gebhart/patrepeval huggingface dataset:
Identification of novel circulatory microRNA signatures linked to patients with ischemic stroke (2018)

MicroRNAs (miRNAs) are involved in growth, development, and occurrence and progression of many diseases. MiRNA-mediated post-transcriptional regulation is poorly understood in vascular biology and pathology. The purpose of this is to determine circulatory miRNAs as early detectable peripheral biomarkers in patients with ischemic stroke (IS). MiRNAs expression levels were measured in IS serum samples and healthy controls using Illumina deep sequencing analysis and identified differentially expressed miRNAs. Differentially expressed miRNAs were further validated using SYBR-green-based quantitative real-time PCR (qRT-PCR) assay in postmortem IS brains, lymphoblastoid IS cell lines, oxygen and glucose deprivation/reoxygenation -treated human and mouse neuroblastoma cells, and mouse models of hypoxia and ischemia (HI)-induced stroke. A total of 4656 miRNAs were differentially expressed in IS serum samples relative to healthy controls. Out of 4656 miRNAs, 272 were found to be significantly deregulated in IS patients. Interestingly, we found several novel and previously unreported miRNAs in IS patients relative to healthy controls. Further analyses revealed that some candidate miRNAs and its target genes were involved in the regulation of the stroke. To the best of our knowledge, this is the first study identified potential novel candidate miRNAs in IS serum samples from the residents of rural West Texas. MiRNAs identified in this study could potentially be used as a biomarker and the development of novel therapeutic approaches for stroke. Further studies are necessary to better understand miRNAs-regulated stroke cellular changes.
Safety and Immunogenicity of a Proteosome- <i>Shigella flexneri</i> 2a Lipopolysaccharide Vaccine Administered Intranasally to Healthy Adults (2001)

We studied the safety and immunogenicity of a Shigella flexneri 2a vaccine comprising native S. flexneri 2a lipopolysaccharide (LPS) complexed to meningococcal outer membrane proteins-proteosomes-in normal, healthy adults. A two-dose series of immunizations was given by intranasal spray, and doses of 0.1, 0.4, 1.0, and 1.5 mg (based on protein) were studied in a dose-escalating design. The vaccine was generally well tolerated. The most common reactions included rhinorrhea and nasal stuffiness, which were clearly dose related (P < or = 0.05). These reactions were self-limited and generally mild. The vaccine elicited S. flexneri 2a LPS-specific immunoglobulin A (IgA), IgG, and IgM antibody-secreting cells (ASCs) in a dose-responsive manner. At doses of 1.0 or 1.5 mg, highly significant (P < 0.001) increases in ASCs of all antibody isotypes occurred and 95% of subjects had an ASC response in at least one antibody isotype. Dose-related serum antibody responses were observed, with geometric mean two- to fivefold rises in specific serum IgA and IgG titers and two- to threefold rises in IgM in the 1.0- and 1.5-mg-dose groups (P < 0.0001 for each isotype). Elevated serum antibody levels persisted through day 70. Increases in fecal IgG and IgA and also in urinary IgA specific for S. flexneri 2a LPS were demonstrated. These were most consistent and approached statistical significance (P = 0.02 to 0.12 for various measures) on day 70 after the first dose. The magnitude of immune responses to intranasally administered proteosome-S. flexneri 2a LPS vaccine is similar to those reported for live vaccine candidates associated with protective efficacy in human challenge models, and further evaluation of this product is warranted.
Detecting deception in the brain: a functional near-infrared spectroscopy study of neural correlates of intentional deception (2005)

Little is known about the neurological underpinnings of deliberate deception. Recent advances in the detection of deception have examined brain responses during experimental deception protocols. A consensus has begun to emerge across the handful of functional magnetic resonance imaging (fMRI) studies that have examined deception implicating areas of the dorsolateral and inferior prefrontal cortex as active during deliberate deception. The purpose of the current study was to determine the utility of functional near-infrared spectroscopy (fNIR), a neuroimaging technique that allows reasonable ecological utility, for the detection of deception. Using a modified version of the Guilty Knowledge Task, participants attempted to conceal the identity of a playing card they were holding while dorsolateral and inferior frontal cortices were monitored with fNIR. The results revealed increased activation in bilateral inferior frontal gyri (BA 47/45) and middle frontal gyri (BA 46/10) when participants were lying. The results provide evidence that inferior and middle prefrontal cortical areas are associated at least some forms of deliberate deception. fNIR has the potential to provide a field-deployable brain-based method for the detection of deception.
Filter Paper Blood Spot Assay of Human Insulin-Like Growth Factor I (IGF-I) and IGF-Binding Protein-3 and Preliminary Application in the Evaluation of Growth Hormone Status (1998)

To facilitate broader applications of insulin-like growth factor I (IGF-I) and IGF-binding protein-3 (IGFBP-3) analysis, we developed procedures for their measurements in extracts of whole blood dried on filter paper. A single 8-mm diameter filter paper disc containing about 13 microL blood was used. IGFBP-3 was efficiently extracted in a buffer within 1 h of incubation. IGF-I extraction involved incubation in buffer followed by acidification and neutralization steps. Blood spot assays showed intra- and interassay coefficients of variation (including interspot variations) of 5.4-16.7% for IGF-I and 6.6-11.7% for IGFBP-3; recoveries were 97 +/- 7.1% and 101 +/- 8.7%, respectively. Recoveries of IGF-I and IGFBP-3 in response to 4- to 8-fold variations in extraction buffer volume were 97 +/- 8.2% and 107 +/- 6.1%, respectively. Dried blood spot IGF-I and IGFBP-3 showed greater than 1-month stability at -20 C, 4 C, and room temperature and retained more than 65% of the immunoreactivity after approximately 1 month at 37 C. Both IGF-I and IGFBP-3 were contained within the plasma fraction of whole blood, and variations (mean +/- SD) in IGF-I (204 +/- 29 micrograms/L) and IGFBP-3 (4.4 +/- 0.48 mg/L) measured in extracts of dried blood spot with adjusted hematocrit of 0.2-0.62 were acceptable. IGF-I and IGFBP-3 in paired plasma and dried blood spot extracts of random samples (n = 46) showed excellent correlation (r > 0.94) with slopes of near unity. Compared to conventional methods, the filter paper procedures were equally effective in distinguishing IGF-I and IGFBP-3 levels in untreated GH receptor-deficient (n = 11) and age-matched normal controls (n = 16). We conclude that blood collected on filter paper is ideal for IGF-I and IGFBP-3 analysis and may find applications in pediatric and large scale infant screening programs.
A multi-resolution multi-size-windows disparity estimation approach (2011)

This paper describes an algorithm for estimating the disparity between 2 images of a stereo pair. The disparity is related to the depth of the objects in the scene. Being able to obtain the depth of the objects in the scene is useful in many applications such as virtual reality, 3D user interfaces, background-foreground segmentation, or depth-image-based synthesis. This last application has motivated the proposed algorithm as part of a system that estimates disparities from a stereo pair and synthesizes new views. Synthesizing virtual views enables the post-processing of 3D content to adapt to user preferences or viewing conditions, as well as enabling the interface with multi-view auto-stereoscopic displays. The proposed algorithm has been designed to fulfill the following constraints: (a) low memory requirements, (b) local and parallelizable processing, and (c) adaptability to a sudden reduction in processing resources. Our solution uses a multi-resolution multi-size-windows approach, implemented as a line-independent process, well-suited for GPU implementation. The multi-resolution approach provides adaptability to sudden reduction in processing capabilities, besides computational advantages; the windows-based image processing algorithm guarantees low-memory requirements and local processing.
Intervals: the connection between computing and the world (2002)

Floating-point arithmetic per se is fundamentally disconnected from computing in science and engineering, and from mathematics, itself. With interval data types, floating-point numbers can be used to establish the required connection. This connection is becoming increasingly important as computers are used to produce answers to fundamentally new questions. Intrinsic compiler support for interval data types from Sun Microsystems Inc. provide the first support for intervals with which commercial interval applications can be developed. The following topics are briefly discussed: Innovations introduced in compiler support for intervals; open questions; and the outlook for computing with intervals.
Treatment of Cytomegalovirus Retinitis With Cytomegalovirus-Specific T-Lymphocyte Infusion (2015)

Cytomegalovirus (CMV) retinitis is a potentially blinding infection that affects immunocompromised patients who are unable to generate a T-cell response against the organism. Infusion of CMV-specific leukocytes has been shown to be effective in patients with systemic CMV infection, especially those resistant to standard therapies. The authors report a case of a patient with CMV viremia with progressive retinitis in whom infusion of third-party donor-derived CMV pp65-specific T cells alone prompted resolution of CMV retinitis. This case suggests a potential role for CMV-specific leukocyte infusion in the treatment of CMV retinitis, especially in cases resistant or refractory to antiviral therapies.
Development of semiconductor detectors for fast neutron radiography (2001)

A high-energy neutron detector has been developed using a semiconductor diode fabricated from bulk gallium arsenide wafers with a polyethylene neutron converter layer. Typical thickness of the diode layer is 250 to 300 μm with bias voltages of 30 to 150 volts. Converter thicknesses up to 2030 μm have been tested. GaAs neutron detectors offer many advantages over existing detectors including positional information, directional dependence, gamma discrimination, radiation hardness, and spectral tailoring. Polyethylene-coated detectors have been shown to detect 14 MeV neutrons directly from a D-T neutron generator without interference from gamma rays or scattered neutrons. An array of small diode detectors can be assembled to perform fast neutron radiography with direct digital readout and real-time display of the image produced. In addition, because the detectors are insensitive to gamma rays and low energy neutrons, highly radioactive samples (such as spent nuclear fuel or transuranic waste drums) could be radiographed.
UV Fluorescent Epoxy Adhesives from Noncovalent and Covalent Incorporation of Coumarin Dyes (2017)

Epoxies are commonly used in art conservation as adhesives for artifact reconstruction and repair. However, with the development of colorless epoxies, it has become more difficult to detect repair work. Fluorescent epoxies would allow for easy detection of the epoxy joints by simple visual inspection under UV light while remaining unnoticeable under normal display lighting. Coumarins are natural dyes that can be added in very small amounts to make thermosets fluoresce. Depending on the functionality of the coumarin used, the dye may be physically encapsulated in the cross-linked polymer or it may be bound to the polymer through covalent bonds. In this paper, we examine the efficacy of coumarin (1) and coumarin 480 (2) as physically encapsulated dyes and 7-hydroxycoumarin (3) and 7-glycidyloxycoumarin (4) as covalently bound dyes in a commercial epoxy thermoset, Epo-Tek 301. All four dyes could be used to make the epoxy fluorescent, but coumarins 1 and 2 slightly reduced the lap shear strength of the thermoset and could be extracted with solvent. In contrast, coumarins 3 and 4 had little effect on the mechanical properties of the epoxy and only minute amounts could be extracted.
<title>Application of Rietveld analysis to crystal structures of titanyl phthalocyanine</title> (1992)

This paper discusses the use of Rietveld analysis to solve crystal structures of titanyl phthalocyanines. Rietveld analysis is based on whole pattern fitting in which every point in the x-ray powder diffraction pattern is used as a measure of one or more Bragg diffraction peaks. Thus the refinement of relatively complicated crystal structures from x-ray patterns containing a relatively small number of resolved diffraction peaks is enabled. Various profile-fitting functions used in Rietveld analysis were parameterized and tested against known crystal structures of type I and type II titanyl phthalocyanine. It was found that a split Pearson VII function was found to best correct for preferred orientation effects observed in the x-ray patterns. The final goodness-of-fit parameters were R(Bragg) equals 0.17 and 0.13 for type I and type II structures, respectively. A computer program was used to generate several unit cells for type IV titanyl phthalocyanine. These unit cells were tested by stereochemical packing analysis to first determine which unit cells allowed for good intermolecular packing arrangements. Energy minimized models were then used as phasing models for Rietveld refinement. A triclinic structure with space group P-1 having an x-ray goodness-of-fit parameter R(Bragg) equals 0.24 was proposed as the most probable crystal structure for type IV titanyl phthalocyanine. The unit cell parameters are a equals 1.083 nm, b equals 1.312 nm, c equals 0.996 nm, alpha equals 72.28 degrees, beta equals 77.25 degrees and gamma equals 104.48 degrees. There are two molecules in the unit cell related by a center of inversion.© (1992) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Assessing risk of fibrosis progression and liver-related clinical outcomes among patients with both early stage and advanced chronic hepatitis C (2017)

Accurate assessments for risk of clinical outcomes can be obtained using routinely collected data across a heterogeneous cohort of patients with CHC. These methods can be applied to predict risk of progression in other chronic liver diseases.
Extraordinary Corrosion Protection from Polymer–Clay Nanobrick Wall Thin Films (2018)

Metals across all industries demand anticorrosion surface treatments and drive a continual need for high-performing and low-cost coatings. Here we demonstrate polymer-clay nanocomposite thin films as a new class of transparent conformal barrier coatings for protection in corrosive atmospheres. Films assembled via layer-by-layer deposition, as thin as 90 nm, are shown to reduce copper corrosion rates by >1000× in an aggressive H<sub>2</sub>S atmosphere. These multilayer nanobrick wall coatings hold promise as high-performing anticorrosion treatment alternatives to costlier, more toxic, and less scalable thin films, such as graphene, hexavalent chromium, or atomic-layer-deposited metal oxides.
Reconstitution of the Human Endothelial Cell Protein C Receptor with Thrombomodulin in Phosphatidylcholine Vesicles Enhances Protein C Activation (1999)

Blocking protein C binding to the endothelial cell protein C receptor (EPCR) on the endothelium is known to reduce protein C activation rates. Now we isolate human EPCR and thrombomodulin (TM) and reconstitute them into phosphatidylcholine vesicles. The EPCR increases protein C activation rates in a concentration-dependent fashion that does not saturate at 14 EPCR molecules/TM. Without EPCR, the protein C concentration dependence fits a single class of sites (Km = 2.17 +/- 0.13 microM). With EPCR, two classes of sites are apparent (Km = 20 +/- 15 nM and Km = 3.2 +/- 1.7 microM). Increasing the EPCR concentration at a constant TM concentration increases the percentage of high affinity sites. Holding the TM:EPCR ratio constant while decreasing the density of these proteins results in a decrease in the EPCR enhancement of protein C activation, suggesting that there is little affinity of the EPCR for TM. Negatively charged phospholipids also enhance protein C activation. EPCR acceleration of protein C activation is blocked by anti-EPCR antibodies, but not by annexin V, whereas the reverse is true with negatively charged phospholipids. Human umbilical cord endothelium expresses approximately 7 times more EPCR than TM. Anti-EPCR antibody reduces protein C activation rates 7-fold over these cells, whereas annexin V is ineffective, indicating that EPCR rather than negatively charged phospholipid provide the surface for protein C activation. EPCR expression varies dramatically among vascular beds. The present results indicate that the EPCR concentration will determine the effectiveness of the protein C activation complex.
Direct sequence OCDMA systems based on fibre grating technology (2005)

Fibre Bragg grating technology enables all-optical encoding and decoding of short pulses at ultrafast chip rates. Such code sequences can be used to implement both all-optical code division multiple access and packet switched systems operating at Gbit/s data rates. (4 pages)
Photonic bandgap fibers (2003)

Photonic bandgap fibers are described using a new Kagome cladding structure. These fibers may potentially guide light in low-index regions. Such fibers offer new dispersion properties, and large design flexibility.
Optimal Design of District Metered Areas in Water Distribution Networks (2014)

The paper presents a multi-objective approach for the automatic partitioning of a water distribution network into District Metering Areas (DMAs). In the proposed methodology, both technical and economic issues are considered, including reduction of water leakages due to pressure management and energy production achievable through the use of turbines. The optimization approach is based on a clear explanation of the objective functions, whose structures are defined with the aim of providing full control to the decision-maker. Concepts from graph theory and cluster analysis methods are combined in a three-step algorithm, which can be easily implemented for software use.
Substituted Bridged Phenyl Piperidines: Orally Active Growth Hormone Secretagogues. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Roentgenology of myofibrogranuloma in walleye, <i>Stizostedion vitreum</i> (1993)

Myofibrogranuloma, a muscle degeneration known only in walleye, Stizostedion vitreum, could not until now be recognized without filleting the fish. Muscle in advanced stages of degeneration shows pronounced granuloma formation, and an increase in calcium concentration (X-ray density) compared with normal tissue is associated with such myopathy. Using X-rays and various anatomical combinations of skin, fillet, and vertebral column, myofibrogranuloma could be recognized in several anatomical combinations.
Live-Attenuated Respiratory Syncytial Virus Vaccine With Deletion of RNA Synthesis Regulatory Protein M2-2 and Cold Passage Mutations Is Overattenuated (2019)

RSV LIDcpΔM2-2 is overattenuated. <b>Clinical Trial Numbers. </b>NCT02890381, NCT02948127.
Determining the contents of protein and amino acids in peanuts using near‐infrared reflectance spectroscopy (2012)

NIRS combined with multivariate calibration has significant potential in determining the protein and amino acid contents of peanuts. This method is suitable for use in an industrial setting owing to its ease of use as well as the relatively low cost of obtaining and running the necessary equipment.
Synthesis and Evaluation of Novel Cyclic Peptide Inhibitors of Lysine-Specific Demethylase 1 (2013)

Lysine specific demethylase 1 (LSD1) selectively removes methyl groups from mono- and dimethylated histone 3 lysine 4 (H3K4), resulting in gene silencing. LSD1 is overexpressed in many human cancers, resulting in aberrant silencing of tumor suppressor genes. Thus, LSD1 is a validated target for the discovery of antitumor agents. Using a ligand-based approach, we designed and synthesized a series of cyclic and linear peptides that are effective inhibitors of LSD1. Linear peptide 7 and cyclic peptide 9 inhibited LSD1 in vitro by 91 and 94%, respectively, at a concentration of 10 μM. Compound 9 was a potent LSD1 inhibitor (IC50 2.1 μM; K i 385 nM) and had moderate antitumor activity in the MCF-7 and Calu-6 cell lines in vitro. Importantly, 9 is significantly more stable to hydrolysis in rat plasma than the linear analogue 7. The cyclic peptides described herein represent important lead structures in the search for inhibitors of flavin-dependent histone demethylases.
<title>Statistical intensity correction and segmentation of MRI data</title> (1994)

Many applications of MRI are facilitated by segmenting the volume spanned by the imagery into the various tissue types that are present. Intensity-based classification of MR images has proven to be problematic, even when advanced techniques such as non- parametric multi-channel methods are used. A persistent difficulty has been accommodating the spatial intensity inhomogeneities that are due to the equipment. This paper describes a statistical method that uses knowledge of tissue properties and intensity inhomogeneities to correct for these intensity inhomogeneities. Use of the Expectation-Maximization algorithm leads to a method (EM segmentation) for simultaneously estimating tissue class and the correcting gain field. The algorithm iterates two components to convergence: tissue classification, and gain field estimation. The result is a powerful new technique for segmenting and correcting MR images. An implementation of the method is discussed, and results are reported for segmentation of white matter and gray matter in gradient-echo and spin-echo images. Examples are shown for axial, coronal and sagittal (surface coil) images. For a given type of acquisition, intensity variations across patients, scans, and equipment have been accommodated without manual intervention in the segmentation. In this sense, the method is fully automatic for segmenting healthy brain tissue. An accuracy assessment was made in which the method was compared to manual segmentation, and to a method based on supervised multi-variate classification, in segmenting white matter and gray matter. The method was found to be consistent with manual segmentation, and closer to manual segmentation than the supervised method.
Session Initiation Protocol (SIP) Extensions for Blocking VoIP Spam Using PSTN Validation (2010)

Verification Involving PSTN Reachability (ViPR) is a new technique for
inter-domain federation of SIP calls. ViPR makes use of a the PSTN as
an introduction mechanism to verify the correctness of mappings from
phone numbers to domains. The PSTN introduction mechanism can also be
used as a techqnique for blocking spam - a SIP caller is only
authorized when they're calling domain has previously called that
same number over the PSTN. This document describes an extension to SIP
which enables authorization of SIP calls based on a prior PSTN
introduction.
Genome Sequence of SG33 Strain and Recombination between Wild-Type and Vaccine Myxoma Viruses (2011)

Myxomatosis in Europe is the result of the release of a South America strain of myxoma virus in 1952. Several attenuated strains with origins in South America or California have since been used as vaccines in the rabbit industry. We sequenced the genome of the SG33 myxoma virus vaccine strain and compared it with those of other myxoma virus strains. We show that SG33 genome carries a large deletion in its right end. Furthermore, our data strongly suggest that the virus isolate from which SG33 is derived results from an in vivo recombination between a wild-type South America (Lausanne) strain and a California MSD-derived strain. These findings raise questions about the use of insufficiently attenuated virus in vaccination.