to limited gene transfer efficacy and difficulty in vector propagation. In view of these obstacles, we have hypothesized that direct analysis of modified adenoviruses during their rescue/propagation is the only straightforward approach that guarantees the selection of functional, targeted vectors with optimized structural integrity and targeting efficiency. Herein, we describe a new schema for Ad vector construction, which allows for the selection of vectors with the optimal modified capsid configuration at the level of viral rescue. Based on our first generation fiber-fibritin molecule, several new fibers employing variant amounts of fibritin and Ad5 fiber shaft were analyzed via this library selection schema. Our selected variant, composed of the entire Ad5 fiber shaft connected to 12th coiled-coil segment of fibritin, is capable of efficient fiber incorporation, ligand display, and CAR-independent transduction. Furthermore, we have concluded that various targeting ligands require individual optimization, which may be accomplished by utilizing this adenoviral library approach.
In Vitro Determination of the Main Effects in the Design of High-Flow Nasal Therapy Systems with Respect to Aerosol Performance (2018)

Aerogen Limited.