gebhart/patrepeval huggingface dataset:
Abstract 14000: miR-322/503 Cluster Drives Cardiac Differentiation by Inhibiting CUG-binding Protein 1 (2014)

Understanding the mechanisms of early cardiac fate determination may lead to better approaches in promoting heart regeneration after injury. MicroRNAs (miRNAs) involved in the process are particularly interesting due to their small profile and relatively shorter path to clinic. With Mesp1 as the marker, we used a Mesp1-Cre/Rosa-EYFP reporter system to track the earliest cardiac progenitors, and identified the miRNAs enriched in these cells. Among them, the miR-322/503 cluster is found to be a powerful regulator of the cardiac program: (1) in a screening of more than 20 CPC-enriched miRNAs, miR-322/503 was the most powerful in driving calcium flux activity in mouse embryonic stem cells (mESCs) differentiation; (2) induced ectopic expression of miR-322/503 to mimic the natural course in mESCs led to α-actinin expression and significant increases of cardiac transcription factors (Tbx5, Mef2C, Nkx2-5 and α-MHC); (3) inhibitors of miR-322 and miR-503 significantly reduced expression of α-actinin and the above cardiac TFs. Remarkably, miR-322/503 regulates the cardiac program by inhibiting an RNA-alternative splicing/decay factor, CUG-binding protein 1 (Celf1), which is also known for a role in myotonic dystrophy pathogenesis. The evidences include (i) miR-322 and miR-503 had a shared target site at 3’UTR of Celf1; (ii) expression patterns of miR-322/503 and Celf1 were mutually exclusive, with the highest Celf1 expression in the brain; (iii) miR-322/503 repressed Celf1 protein expression in a dose-dependent manner; (iv) Celf1-shRNA induced up-regulation of cardiac transcription factors and α-actinin, mimicking the function of miR-322/503; (v) ectopic Celf1 expression repressed expression of cardiac transcription factors, while promoted expressions of early neural markers, including Sox1, Zic1, Nestin and Pax6. In summary, we have identified a miR-322/503-Celf1 pathway that promotes cardiac differentiation by preventing activation of other lineages. This new regulatory mechanism may be used to direct cardiac regeneration after heart injury, and treat myotonic dystrophy where Celf1 up-regulation is responsible for skeletal muscle wasting and other symptoms.
Autoantibodies to the presumptive cytoplasmic domain of platelet glycoprotein IIIa in patients with chronic immune thrombocytopenic purpura [published erratum appears in Blood 1991 Dec 1;78(11):3109] (1991)

Abstract Chronic immune thrombocytopenic purpura (ITP) is an autoimmune disorder due to autoantibodies against platelets that result in their destruction. In some patients, these autoantibodies bind to platelet glycoprotein (GP) IIIa. With the aim of better defining the antigenic epitopes, plasma from 13 selected patients with chronic ITP known to have anti-GPIIb/IIIa autoantibodies was tested for reactivity with nine synthetic peptides corresponding to different regions of the GP IIIa molecule. Of these plasmas, five bound significantly (P less than .001) with either peptide 8 (amino acids 721–744) or peptide 9 (amino acids 742–762), which together form most of the carboxyterminal region presumed to be the cytoplasmic domain. Three of these positive plasmas, were tested further. In two of these positive plasmas, the anti-peptide antibodies represented greater than 80% of the detectable circulating autoantibody. To further evaluate the importance of the carboxyterminal region as an antigenic site, the chronic ITP plasmas were tested against Chinese hamster ovary cells transfected with GPIIb and either whole GPIIIa or GPIIIa lacking amino acids 728 to 762. Ten of the 13 plasmas required the presence of this region for significant autoantibody binding. We conclude that the carboxyterminal region is an important area for stimulating antiplatelet autoantibody formation in some patients with chronic ITP. It is not known whether these autoantibodies to the presumed cytoplasmic domain play an important role in the pathogenesis of the disease or occur as a secondary phenomenon during the course of platelet destruction.
Glycosyltransferases of Small Molecules: Their Roles in Plant Biology (2010)

Abstract Glycosyltransferases are enzymes that transfer sugars from nucleotide sugars to a wide range of small molecule acceptors, from hormones and secondary metabolites to biotic and abiotic chemicals. This alters the hydrophilicity of the acceptors, their stability and chemical properties, their subcellular localization and often their bioactivity. Glycosyltransferases form a large multigene family in the plant kingdom and can be identified by a signature motif in their primary sequence. Considerable progress has been made in understanding the biochemistry of glycosyltransferases and the role of these enzymes in the plant. This article outlines our current knowledge of these enzymes, drawing on information gained from recent in vitro and in planta studies. Key concepts: There is a class of glycosyltransferases (GTs) that transfers sugars to small molecule acceptors. In plants, these acceptors can be natural products such as hormones and secondary metabolites, as well as nonnatural products, such as herbicides and pesticides. Glycosylation changes the properties of the acceptors, increasing water solubility and leading to transport of glycosides from the cytosol. Glycosylation can also affect activity of the acceptors, both in the plant, such as inactivation of hormones and in industrial applications, such as bioactivity and bioavailability.
Surface plasmon optical characterization of lipid monolayers at 5 μm lateral resolution (1990)

Surface plasmon microscopic pictures recorded as a function of the angle of incidence of the coupling laser beam can be quantitatively evaluated and yield optical thicknesses of ultrathin coatings with an areal resolution of 5×5 μm2. This is demonstrated for a lipid monolayer transferred to a solid support in its phase transition region. The coexisting amorphous and crystalline domains can be analyzed simultaneously.
Pore-forming fillers for molten carbonate matrices (1981)

A molten carbonate fuel cell is described including a cathode electrode of electrically conducting or semiconducting lanthanum containing material and an electrolyte containing matrix of an electrically insulating lanthanum perovskite. In addition, in an embodiment where the cathode electrode is LaMnO/sub 3/, the matrix may include LaAlO/sub 3/ or a lithium containing material such as LiAlO/sub 2/ or Li/sub 2/TiO/sub 3/.
Structural basis for germline gene usage of a potent class of antibodies targeting the CD4 binding site of HIV-1 gp120 (2012)

Background:\nA large number of anti-HIV-1 antibodies targeting the\nCD4 binding site (CD4bs) on gp120 have recently been\nreported. These antibodies, typified by VRC01, are\nremarkable for both their breadth and potency. Crystal\nstructures have revealed a common mode of binding for\nseveral of these antibodies; however, the precise relationship\namong CD4bs antibodies remains to be defined.\nMethods:\nWe analyze existing structural and sequence data, propose\na set of signature features for potent VRC01-like\n(PVL) antibodies, and test the importance of these features\nby mutagenesis.\nResults:\nA group of highly potent CD4bs antibodies, previously\nisolated from 5 different individuals, all derive from the\nhuman VH1-2 gene segment and share a set of characteristic\nresidues, including W50, N58, R71, and W100B.\nMutagenesis studies on a half-germline version of a\nVRC01-like antibody confirm that these signature residues\nare critical for gp120 binding. Neutralization assays\nwith viruses mutated at sites that contact these critical\nantibody residues also confirm the significance of these\ninteractions.\nConclusion:\nThe signature features explain why PVL antibodies derive\nfrom a single germ-line human VH gene segment and\nwhy certain gp120 sequences are associated with antibody\nresistance. This analysis also suggests that\nimmunization experiments to elicit VRC01-like antibodies\nmay be problematic in mice or rabbits since they\nlack germ-line VH genes with all the critical residues.\nOur results bear on vaccine development and structure-based\ndesign to improve the potency and breadth of anti-\nCD4bs antibodies.
Uptake of uranium from seawater by amidoxime-based polymeric adsorbent marine testing (2013)

Amidoxime-based polymer adsorbents in the form of functionalized fibers were prepared at the Oak Ridge National Laboratory (ORNL) and screened in laboratory experiments, in terms of uranium uptake capacity, using spiked uranium solution and seawater samples. Batch laboratory experiments conducted with 5-gallon seawater tanks provided equilibrium information. Based on results from 5-gallon experiments, the best adsorbent was selected for field-testing of uranium adsorption from seawater. Flow-through column tests have been performed at different marine sites to investigate the uranium uptake rate and equilibrium capacity under diverse biogeochemistry. The maximum amount of uranium uptake from seawater tests at Sequim, WA, was 3.3 mg U/g adsorbent after eight weeks of contact of the adsorbent with seawater. This amount was three times higher than the maximum adsorption capacity achieved in this study by a leading adsorbent developed by the Japan Atomic Energy Agency (JAEA), which was 1.1 mg U/g adsorbent at equilibrium. The initial uranium uptake rate of the ORNL adsorbent was 2.6 times higher than that of the JAEA adsorbent under similar conditions. A mathematical model derived from the mass balance of uranium was employed to describe the data. (authors)
SU-GG-I-151: Background Subtraction From X-Ray Projection Images Using Prior Information: A Phantom Study (2008)

Purpose: Kilovoltage image guidance is increasingly available for daily imaging in radiotherapy departments. Improving image quality on the projection of a section of the anatomy can be of interest for some imaging techniques. Our purpose is to investigate a proof-of-principle background subtraction technique that improves contrast resolution in x-ray projection images, by isolating the structures belonging to a selected slice of the anatomy, using prior CT information. Method and Materials: we acquired X-ray projection images of a phantom with a CBCT Varian On-Board Imager over a full gantry turn, using a standard CBCT acquisition technique. The CBCT scanner was equipped with antiscatter grid, without a bowtie filter. The dataset was comprised of a reconstructed CBCT image and the set of 2D projections used to reconstruct the CBCT image using the standard FDK algorithm. In the reconstructed CT image we selected sets of slices parallel to the axis of gantry rotation on the CBCT reconstructed images, and obtained a background image by forward projecting the full CBCT image minus the voxels belonging to the selected slice. No denoising was applied to the background image. The background was subtracted from the full projection to give an attenuation map of the selected slices. Results: the background-subtracted X-ray projections of selected slices of the Catphan phantom show a higher contrast than the projections of the full phantom. The CNR of the imaged slices improved by a factor of two with respect to the full projection. Conclusion: Background-subtracted X-ray projection images could show enhanced low contrast resolution when imaging pre-selected slices of a previously imaged anatomy. Investigation supported by NCI grant R01CA117997.
Silk Protein Bioresorbable, Drug‐Eluting Ear Tubes: Proof‐of‐Concept (2019)

Otitis media with effusion (OEM) is a common pediatric pathology treated with topical fluoroquinolones (ear drops) and tympanoplasty tube, also referred to as ear tube, implantation for middle ear drainage. Commercially available ear tubes are fabricated using poly (lactic-co-glycolic acid) synthetic materials that are associated with long-complications due to premature extrusion. Resorbable materials have emerged as desirable alternatives to reduce extrusion-related complications, but often limited by fast resorption rates. Therefore, resorbable tubes with long-term functional integrity are required for future clinical translation. In this communication, a proof-of-concept study is reported on a bioresorbable and drug-eluting silk ear tube device. Preliminary in vitro assessments reveal time-dependent drug elution and antimicrobial properties, while maintaining long-term functional integrity in vivo. This report provides evidence of a silk ear tube with potential for future clinical translation and OEM treatment.
Coal gasification vessel. [Patent application] (1981)

A vessel system comprises an outer shell of carbon fibers held in a binder, a coolant circulation mechanism and control mechanism and an inner shell comprised of a refractory material and is of light weight and capable of withstanding the extreme temperature and pressure environment of, for example, a coal gasification process. The control mechanism can be computer controlled and can be used to monitor and modulate the coolant which is provided through the circulation mechanism for cooling and protecting the carbon fiber and outer shell. The control mechanism is also used to locate any isolated hot spots which may occur through the local disintegration of the inner refractory shell.
Basophil CD203c Levels Are Increased at Baseline and Can Be Used to Monitor Omalizumab Treatment in Subjects with Nut Allergy (2010)

Subjects with nut allergy show an increase of basophil CD203c levels at baseline and following rapid ex vivo stimulation with nut allergen. Both can be reduced by omalizumab therapy. These results highlight the potential of using basophil CD203c levels for baseline diagnosis and therapeutic monitoring in subjects with nut allergy.
Perceptual evaluation of speech quality (PESQ) the new ITU standard for end-to-end speech quality assessment: Part I: Time-delay compensation (2002)

A new model for the perceptual evaluation of speech quality (PESQ) was recently standardized by the International Telecommunications Union as Recommendation P.862. Unlike previous codec assessment models, such as PSQM and MNB (ITU-T P.861), PESQ is able to predict subjective quality with good correlation in a very wide range of conditions, which may include coding distortions, errors, noise, filtering, delay, and variable delay. In Part I time-delay identification techniques are introduced and some causes of variable delay are outlined before the processes that are integrated into PESQ and specified in P.862 are described. More information on the structure of PESQ as well as performance results will be given in Part II.
All‐Dielectric Meta‐Optics for High‐Efficiency Independent Amplitude and Phase Manipulation (2021)

Optical metasurfaces, composed of subwavelength scattering elements, demonstrate remarkable control over the transmitted amplitude, phase, and polarization of light. However, manipulating the amplitude upon transmission, without the use of surface waves, requires loss if a single metasurface is used. Herein, high‐efficiency independent manipulation of the amplitude and phase of a beam is described using two lossless phase‐only metasurfaces separated by a distance. With this configuration, optical components such as combined beam‐forming and splitting devices are experimentally demonstrated, as well as those for forming complex‐valued, 3D holograms. The compound meta‐optic platform provides a promising approach for achieving high‐performance holographic displays and compact optical components, while exhibiting a high overall efficiency.
Generation of PRL-3- and PRL-1-Specific Monoclonal Antibodies as Potential Diagnostic Markers for Cancer Metastases (2005)

Using several approaches, we show that PRL-3- or PRL-1-specific mAbs react only to their respective antigen. The expression of PRL-3 in >10% of primary colorectal cancer samples indicates that PRL-3 may prime the metastatic process. These mAbs will be useful as markers in clinical diagnosis for assessing tumor aggressiveness.
Identification of STAT3 as a substrate of receptor protein tyrosine phosphatase T (2007)

Protein tyrosine phosphatase (PTP) receptor T (PTPRT) is the most frequently mutated PTP in human cancers. However, the cell signaling pathways regulated by PTPRT have not yet been elucidated. Here, we report identification of signal transducer and activator of transcription 3 (STAT3) as a substrate of PTPRT. Phosphorylation of a tyrosine at amino acid Y705 is essential for the function of STAT3, and PTPRT specifically dephosphorylated STAT3 at this position. Accordingly, overexpression of normal PTPRT in colorectal cancer cells reduced the expression of STAT3 target genes. These studies illuminate a mechanism regulating the STAT3 pathway and suggest that this signaling pathway plays an important role in colorectal tumorigenesis.
Manufacture of Clinical-Grade Universal Antigen Presenting Cells (UAPC) for the Ex Vivo Expansion and Activation of Natural Killer (NK) Cells (2018)

Abstract NK cells are potent cellular immunotherapeutic agents against a wide array of human malignancies. Ex vivo expansion of NK cells to achieve clinically relevant numbers must overcome poor in vitro growth kinetics, low starting percentages within the mononuclear cell fraction (especially from autologous donors with active disease), and limited in vivo life span. We targeted three universally critical NK signaling pathways, namely IL-21, 4-1BB, and SLAM family member 4 (SLAMF4), to increase NK cell proliferation and enhance survival. We genetically-engineered HLA-A-ve and -B-ve K562 cells to enforce expression of membrane-bound IL-21 (mbIL21), 4-1BB-L, and CD48, forming a universal antigen presenting cell (UAPC) to generate highly potent clinical-grade umbilical cord blood (CB-NK) or peripheral blood NK cells (PB-NK). While the mbIL21 and 4-1BB signaling nexuses have been utilized previously, we highlight here SLAMF-mediated immunological sculpting of NK cells for clinical applications. SLAMF triggering of co-receptors modulate NK cell activation, in particular through high-avidity interactions between SLAMF4 (2B4/CD244) and its heterophilic, robust affinity, and physiological ligand CD48, a glycosyl-phosphatidyl-inositol (GPI)-anchored cell surface protein. Upon ligand binding and receptor phosphorylation, SLAMF4 recruits PTPN11/SHP-2 and SH2D1A/SAP for downstream signaling, including significant increases in NK cell-mediated cytotoxicity, granule exocytosis, and production of IFN-γ and IL-2. Other than a subset of low surface density expressers from aging subjects consistently associated with inefficient and impaired activating signal transduction, the majority of NK cells express SLAMF4. The functional prominence of SLAMF4, presently recognized as an activating co-receptor, is also evidenced by loss-of-function mutations associated with X-linked lymphoproliferative (XLP) disease. We achieved log-scale expansion of NK cells with UAPC (>1000 fold in 2 weeks), with excellent purity (>99% CD56+ve/CD3−ve and < 1% CD3+ve cells), without indications of senescence/exhaustion, even after 4 weeks of culture. Surface molecular phenotypes of UAPC-expanded CB-NK cells exhibited a phenotype similar to CB-NK cells expanded without SLAMF4. Synergistic signals from IL-21/STAT3, 4-1BB/4-1BBL, and SLAMF4 drive tonic NK propagation, supporting their clinical application. Our novel and clinically accessible platform technology for generation of high purity CB-NKs, a promising source of fresh and cryopreserved allogeneic NK cells, is well-suited for adoptive cancer immunotherapy. Disclosures Champlin: Sanofi: Research Funding; Otsuka: Research Funding. Shpall:Affirmed GmbH: Research Funding. Rezvani:Affirmed GmbH: Research Funding.
Transposition of the <i>Tol2</i> Element, an <i>Ac</i>-Like Element From the Japanese Medaka Fish <i>Oryzias latipes</i>, in Mouse Embryonic Stem Cells (2004)

The Tol2 transposable element of the Japanese medaka fish belongs to the hAT family of transposons including hobo of Drosophila, Ac of maize, and Tam3 of snapdragon. To date, Tol2 is the only natural transposon in vertebrates that has ever been shown to encode a fully functional transposase. It has not been known, however, whether Tol2 can transpose in vertebrates other than fish. We report here transposition of Tol2 in mouse embryonic stem (ES) cells. We constructed a transposon donor plasmid containing a nonautonomous Tol2 element with the neomycin resistance gene and a helper plasmid capable of expressing the transposase and introduced the donor plasmid with various amounts of the helper plasmid by electroporation into mouse ES cells. The number of G418-resistant ES colonies increased as the amount of helper plasmid was increased, in a dose-dependent manner, indicating that the transposase activity elevated the integration efficiency. These G418-resistant ES colonies were cloned and the structure of the junction of the integrated Tol2 element and the genomic DNA was analyzed by inverse PCR. In those clones, Tol2 was surrounded by mouse genomic sequences and an 8-bp direct repeat was created adjacent to both ends of Tol2, indicating that Tol2 was integrated in the genome through transposition. The Tol2 transposon system is thus active in mouse as well as in fish. We propose that it should be used as a genetic tool to develop novel gene transfer, transgenesis, and mutagenesis methods in mammals.
Functional endothelial cells derived from rhesus monkey embryonic stem cells (2003)

We have used rhesus monkey embryonic stem (ES) cells to study endothelial cell development. Rhesus ES cells (R366.4 cell line) exposed to medium containing vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), insulin-like growth factor (IGF), and epidermal growth factor (EGF) assumed a relatively uniform endothelial cell morphology and could be propagated and expanded with a consistent phenotype and normal karyotype. When placed in Matrigel, these rhesus ES cell-derived endothelial cells (RESDECs) formed capillary-like structures characteristic of endothelial cells. Immunohistochemical and flow cytometric analysis of RESDECs showed that they take up acetylated low-density lipoprotein (LDL), express CD146, von Willebrand factor, and the integrin alpha v beta 3, and bind the lectin ulex europaeus agglutinin-1. These cells also express the VEGF receptor Flk-1 and secrete VEGF. When introduced in a Matrigel plug implanted subcutaneously in mice, RESDECs formed intact vessels and recruited new endothelial cell growth. In vivo function was demonstrated by coinjection of RESDECs with murine tumor cells subcutaneously into immunocompromised adult mice. RESDECs injected alone did not form measurable tumors. Tumor cells grew more rapidly and had increased vascularization when coinjected with the RESDECs. Immunohistochemical staining demonstrated that the RESDECs participated in forming the tumor neovasculature. RESDECs provide a novel means to examine the mechanisms of endothelial cell development, and may open up new therapeutic strategies.
Dual-sensor Streamer Increases Data Bandwidth Leading to Improved Penetration and Higher Resolution (2009)

The use of a dual-sensor streamer allows the exact removal of the receiver ghost. The bandwidth of the seismic data is consequently increased, providing better penetration and greater resolution. In addition, seismic velocities and earth attenuation are estimated more accurately. These results are illustrated with case studies from basins worldwide.