gebhart/patrepeval huggingface dataset:
Exon skipping of FcεRIβ eliminates expression of the high-affinity IgE receptor in mast cells with therapeutic potential for allergy (2016)

Allergic diseases are driven by activation of mast cells and release of mediators in response to IgE-directed antigens. However, there are no drugs currently available that can specifically down-regulate mast cell function in vivo when chronically administered. Here, we describe an innovative approach for targeting mast cells in vitro and in vivo using antisense oligonucleotide-mediated exon skipping of the β-subunit of the high-affinity IgE receptor (FcεRIβ) to eliminate surface high-affinity IgE receptor (FcεRI) expression and function, rendering mast cells unresponsive to IgE-mediated activation. As FcεRIβ expression is restricted to mast cells and basophils, this approach would selectively target these cell types. Given the success of exon skipping in clinical trials to treat genetic diseases such as Duchenne muscular dystrophy, we propose that exon skipping of FcεRIβ is a potential approach for mast cell-specific treatment of allergic diseases.
Colloidal gold immunolabeling of immunoglobulin-binding sites and beta antigen in group B streptococci (1990)

We have characterized the immunoglobulin A (IgA)-Fc-binding properties and beta-antigen expression of several strains of group B streptococci by using ultrastructural immunocytochemistry. Colloidal gold-labeled tracers were used with intact and sectioned bacteria in order to gain information regarding the location and distribution of cell surface and cytoplasmic IgA-Fc-binding molecules and beta antigen. Colloidal gold (5- or 15-nm particles) was conjugated to IgA to characterize IgA-binding properties and to IgG to test for IgG binding. Rabbit anti-beta antiserum was reacted with the bacteria and then with protein G labeled with 15-nm colloidal gold particles. A double-labeling technique was used for simultaneous localization of IgA-Fc- and anti-beta-antibody-binding properties on sectioned bacteria. The data corroborated previous results which indicated that (i) IgA-Fc-binding and IgA-Fc-nonbinding forms of beta antigen can be secreted by strains which do not express beta antigen on the cell surfaces (HG806, VC75); (ii) differences in levels of expression of beta antigen and/or IgA-Fc-binding proteins can be detected among various group B isolates; (iii) group B streptococci do not express human IgG-Fc-binding proteins; and (iv) not all forms of beta antigen are capable of binding human IgA.
Terahertz quantum cascade lasers using resonant-phonon depopulation and metal-metal waveguides (2004)

The recent extension of quantum cascade lasers (QCLs) from the mid-infrared to the terahertz frequency range (1-10 THz) promises to help address the relative lack of compact, coherent radiation sources in this spectral regime. We report our recent development of terahertz QCLs based on a resonant phonon depopulation scheme coupled with high-confinement, low-loss, metal-metal waveguides for mode confinement. A 3.2 THz laser (λ≈ 93.4 μm) is presented that operates in continuous wave mode up to a temperature of 93 K and up to 133 K in pulsed mode. Also presented is a 2.1 THz laser (λ ≈ 141 μm) that lases up to 40 K in continuous wave mode and 72 K in pulsed mode.
222 Beyond the Bench: Surgical Technique Development for Implantation of a Novel Penile Prosthesis in Human Corpora Cavernosa (2018)

With development of a novel class of penile prosthesis that uses shape memory alloys (SMA), we sought to develop and troubleshoot the optimal surgical technique for implantation into the corpora cavernosa of human cadavers as no established technique exists. Development of such surgical techniques is necessary to move forward to human applications. Two pelvic human cadavers were obtained. A lasercut SMA prosthesis that has been previously described surrounding a spongy core and covered in a latex sheath was inserted into the corpora cavernosa through various established surgical approaches: (1) transglanular, (2) subcoronal, and (3) penoscrotal. Challenges in technique were documented and activation/deactivation of the device was carried out. Similar to malleable penile prosthesis implantation, techniques for inserting a cylindrical device involved creating a space in the corpora using standard dilation techniques. Unlike malleables, we are able to crimp our device and reduce cross sectional diameter prior to implantation. The numerous ribs in our prototype, despite being encased in a latex sheath, made implantation from a distal approach (transglanular and subcoronal) challenging. A penoscrotal approach was more successful. Seating the prototype into the proximal crura was also difficult, as our prototype did not have rear tip extenders or proximal tapering. Fixation proximally was found to be important for stability. During the activation process with magnetic induction, the intrapelvic portion was difficult to access, while the penile component responded readily and demonstrated a force resistant to buckling of 1.2 kgf.
A novel polyamine blockade therapy activates an anti-tumor immune response (2017)

Most tumors maintain elevated levels of polyamines to support their growth and survival. This study explores the anti-tumor effect of polyamine starvation via both inhibiting polyamine biosynthesis and blocking the upregulated import of polyamines into the tumor. We demonstrate that polyamine blockade therapy (PBT) co-treatment with both DFMO and a novel polyamine transport inhibitor, Trimer PTI, significantly inhibits tumor growth more than treatment with DFMO or the Trimer PTI alone. The anti-tumor effect of PBT was lost in mice where CD4<sup>+</sup> and CD8<sup>+</sup> T cells were antibody depleted, implying that PBT stimulates an anti-tumor immune effect that is T-cell dependent. The PBT anti-tumor effect was accompanied by an increase in granzyme B<sup>+</sup>, IFN-γ<sup>+</sup> CD8<sup>+</sup> T-cells and a decrease in immunosuppressive tumor infiltrating cells including Gr-1<sup>+</sup>CD11b<sup>+</sup> myeloid derived suppressor cells (MDSCs), CD4<sup>+</sup>CD25<sup>+</sup> Tregs, and CD206<sup>+</sup>F4/80<sup>+</sup> M2 macrophages. Stimulation with tumor-specific peptides elicited elevated antigen-specific IFN-γ secretion in splenocytes from PBT-treated mice, indicating that PBT treatment stimulates the activation of T-cells in a tumor-specific manner. These data show that combined treatment with both DFMO and the Trimer PTI not only deprives polyamine-addicted tumor cells of polyamines, but also relieves polyamine-mediated immunosuppression in the tumor microenvironment, thus allowing the activation of tumoricidal T-cells.
<title>Polymer microlens arrays fabricated using the hydrophobic effect</title> (2000)

We report a means of fabricating hydrophilic domains in a hydrophobic background by lithographically patterning an adhesive hydrophobic layer. Organic polymer microlenses have been fabricated on these substrates using a dip-coating technique. Various lens shapes (circular, elliptical, square) have been fabricated on a variety of substrates (SiO<SUB>2</SUB>, SiN, GaAs, InP, etc), ranging in size from 2 - 500 micrometers in diameter, and having fill factors of up to 90%. Plano-convex and double-convex lenses have been fabricated as fast as f/1.38 and f/1.2, respectively. The performance of arrays of these microlenses was quantitatively analyzed and optimized.
High calcium cementless fly ash binder with low environmental footprint: Optimum Taguchi design (2018)

Abstract Despite the myriad of research efforts on exploiting fly ash as an alternative binder, its current role in industry is largely restricted to the supplementary use, which enables only partial replacement of conventional portland cement. Herein, we propose an unprecedented binder composite with the promising early‐age strength, which is cost‐effective and reduces the CO 2 footprint compared with portland cement. The major constituent is fly ash occupying 76.4%‐80.3% by the total mass of the constituents, while calcium oxide, nanosilica, and the minimum amounts of sodium‐based activators are added to induce the early‐age strength development. Optimization of the composition via the Taguchi design of experiments produced the early (7‐day) compressive strength of 16.18 MP a. This value is encouraging considering that it is comparable to that of conventional portland cement and that a cementless composition with the minimum amounts of sodium‐based activators was employed. The extensive materials analysis demonstrates that the starting Ca/Na molar ratio and the amount of nanosilica play instrumental roles in strength development by influencing the formation of key reaction products, which include the sodium‐substituted AF m phase (the U‐phase), katoite and portlandite. Overall, the promising early‐age strength coupled with the significantly decreased amount of sodium‐based chemicals and the reduced CO 2 footprint will lay a foundation for development of low‐cost, environmentally friendly binder in diverse industries.
A linear magnetic motor and generator (1980)

In linear magnetic motor and generator suitable for remote and hostile environments, magnetic forces drive reciprocating shaft along its axis. Actuator shaft is located in center of cylindrical body and may be supported by either contacting or noncontacting bearings. When device operates as bidirectional motor, drive coil selectively adds and subtracts magnetic flux to and from flux paths, producing forces that drive actuator along axis. When actuator is driven by external reciprocating engine, device becomes ac generator.
Nonenzymatic and Metal-Free Organocatalysis for in Situ Regeneration of Oxidized Cofactors by Activation and Reduction of Molecular Oxygen (2016)

The application of synthetic flavinium organocatalysts for the in situ regeneration of oxidized cofactors NAD(P)+ using O2 as the terminal oxidant without any special illumination or equipment is reported. With the aid of the highly active bridged flavinium catalyst, the rate of NAD(P)H oxidation is accelerated by 3 orders of magnitude. The results show that the catalytic activity of the bridged flavinium catalyst is not dependent on light but on only oxygen. Furthermore, this catalyst is compatible with various preparative enzymatic oxidation reactions. A hydride transfer mechanism is proposed for the presented system.
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii (2003)

Although, the S. cerevisiae genome is rightly considered as one of the most accurately sequenced and annotated eukaryotic genomes, we have shown that it still benefits substantially from comparison to the completed sequence and syntenic gene map of A. gossypii, an evolutionarily related fungus. This type of approach will strongly support the annotation of more complex genomes such as the human and murine genomes.
Activation of metal–organic framework materials (2013)

Crystalline metal–organic frameworks (MOFs) have emerged as a highly desirable class of solid-state materials. Some of their most attractive features include exceptionally high porosities as well as surface areas. A key aspect to the realization of high porosity is the removal of guest molecules from the framework while still maintaining its structural integrity (i.e., “activation”). This contribution highlights the strategies utilized to date for activating MOFs, including: (i) conventional heating and vacuum; (ii) solvent-exchange; (iii) supercritical CO2 (scCO2) exchange; (iv) freeze-drying; and (v) chemical treatment.
Growth of a Tryptophanase-producing Thermophile, Symbiobacterium thermophilum gen. nov., sp. nov., Is Dependent on Co-culture with a Bacillus sp. (1988)

An obligately symbiotic bacterium, strain T, associating with a specific strain S of a thermophilic Bacillus sp. was isolated during screening for micro-organisms that produce heat-stable tryptophanase and β-tyrosinase. A colony containing both strains was finally isolated by successive selection with bacitracin. In mixed culture with Bacillus strain S under low aeration conditions at 60 °C, growth of strain T was initiated following lysis of the Bacillus cells. No independent growth of strain T was observed in any of the media tested, even in the presence of other thermophilic Bacillus strains or cell-free extracts of strain S or its killed cells. No physical adhesion between cells of strains S and T was observed microscopically. Tryptophanase and β-tyrosinase production by strain T were induced by l-tryptophan and L-tyrosine, respectively. The name Symbiobacterium thermophilum gen. nov., sp. nov. is proposed for strain T which is a Gram-negative rod (0·25–0·35 µm diameter) with a multilayer surface structure containing meso-diaminopimelic acid. The G+C content of the DNA is 65·1 mol%; iso-C15:0, iso-c17:0 and anteiso-C17:0 acids are the major cellular fatty acids. The type strain is strain IAM 13621.
Simple and high sensitive focus monitoring utilizing an aperture on backside of photomask (2003)

A simple and high sensitive focus monitoring has been developed utilizing an aperture in Cr film formed on backside of photomask. A special mask for focus monitoring is developed such that two mark patterns on the front side of the mask are irradiated by different illuminations. The different illuminations for the two marks are generated from usually used illumination with modulation by an aperture on the backside of the mask. In this work, two complementally halves of usually used illumination are effectively generated. Because illumination for each mark pattern on front side of the mask is strongly asymmetric in incident angle such that illumination beam impinged from only one side of the space, imaging of the large size mark pattern is carried out obliquely on the wafer. As a result, image is laterally shifted with focus. The direction of lateral image shift is opposite to that of another mark which is irradiated with illumination beams from opposite side of the space. Thus, the relative displacement between the two mark images may become a measure of focus. Because this focus monitor works under purely geometrical optics, focus monitoring of multiple steppers, which are working under different wavelength, can be performed with the same one photomask. In experiments, the two mark patterns, which are inner and outer box patterns, are printed with overlaying each other by double exposure with stepping of wafer stage. Then, mutual displacement of mark patterns is measured by a commercially available overlay measurement tool whose resolution is a few nm. Very high focus sensitivity (Δx/Δz) of ~0.9 is observed for NA=0.68 optics with strong annular illumination. Because of the high focus sensitivity and high resolution of overlay measurement, focus monitoring with very high resolution of a few nm can be achieved.
Fast and memory effective i-vector extraction using a factorized sub-space (2013)

Most of the state-of-the-art speaker recognition systems use a compact representation of spoken utterances referred to as i-vectors. Since the standard i-vector extraction procedure requires large memory structures and is relatively slow, new approaches have recently been proposed that are able to obtain either accurate solutions at the expense of an increase of the computational load, or fast approximate solutions, which are traded for lower memory costs. We propose a new approach particularly useful for applications that need to minimize their memory requirements. Our solution not only dramatically reduces the storage needs for i-vector extraction, but is also fast. Tested on the female part of the tel-tel extended NIST 2010 evaluation trials, our approach substantially improves the performance with respect to the fastest but inaccurate eigen-decomposition approach, using much less memory than any other known method.
Solid H/sub 2//D/sub 2/ gas generators (1987)

This patent describes a thermally stable, solid reactant hydrogen and deuterium gas generator compositions comprising in weight percentages as follows: an oxidizer compound selected from the group of oxidizer compounds: LiNO/sub 3/ and KNO/sub 3/ from about 59 to about 15; binder of polytetrafluorethylene from about 2 to about 15; and magnesium borohydride diammoniate in an amount from about 80 to about 90 as a source of hydrogen gas or the equivalent weight of the deuterated analog of the magnesium borohydride diammoniate is a source of deuterium gas.
Mathematical Language Processing: Automatic Grading and Feedback for Open Response Mathematical Questions (2015)

While computer and communication technologies have provided effective means to scale up many aspects of education, the submission and grading of assessments such as homework assignments and tests remains a weak link. In this paper, we study the problem of automatically grading the kinds of open response mathematical questions that figure prominently in STEM (science, technology, engineering, and mathematics) courses. Our data-driven framework for mathematical language processing (MLP) leverages solution data from a large number of learners to evaluate the correctness of their solutions, assign partial-credit scores, and provide feedback to each learner on the likely locations of any errors. MLP takes inspiration from the success of natural language processing for text data and comprises three main steps. First, we convert each solution to an open response mathematical question into a series of numerical features. Second, we cluster the features from several solutions to uncover the structures of correct, partially correct, and incorrect solutions. We develop two different clustering approaches, one that leverages generic clustering algorithms and one based on Bayesian nonparametrics. Third, we automatically grade the remaining (potentially large number of) solutions based on their assigned cluster and one instructor-provided grade per cluster. As a bonus, we can track the cluster assignment of each step of a multistep solution and determine when it departs from a cluster of correct solutions, which enables us to indicate the likely locations of errors to learners. We test and validate MLP on real-world MOOC data to demonstrate how it can substantially reduce the human effort required in large-scale educational platforms.
X-ray structure of <i>Arthrobacter globiformis</i> M30 ketose 3-epimerase for the production of <scp>D</scp>-allulose from <scp>D</scp>-fructose (2018)

The X-ray structure of ketose 3-epimerase from Arthrobacter globiformis M30, which was previously reported to be a D-allulose 3-epimerase (AgD-AE), was determined at 1.96 Å resolution. The crystal belonged to the hexagonal space group P 6 5 22, with unit-cell parameters a = b = 103.98, c = 256.53 Å. The structure was solved by molecular replacement using the structure of Mesorhizobium loti L-ribulose 3-epimerase (MlL-RE), which has 41% sequence identity, as a search model. A hexagonal crystal contained two molecules in the asymmetric unit, and AgD-AE formed a homotetramer with twofold symmetry. The overall structure of AgD-AE was more similar to that of MlL-RE than to the known structures of D-psicose (alternative name D-allulose) 3-epimerases (D-PEs or D-AEs), although AgD-AE and MlL-RE have different substrate specificities. Both AgD-AE and MlL-RE have long helices in the C-terminal region that would contribute to the stability of the homotetramer. AgD-AE showed higher enzymatic activity for L-ribulose than D-allulose; however, AgD-AE is stable and is a unique useful enzyme for the production of D-allulose from D-fructose.
The Use of Fluorogenic Substrates To Measure Fungal Presence and Activity in Soil (1998)

Our objective was to determine if 4-methylumbelliferyl-labelled enzyme substrates could be used to detect and quantify specific components of chitinase and cellulase activities as specific indicators of the presence and activity of fungal biomass. The fluorogenic substrates 4-methylumbelliferyl (MUF) N-acetyl-beta-D-glucosaminide and MUF beta-D-lactoside were used for the detection and quantification of beta-N-acetylglucosaminidase (EC 3.2.1.30) (NAGase) and endo 1,4-beta-glucanase (EC 3.2.1.4)/cellobiohydrolase (EC 3.2.1.91) (CELase), respectively. Culture screenings on solid media showed a widespread ability to produce NAGase among a taxonomically diverse selection of fungi on media with and without added chitin. NAGase activity was expressed only in a limited number of bacteria and on media supplemented with chitin. The CELase activity was observed only in a limited number of fungi and bacteria. Bacterial CELase activity was expressed on agar media containing a cellulose-derived substrate. In soil samples, NAGase activity was significantly correlated with estimates of fungal biomass, based on the content of two fungus-specific indicator molecules, 18:2 omega 6 phospholipid fatty acid (PLFA) and ergosterol. CELase activity was significantly correlated with the PLFA-based estimate of fungal biomass in the soil, but no correlation was found with ergosterol-based estimates of fungal biomass.
Design of High-Efficiency Matching Networks for Capacitive Wireless Power Transfer Systems (2020)

Matching networks are an efficient means of providing large voltage or current gain and reactive compensation in high-frequency wireless power transfer (WPT) systems. This article introduces an analytical optimization approach for the design of L-section matching networks in capacitive WPT systems, which maximizes the network efficiency while achieving the required overall gain and compensation. The proposed approach identifies the optimal number of matching network stages and the optimal distribution of gains and compensations among these stages. Compared with the conventional approach to designing matching networks for capacitive WPT systems, the proposed approach results in higher and flatter efficiency for a wide range of air-gap voltages. The proposed approach also offers a better tradeoff between efficiency and power transfer density while meeting electric field safety requirements. The efficiency predictions of the proposed design approach are experimentally validated using three 6.78-MHz 100-W prototype capacitive WPT systems: one with single-stage matching networks, one with two-stage matching networks, and another with three-stage matching networks. The measured matching network efficiencies of the prototype systems are in close agreement with the theoretical predictions. The prototype system with two-stage matching networks is also compared with a prototype system designed using the conventional approach and is shown to achieve significantly higher efficiency.
Physicochemical and Biological Characterization of Recombinant Human Inhibin A (1990)

Recombinant human inhibin A was isolated from recombinant mammalian cell line culture media. Two forms of inhibin were identified with Mr of 34 and 31 Kd composed of subunits (alpha, beta) of 24 and 15 Kd and 21 and 15 Kd respectively. Both forms are bioactive in an inhibin in vitro bioassay and immunoactive with potencies comparable to or higher than purified bovine inhibin. Amino acid analyses and NH2-terminal sequences of each of the subunits are consistent with those predicted from their cDNA structures. The inhibin alpha- but not beta-subunit is glycosylated based on its binding to the lectins concanavalin A and wheat germ lectin. The difference in molecular weight of 31 and 34 Kd inhibin is attributed to variation in glycosylation of the alpha-subunit. The 31+34 Kd inhibin is heterogeneous on isoelectric focusing gels consisting of four isoforms in the pH range 6.2-7.6. Inhibition also exhibits in vivo biological activity by suppressing serum FSH but not LH in castrate male rats. These physicochemical and biological characteristics of recombinant human inhibin are similar to those described for native inhibin isolated from a variety of other species.