gebhart/patrepeval huggingface dataset:
Suppression of Thyrotropin Receptor Constitutive Activity by a Monoclonal Antibody with Inverse Agonist Activity (2007)

TSH binding to the TSH receptor (TSHR) induces thyrocyte growth and proliferation primarily by activating the adenylyl cyclase signaling pathway. Relative to the other glycoprotein hormone receptors, the TSHR has considerable ligand-independent (constitutive) activity. We describe a TSHR monoclonal antibody (CS-17) with the previously unrecognized property of being an inverse agonist for TSHR constitutive activity. This property is retained, even when constitutive activity is extremely high consequent to diverse TSHR extracellular region mutations. A similar effect on an activating mutation at the base of the sixth transmembrane helix (not accessible to direct CS-17 contact) indicates that CS-17 is acting allosterically. Administered to mice in vivo, CS-17 reduces serum T(4) levels. The CS-17 epitope is conformational and a significant portion lies in the C-terminal region of the TSHR leucine-rich domain (residues 260-289). By interacting with the large TSHR extracellular domain, CS-17 is, to our knowledge, the first antibody reported to be an inverse agonist for a member of the G protein receptor superfamily. After humanization of its murine constant region, CS-17 has the potential to be an adjunctive therapeutic agent in athyreotic patients with residual well-differentiated thyroid carcinoma as well as pending definitive treatment in some selected hyperthyroidism states.
Stance classification of multi-perspective consumer health information (2018)

While search engines are effective in answering direct factual questions such as, 'What are the symptoms of a disease X?', they are not so effective in addressing complex consumer health queries, which do not have a single definitive answer, such as, 'Is treatment X effective for disease Y?'. Instead, the users are presented with a vast number of search results with often contradictory perspectives and no definitive answer. We denote such queries as Multi-Perspective Consumer Health Information (MPCHI) queries for which there is no single 'Yes or No' answer. While ascertaining the credibility of the claims requires domain expertise, an efficient categorization of the search results according to their stance (support or oppose) to the queries will help the searcher in decision making. Hence, this paper focuses on the problem of stance classification for MPCHI data at sentence level, presenting a new data set for MPCHI queries. Unlike typical debate or argumentative text, the linguistic characteristics of MPCHI is quite different, with extensive use of scientific formal language and absence of opinion bearing words. Hence, such inherently different characteristic of MPCHI text requires going beyond traditional Bag of Words (BoW) features for stance classification. Hence, we propose using a rich non-traditional set of features such as medical semantic relations, stance vectors, sentiment polarity, textual entailment, and study their impact on MPCHI stance classification using an SVM and a neural network classifier. We find that using novel non-traditional features improves MPCHI stance classification performance over traditional BoW model by 24% for the SVM classifier, and 44% for the neural network classifier respectively, for the best feature combination.
Pediatric <i>Clostridioides difficile</i> Infection: Diagnosis and Diagnostic Stewardship (2021)

Although the pathogenesis of Clostridioides difficile infection (CDI) is complex and incompletely understood, it is believed that the elaboration of C. difficile toxins is necessary for disease. There are a variety of tests available for the detection of both the C. difficile organism and its toxins; however, each has limitations and the best application of these tests to the diagnosis of CDI in children remains uncertain. Nucleic acid amplification tests are unable to reliably discriminate between CDI and C. difficile colonization, while commercially available enzyme immunoassays for toxin detection lack sensitivity. An understanding of preanalytic factors, relevant patient features, and test performance characteristics is essential to the accurate diagnosis of CDI in children. Specific diagnostic stewardship strategies can also increase the likelihood that positive tests reflect disease rather than colonization. Ultimately, CDI remains a clinical diagnosis and clinical judgment is essential when interpreting test results, regardless of the methods used.
Multilayered microfluidic probe heads (2009)

Microfluidics have emerged as powerful processing and analytical tools. However, as they are usually closed systems, they are difficult to use with large samples and surfaces that cannot pass inside their conduits. Here, we extend our previously reported microfluidic probe (MFP) concept, in which a focused stream of liquid is scanned over a surface, for which heads were fabricated using one Si wafer and a molded poly(dimethylsiloxane) (PDMS) block. The new heads comprise a microfabricated Si lid, a chip for hydrodynamic flow confinement (HFC) and standard ports and fittings. The HFC chip carries the smallest structures needed for focusing the liquid on the surface; the Si lid is bonded to the HFC chip using a polyimide adhesive and has macroscopic vias for bonding standard ports and fittings. These heads are easy to fabricate at high yield, have high-resolution potential and are compatible with a large number of chemicals and solvents. We exemplify this by patterning proteins on a surface, directly developing a resist using a high-pH developer, and producing tapered structures in a resist. This work should foster the adoption of MFPs for processing, patterning and analyzing surfaces under microfluidic conditions.
Development of a pan-retrovirus detection system for multiple sclerosis studies (1997)

These findings lend further support to the concept of retroviral involvement in MS.
Apparatus for measuring the damping coefficient of torsional-vibration dampers (1980)

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Effective browsing of web image search results (2004)

The rapid development of web image search engines has enabled users to search hundred million of images available on the Web. However, due to the unsatisfactory performance of current search technologies, people still need to spend much time in navigating through the large number of result pages to find images of their interest. In this paper, we analyze the user information needs for web image search results browsing and propose to employ a similarity-based organization to present the search results. A user study is carried out to compare our approach with a ranking-based list interface and a cluster-based interface. Experimental results show that similarity-based presentation can help users to explore image search results more naturally and efficiently
Stem cell approaches for retinal repair (2009)

Retinal degenerations are significant causes of vision loss. Efforts to stimulate regeneration of retinal neurons from Muller glia have recently been successful for amacrine cells, but not for photoreceptors. Cell replacement using transplantation offers an alternative therapy to potentially restore visual function to individuals who have lost their sight from photoreceptor degeneration. To provide a source of new retinal neurons for cell based therapies, we developed methods to derive retinal progenitors from human ES cells. We have found that the photoreceptors derived from human ES cells can be transplanted to mice with inherited retinal degeneration, and that they restore light response to the animals. We have also recently developed methods to purify the photoreceptors prior to transplantation. These results provide a proof of principle that human ES cells can be useful in cell replacement therapies for retinal degenerations.
Basal plane dislocation reduction for 8° off-cut, 4H-SiC using <i>in situ</i> variable temperature growth interruptions (2008)

In situ growth interrupts were executed during the growth of 8° off-cut 4H-SiC epitaxial layers to determine the dependence of the efficiency for converting basal plane dislocations (BPDs) to threading edge dislocations (TEDs) on the interrupt temperature. Three samples were grown with 15min growth interrupts executed near the middle of a 30–40μm thick, n-type doped layer at 1400, 1500, and 1580°C. Ultraviolet photoluminescence (UVPL) mapping of these layers reveals the BPDs and permits the observation of how these defects extend into and through the epilayer. From the lateral length of the BPDs in the UVPL wafer map, it was determined whether or not the BPD converted into a TED at the growth interrupt interface. The percentage of BPDs that converted for the 1400, 1500, and 1580°C interrupts were 20%, 28%, and 51%, respectively. The proposed cause for the higher conversion rate at the interrupt temperature of 1580°C is the higher etching rate that occurs at this temperature, and it is presumed that there is an enhanced etch rate where the BPD intersects the surface which will result in etch pit decorations. It was also observed that no new in-grown stacking faults formed at the growth interrupt interface, as has been observed for ex situ growth interrupts.
Nanoparticles and ultrasound for delivery of model macromolecular anti-cancer drugs in tumors (2003)

Penetration of macromolecular anti-cancer agents from blood into tumor cells is poor due to the physiological barriers: tumor capillary wall, interstitium, and cancer cell membrane. We proposed to use laser- or ultrasound-induced cavitation to enhance anti-cancer drug delivery through these barriers. Interaction of ultrasound with exogenous nanoparticles with certain acoustic properties may provide cavitation selectively in tumors and, therefore, may provide safe and efficient delivery of anti-cancer drugs in cancer cells without damage to normal tissues. In this paper, we studied enhanced delivery of model macromolecular anti-cancer drugs with ultrasound-induced cavitation in mice bearing human colon (KM20) and breast (MCF-7) tumors. Fluorescent rhodamine-dextrans of different molecular weight (10, 70, and 2,000 kDa) served as model drugs simulating antisense oligonucleotides, antibodies, and genes, respectively. Immunohistochemical staining of tumor vasculature with CD31 was used to visualize tumor blood vessels. Our studies demonstrated enhanced penetration of the drugs from blood vessels into tumor interstitium when ultrasound was applied in combination with polymer nanoparticle injections. Our results suggest that this drug delivery technique can potentially be used for efficient cancer chemo- and biotherapy.
<title>Fiber optic fire sensor</title> (1993)

A passive fiber optic fire sensor that uses transmission quality silica fiber is described. The fiber optic is used only to direct radiation from a fire down to a detector, as a light conduit. The sensor is characterized by resistance to high temperature environments, dirt, and electromagnetic fields. It is small, compact, lightweight, and senses fires from a wide variety of sources.
Detection of Glycosylated Markers From Cancer Stem Cells With ColoSTEM Dx Kit for Earlier Prediction of Colon Cancer Aggressiveness (2022)

Nowadays, colon cancer prognosis still difficult to predict, especially in the early stages. Recurrences remain elevated, even in the early stages after curative surgery. Carcidiag Biotechnologies has developed an immunohistochemistry (IHC) kit called ColoSTEM Dx, based on a MIX of biotinylated plant lectins that specifically detects colon cancer stem cells (CSCs) through glycan patterns that they specifically (over)express. A retrospective clinical study was carried out on tumor tissues from 208 non-chemotherapeutic-treated and 21 chemotherapeutic-treated patients with colon cancer, which were stained by IHC with the MIX. Clinical performances of the kit were determined, and prognostic and predictive values were evaluated. With 78.3% and 70.6% of diagnostic sensitivity and specificity respectively, our kit shows great clinical performances. Moreover, patient prognosis is significantly poorer when the MIX staining is "High" compared to "Low", especially at 5-years of overall survival and for early stages. The ColoSTEM Dx kit allows an earlier and a more precise determination of patients' outcome. Thus, it affords an innovating clinical tool for predicting tumor aggressiveness earlier and determining prognosis value regarding therapeutic response in colon cancer patients.
Peramivir Phosphonate Derivatives as Influenza Neuraminidase Inhibitors (2016)

Peramivir is a potent neuraminidase (NA) inhibitor for treatment of influenza infection by intravenous administration. By replacing the carboxylate group in peramivir with a phosphonate group, phosphono-peramivir (6a), the dehydration and deoxy derivatives (7a and 8a) as well as their corresponding monoalkyl esters are prepared from a pivotal intermediate epoxide 12. Among these phosphonate compounds, the dehydration derivative 7a that has a relatively rigid cyclopentene core structure exhibits the strongest inhibitory activity (IC50 = 0.3-4.1 nM) against several NAs of wild-type human and avian influenza viruses (H1N1, H3N2, H5N1, and H7N9), although the phosphonate congener 6a is unexpectedly less active than peramivir. The inferior binding affinity of 6a is attributable to the deviated orientations of its phosphonic acid and 3-pentyl groups in the NA active site as inferred from the NMR, X-ray diffraction, and molecular modeling analyses. Compound 7a is active to the oseltamivir-resistant H275Y strains of H1N1 and H5N1 viruses (IC50 = 73-86 nM). The phosphonate monoalkyl esters (6b, 6c, 7b, 7c, 8b, and 8c) are better anti-influenza agents (EC50 = 19-89 nM) than their corresponding phosphonic acids (EC50 = 50-343 nM) in protection of cells from the viral infection. The phosphonate monoalkyl esters are stable in buffer solutions (pH 2.0-7.4) and rabbit serum; furthermore, the alkyl group is possibly tuned to attain the desired pharmacokinetic properties.
Susceptibility of strain-hardening cementitious composite to curing conditions as a retrofitting material for RC beams (2021)

Strain-hardening cement-based composites (SHCC) have recently been developed as repair materials for the improvement of crack control and strength of flexural members. This work focuses on strengthening and flexural enhancement using SHCC layer in tensile regions of flexural members under three different curing conditions. The curing conditions simulate the effect of different environmental conditions prevailing in the central and coastal regions of the Arabian Peninsula on the properties of SHCC as a retrofitting material. In this investigation, beams with SHCC layer were compared to control beams. The beams with SHCC layer of 50-mm thickness were cast. The results revealed that the flexural behavior and the load-carrying capacity of the normal concrete beam specimens under hot and dry environmental conditions were significantly reduced, lowering the ductility of the section. However, compressive strength is comparatively unaffected. Similarly, the hot curing conditions have also led to a notable reduction in the loading capacity of the beam with SHCC layer with a slight effect on its stiffness. On the other hand, steam-curing conditions have shown improvement in load-carrying capacity and a reduction in section ductility of the beam with SHCC layer. It was found that the structural unit retrofitted with SHCC layer was a curing-regime dependent as the tensile and strain-hardening properties of SHCC are highly sensitive to the alteration in the cement hydration process. A normal curing regime was found effective and satisfying the practical, cost, and performance requirements. Accordingly, a normal curing regime could be implemented to retrofit reinforced concrete (RC) beams with SHCC layers as recommended in the study.
Catadioptric projectors (2009)

We present a catadioptric projector analogous to a catadioptric camera by combining a commodity digital projector with additional optical units. We show that, by using specially shaped reflectors/refractors, catadioptric projectors can offer an unprecedented level of flexibility in aspect ratio, size, and field of view. We also present efficient algorithms to reduce projection artifacts in catadioptric projectors, such as distortions, scattering, and defocusing. Instead of recovering the reflector/refractor geometry, our approach directly models the light transport between the projector and the viewpoint using the light transport matrix (LTM). We show how to efficiently approximate the pseudo inverse of the LTM and apply it to find the optimal input image that produces least projection distortions. Furthermore, we present a projection defocus analysis for reflector and thin refractor based catadioptric projectors. We show that defocus blur can be interpreted as spatially-varying Gaussian blurs on the input image. We then measure the kernels directly from the LTM and apply deconvolution to optimize the input image. We demonstrate the practical uses of catadioptric projectors in panoramic and omni-directional projections. Our new system achieves much wider field-of-view projection while maintaining sharpness and low geometric and photometric distortions.
Amantadine and dansylcadaverine inhibit vesicular stomatitis virus uptake and receptor-mediated endocytosis of alpha 2-macroglobulin. (1982)

The entry of many animal viruses into their host cells often proceeds via a specialized internalization pathway involving clathrin-coated regions of the plasma membrane. We have examined the effect of dansylcadaverine and amantadine on the entry of vesicular stomatitis virus (VSV) into mouse cells. Both compounds inhibit VSV entry as determined by fluorescence and electron microscopy, 3H-labeled VSV uptake, and VSV-dependent RNA synthesis assays. They also inhibit the uptake of alpha 2-macroglobulin, a protein that binds to specific membrane receptors and follows the same route of internalization. Dansylcadaverine is 20-fold more potent than amantadine in blocking virus and alpha 2-macroglobulin uptake. One cellular target for both of these amine-containing compounds appears to be the clustering of membrane-bound ligands or particles in clathrin-coated pits.
Purification and Assembly of DNA-Stabilized Boron Nitride Nanotubes into Aligned Films (2019)

The liquid phase processing including dispersion, purification, and assembly of boron nitride nanotubes (BNNTs) is important for effectively translating unique properties of BNNTs into assembled solid materials, such as films and fibers. Short single-stranded DNA (ssDNA) has been the biopolymer of choice to achieve efficient sorting and assembly of carbon nanotubes, which are structural analogues to BNNTs. Here, we demonstrated a highly efficient aqueous dispersion of BNNTs using (GT)20 ssDNA and the subsequent removal of non-nanotube impurities from dispersions of as-synthesized BNNT material by a membrane filtration approach. The surface coating of BNNTs by DNA creates uniform dispersions at a nanotube concentration of as high as ≈11.5 mass %, leading to the formation of solid aligned films after solvent evaporation without applied shear, therefore demonstrating the first example of BNNT films produced by spontaneous alignment of nanotubes. Our findings provide important insights for producing macroscopic assemblies of aligned BNNT films for potential applications in thermal interface material and electronic and optoelectronic devices.
Antibody mediated CDCP1 degradation as mode of action for cancer targeted therapy (2013)

CUB-domain-containing-protein-1 (CDCP1) is an integral membrane protein whose expression is up-regulated in various cancer types. Although high CDCP1 expression has been correlated with poor prognosis in lung, breast, pancreas, and renal cancer, its functional role in tumor formation or progression is incompletely understood. So far it has remained unclear, whether CDCP1 is a useful target for antibody therapy of cancer and what could be a desired mode of action for a therapeutically useful antibody. To shed light on these questions, we have investigated the cellular effects of a therapeutic antibody candidate (RG7287). In focus formation assays, prolonged RG7287 treatment prevented the loss of contact inhibition caused by co-transformation of NIH3T3 cells with CDCP1 and Src. In a xenograft study, MCF7 cells stably overexpressing CDCP1 reached the predefined tumor volume faster than the parental MCF7 cells lacking endogenous CDCP1. This tumor growth advantage was abolished by RG7287 treatment. In vitro, RG7287 induced rapid tyrosine phosphorylation of CDCP1 by Src, which was accompanied by translocation of CDCP1 to a Triton X-100 insoluble fraction of the plasma membrane. Triggering these effects required bivalency of the antibody suggesting that it involves CDCP1 dimerization or clustering. However, this initial activation of CDCP1 was only transient and prolonged RG7287 treatment induced internalization and down-regulation of CDCP1 in different cancer cell lines. Antibody stimulated CDCP1 degradation required Src activity and was proteasome dependent. Also in three different xenograft models with endogenous CDCP1 expression RG7287 treatment resulted in significant tumor growth inhibition concomitant with substantially reduced CDCP1 levels as judged by immunohistochemistry and Western blotting. Thus, despite transiently activating CDCP1 signaling, the RG7287 antibody has a therapeutically useful mode of action.
3D ISAR Imaging Algorithm Based on Amplitude Monopulse Processing at W Band (2019)

This paper introduces an inverse synthetic aperture radar (ISAR) imaging algorithm for performing high resolution three dimensional (3D) imaging of moving targets at millimeter wave (MMW). The algorithm takes full advantage of the available spatial modalities resulting from an amplitude monopulse antenna configuration designed to operate over the 92-96 GHz band. Using the simulated antenna patterns, this novel ISAR approach accurately estimates the 3D spatial locations of the scatterers in the scene and can operate robustly at relatively low signal-to-noise ratio (SNR) levels. The approach should be broadly useful for generating high resolution imagery in long range MMW monopulse tracking radars.
Global Gene Expression Profiles of <i>Bacillus subtilis</i> Grown under Anaerobic Conditions (2000)

Bacillus subtilis can grow under anaerobic conditions, either with nitrate or nitrite as the electron acceptor or by fermentation. A DNA microarray containing 4,020 genes from this organism was constructed to explore anaerobic gene expression patterns on a genomic scale. When mRNA levels of aerobic and anaerobic cultures during exponential growth were compared, several hundred genes were observed to be induced or repressed under anaerobic conditions. These genes are involved in a variety of cell functions, including carbon metabolism, electron transport, iron uptake, antibiotic production, and stress response. Among the highly induced genes are not only those responsible for nitrate respiration and fermentation but also those of unknown function. Certain groups of genes were specifically regulated during anaerobic growth on nitrite, while others were primarily affected during fermentative growth, indicating a complex regulatory circuitry of anaerobic metabolism.
Terahertz antenna for arrays of hundreds of pixels (2012)

Array technology is currently being applied to terahertz (THz) remote sensing systems to improve sensitivity and scanning speed. An integral component to these arrayed systems is the antenna feed structures since they must satisfy challenging manufacturing requirements to support the high densities and high pixel counts required. This paper reviews the current technologies used for THz antennae and discusses their impediments to arraying. Several new antenna designs are efficiently arrayed are discussed.