gebhart/patrepeval huggingface dataset:
A New Ebola Virus Nonstructural Glycoprotein Expressed through RNA Editing (2011)

Ebola virus (EBOV), an enveloped, single-stranded, negative-sense RNA virus, causes severe hemorrhagic fever in humans and nonhuman primates. The EBOV glycoprotein (GP) gene encodes the nonstructural soluble glycoprotein (sGP) but also produces the transmembrane glycoprotein (GP₁,₂) through transcriptional editing. A third GP gene product, a small soluble glycoprotein (ssGP), has long been postulated to be produced also as a result of transcriptional editing. To identify and characterize the expression of this new EBOV protein, we first analyzed the relative ratio of GP gene-derived transcripts produced during infection in vitro (in Vero E6 cells or Huh7 cells) and in vivo (in mice). The average percentages of transcripts encoding sGP, GP₁,₂, and ssGP were approximately 70, 25, and 5%, respectively, indicating that ssGP transcripts are indeed produced via transcriptional editing. N-terminal sequence similarity with sGP, the absence of distinguishing antibodies, and the abundance of sGP made it difficult to identify ssGP through conventional methodology. Optimized 2-dimensional (2D) gel electrophoresis analyses finally verified the expression and secretion of ssGP in tissue culture during EBOV infection. Biochemical analysis of recombinant ssGP characterized this protein as a disulfide-linked homodimer that was exclusively N glycosylated. In conclusion, we have identified and characterized a new EBOV nonstructural glycoprotein, which is expressed as a result of transcriptional editing of the GP gene. While ssGP appears to share similar structural properties with sGP, it does not appear to have the same anti-inflammatory function on endothelial cells as sGP.
Can ferrohydrodynamic instabilities be useful in transducers? [Instrumentation Notes] (2011)

Magnetic fluids are formed when magnetic particles are dispersed in a carrier liquid and suitably coated [1], [2]. Coating the particles provides an elastic shield which avoids particle friction, and it can be also used to implement bio-assay strategies. There are two types of magnetic fluids: magneto-rheological fluids and ferrofluids. The size of the dispersed particles is what distinguishes the two types of magnetic fluids: magnetorheological fluids containing magnetic particles with a diameter on the order of microns and the fluids change from a liquid to a solid in response to a high magnetic field while ferrofluids are colloidal suspensions of magnetic nanoparticles that maintain their liquid state in the presence of a strong magnetic field. In the case of ferrofluids, the higher the magnetization strength, the greater the magnetic pressure exerted by the fluid [3]. Magnetic fields applied to a ferrofluidic volume and the consequent magnetic force causes the alignment of the ferrofluidic particles in the direction of the field and modifies the viscosity and the control of the ferrofluid mass position. Interest in ferrofluids and magnetic particles exists because of the possibility of efficiently converting valuable elastic energy into mechanical energy in many applications. In this column, we describe some of the uses of ferrofluids and highlight ways to exploit its ferrohydrodynamic instabilities.
Primary structure of rat monoamine oxidase A deduced from cDNA and its expression in rat tissues. (1990)

The cDNA for rat monoamine oxidase A (MAO-A) mRNA was isolated from a liver cDNA library in λ gtll as the cDNA species cross-hybridizing with rat monoamine oxidase B (MAO-B) cDNA. The primary structure of the protein, deduced from the nucleotide sequence, consisted of 526 amino acid residues and its molecular mass was calculated to be 59.6 kD. The amino acid sequence shows about 70% identity with that of rat MAO-B. Northern blot analysis showed that MAO-A mRNA was expressed in various rat tissues and the highest expression was observed in heart. The MAO-B mRNA was quite different from MAO-A mRNA in the tissue-specific expression and liver had the highest level of the mRNA.
Nonplanarity at Tri‐Coordinated Aluminum and Gallium: Cyclic Structures for X<sub>3</sub>H<sub>n</sub><sup>m</sup> (X: B, Al, Ga) (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Phenomenological model for interpreting the clinical significance of the in vitro optical transfer function (1993)

We describe a methodology to predict the outcome of clinical tests caused by changes made to the optical elements of the human eye. This formalism, called the expected visual outcome model, is based on in vitro measurements of the optical transfer function and takes into account a simple model of human threshold performance. The clinical tests under consideration are high-contrast visual acuity and contrast sensitivity. Using the expected visual outcome, we describe a useful performance index called the predicted visual acuity graph, which can be measured clinically. The theoretical results are compared with visual function measured in patients with pseudophakic (multifocal and monofocal) implants.
Impact of speckle on laser range-gated shortwave infrared imaging system target identification performance (2003)

The U.S. Army and the U.S. Air Force are investigating laser range-gated shortwave IR (LRG-SWIR) imaging systems for use in target identification. When coupled to an electron-bombarded CCD, the imaging system can obtain high-resolution images at long ranges. Speckle, an image artifact inherent in laser-illuminated imaging systems, results from interference patterns caused by the coherent illumination. Laser speckle degrades target identification performance but can be reduced by averaging successive LRG-SWIR images. This research is a first attempt at quantifying target identification performance degradation associated with laser speckle. The research begins with a laboratory experiment to verify a speckle model that includes power spectral density and intensity probability density functions. An LRG-SWIR sensor simulation is developed that includes coherent illumination resulting in speckle target images. A field demonstration is performed to verify the fidelity of the simulation. The simulation is then applied to the U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) target identification set with various levels of image averaging and blur. Observer performance results are analyzed in terms of target identification probability and the effects of various levels of blur and speckle are characterized.
Respiratory Syncytial Virus Limits α Subunit of Eukaryotic Translation Initiation Factor 2 (eIF2α) Phosphorylation to Maintain Translation and Viral Replication (2010)

The impact of respiratory syncytial virus (RSV) on morbidity and mortality is significant in that it causes bronchiolitis in infants, exacerbations in patients with obstructive lung disease, and pneumonia in immunocompromised hosts. RSV activates protein kinase R (PKR), a cellular kinase relevant to limiting viral replication (Groskreutz, D. J., Monick, M. M., Powers, L. S., Yarovinsky, T. O., Look, D. C., and Hunninghake, G. W. (2006) J. Immunol. 176, 1733-1740). It is activated by autophosphorylation, likely triggered by a double-stranded RNA intermediate during replication of the virus. In most instances, ph-PKR targets the alpha subunit of eukaryotic translation initiation factor 2 (eIF2alpha) protein via phosphorylation, leading to an inhibition of translation of cellular and viral protein. However, we found that although ph-PKR increases in RSV infection, significant eIF2alpha phosphorylation is not observed, and inhibition of protein translation does not occur. RSV infection attenuates eIF2alpha phosphorylation by favoring phosphatase rather than kinase activity. Although PKR is activated, RSV sequesters PKR away from eIF2alpha by binding of the kinase to the RSV N protein. This occurs in conjunction with an increase in the association of the phosphatase, PP2A, with eIF2alpha following PKR activation. The result is limited phosphorylation of eIF2alpha and continued translation of cellular and viral proteins.
A Liver Level Set (LLS) Algorithm for Extracting Liver's Volume Containing Disconnected Regions Automatically (2008)

In this paper a specified method is presented to facilitate segmentation of liver volume from CT images that contain disconnected regions automatically. The disconnected region appears because the physic of the liver containing multi-lobe structure, thus different lobe make different region in a single slice image. Most of the available liver segmentation algorithms that are based on gray level operation such as thresholding and active contour fail to extract the liver volume from these images automatically. Thus the core of the algorithm is a level set function that has the availability to manage separating and joining liver boundary routinely. The liver level set (LLS) is separated into two stages which a pre-processing stage and a level set with a hybrid energy minimization algorithm. The current slice is initialized by previous segmented liver boundary allowing changes in liver boundary topological changes to be inherited. The result show a respective segmentation with average 85% DCS when comparing with manual segmentation.
Intrusion Detection System Requirements. A Capabilities Description in Terms of the Network Monitoring and Assessment Module of CSAP21 (2000)

This paper presents the intrusion detection and vulnerability scanning capabilities that the authors consider necessary for the U.S. Air Force computer network. These capabilities are described as requirements for the Network Monitoring and Assessment (NMA) module of the Computer Security Assistance Program for the Twenty-First Century (CSAP21) architecture. The advantage of this approach is that it provides a global and comprehensive context in which to describe intrusion detection system (IDS) requirements. The authors have adapted and organized requirements derived from a number of sources, including intrusion monitoring practitioners.
Limits and Opportunities of Big Data For Macro-Prudential Modeling of Financial Systemic Risk (2014)

We explore the use of "big data", i.e. large unstructured data sets, within financial risk analysis. We conclude it has value, but structured data remain critical. We show that forward-looking financial analysis on the systemic level needs a data structure that represents financial contracts as algorithms that produce state contingent cash flows. Currently the industry lacks such a standard, which precludes meaningful systemic forward-looking analysis. We introduce ACTUS as an emerging standard that will enable consistent analysis on all levels. This standard will also create an infrastructure for macro financial analysis.
The Epstein-Barr virus immortalizing protein EBNA-2 is targeted to DNA by a cellular enhancer-binding protein. (1993)

The Epstein-Barr virus nuclear antigen EBNA-2 is essential for Epstein-Barr virus-induced immortalization of B cells. EBNA-2 is a transcriptional activator capable of modifying the expression of specific viral and cellular genes. However, the mechanism of EBNA-2 transactivation has been an enigma. We used a fractionated extract of CA46 lymphoblastoid cells and bacterially expressed EBNA-2 polypeptides to demonstrate that EBNA-2 is targeted to the Epstein-Barr virus latency C promoter (Cp) through interaction with a cellular DNA binding protein designated Cp binding factor 1 (CBF1). A glutathione S-transferase-EBNA-2 fusion protein containing aa 252-425 of EBNA-2 interacted with CBF1 to yield a slowly migrating complex in an electrophoretic mobility shift assay. Mutation of EBNA-2 aa 323 and 324, which lie within a highly conserved amino acid motif, abolished the interaction with CBF1. This same mutation also abolished the ability of EBNA-2 to activate the Cp in a cotransfection assay. The binding site for CBF1 was localized to residues -359 to -388 of the Cp by using an electrophoretic mobility shift assay and DNase I footprinting. Introduction of multiple copies of the CBF1 binding site upstream of a minimal heterologous promoter conferred EBNA-2 responsiveness on that promoter. Mutation of a core sequence CNGTGGGAA abolished CBF1 binding, and the mutated sequence was unable to mediate EBNA-2 transactivation. The CBF1 core sequence also occurs in other EBNA-2-responsive promoters suggesting that CBF1 may mediate EBNA-2 transactivation of both cellular and viral targets.
Pain Management Via Local Anesthetics and Responsive Hydrogels (2015)

Acute and chronic pain control is a significant clinical challenge that has been largely unmet. Local anesthetics are widely used for the control of post-operative pain and in the therapy of acute and chronic pain. While a variety of approaches are currently used to prolong the duration of action of local anesthetics, an optimal strategy to achieve neural blockage for several hours to days with minimal toxicity has yet to be identified. Several drug delivery systems such as liposomes, microparticles and nanoparticles have been investigated as local anesthetic delivery vehicles to achieve prolonged anesthesia. Recently, injectable responsive hydrogels raise significant interest for the localized delivery of anesthetic molecules. This paper discusses the potential of injectable hydrogels to prolong the action of local anesthetics.
Highly Efficient Solvent‐Free Condensation of Carboxylic Acids with Alcohols Catalysed by Zinc Perchlorate Hexahydrate, Zn(ClO<sub>4</sub>)<sub>2</sub>⋅6 H<sub>2</sub>O (2005)

Abstract Zinc perchlorate hexahydrate, Zn(ClO 4 ) 2 ⋅6 H 2 O, efficiently catalyses the esterification between nearly equimolar amounts of carboxylic acids and alcohols. The reaction works under solvent‐free conditions at relatively low temperatures. Excellent results were obtained with a wide range of substrates.
Postproduction Processing of Electrospun Fibres for Tissue Engineering (2012)

Electrospinning is a commonly used and versatile method to produce scaffolds (often biodegradable) for 3D tissue engineering.(1, 2, 3) Many tissues in vivo undergo biaxial distension to varying extents such as skin, bladder, pelvic floor and even the hard palate as children grow. In producing scaffolds for these purposes there is a need to develop scaffolds of appropriate biomechanical properties (whether achieved without or with cells) and which are sterile for clinical use. The focus of this paper is not how to establish basic electrospinning parameters (as there is extensive literature on electrospinning) but on how to modify spun scaffolds post production to make them fit for tissue engineering purposes--here thickness, mechanical properties and sterilisation (required for clinical use) are considered and we also describe how cells can be cultured on scaffolds and subjected to biaxial strain to condition them for specific applications. Electrospinning tends to produce thin sheets; as the electrospinning collector becomes coated with insulating fibres it becomes a poor conductor such that fibres no longer deposit on it. Hence we describe approaches to produce thicker structures by heat or vapour annealing increasing the strength of scaffolds but not necessarily the elasticity. Sequential spinning of scaffolds of different polymers to achieve complex scaffolds is also described. Sterilisation methodologies can adversely affect strength and elasticity of scaffolds. We compare three methods for their effects on the biomechanical properties on electrospun scaffolds of poly lactic-co-glycolic acid (PLGA). Imaging of cells on scaffolds and assessment of production of extracellular matrix (ECM) proteins by cells on scaffolds is described. Culturing cells on scaffolds in vitro can improve scaffold strength and elasticity but the tissue engineering literature shows that cells often fail to produce appropriate ECM when cultured under static conditions. There are few commercial systems available that allow one to culture cells on scaffolds under dynamic conditioning regimes--one example is the Bose Electroforce 3100 which can be used to exert a conditioning programme on cells in scaffolds held using mechanical grips within a media filled chamber.(4) An approach to a budget cell culture bioreactor for controlled distortion in 2 dimensions is described. We show that cells can be induced to produce elastin under these conditions. Finally assessment of the biomechanical properties of processed scaffolds cultured with or without cells is described.
Use of High Specific Activity StarFire™ Oligonucleotide Probes to Visualize Low-Abundance Pre-mRNA Splicing Intermediates in <i>S. pombe</i> (2000)

An oligonucleotide labeling system was developed that can produce radiolabeled hybridization probes with tenfold or more higher specific activity than is obtained by traditional 5'-end-labeling with polynucleotide kinase. Yet the system is as rapid and simple as kinase labeling. The reaction uses the Klenow fragment of E. coli DNA polymerase to add alpha-32P-dA residues to the 3'-end of an oligonucleotide in a primer-extension reaction. Unlike other methods of radioactive tailing (e.g., terminal transferase), a single species is produced of both known length and known specific activity. The reaction is efficient, and over 90% of probe molecules are routinely labeled. Using this method of labeling, an oligonucleotide was shown to be tenfold more sensitive in detecting target DNA sequences in a dot blot hybridization assay, compared to the same oligonucleotide labeled using polynucleotide kinase. Northern blots of Schizosaccharomyces pombe RNA were probed with an oligonucleotide specific for intron 1 of the tf2d gene, a TATA-box binding transcription factor. Kinase-labeled tf2d probe detected only unspliced RNA, while the same oligonucleotide labeled using the new method detected both unspliced tf2d RNA and rare pre-mRNA splicing intermediates.
A 3D laser and vision based classifier (2009)

This paper presents a method for modelling semantic content in scenes, in order to facilitate urban driving. More specifically, it presents a 3D classifier based on Velodyne data and monocular color imagery. The system contains two main components: a ground model and an object model. The ground model is a novel extension of elevation maps using Conditional Random Fields. It allows estimation of ground type (grass vs. asphalt) in addition to modelling the geometry of the scene. The object model involves two segmentation procedures. The first is a novel extension of elevation maps to a hierarchical clustering algorithm. The second is a new algorithm for defining regions of interest in images, which reasons jointly in the 3D Cartesian frame and the image plane. These two procedures provide a segmentation of the objects in the 3D laser data and in the images. Based on the resulting segmentation, object classification is implemented using a rule based system to combine binary deterministic and probabilistic features. The overall 3D classifier is tested on logs acquired by the MIT Urban Grand Challenge 2007 vehicle. The classifier achieves an accuracy of 89% on a set of 500 scenes involving 16 classes. The proposed approach is evaluated against seven other standard classification algorithms, and is shown to produce superior performance.
Wide-band superconducting coplanar delay lines (2005)

Two 25-ns high-temperature superconductor delay lines with novel double-spiral meander line structures were fabricated and measured, one based on the conventional coplanar waveguide (CPW) and the other based on the conductor-backed CPW. Compared with other published studies, the performance of the Conductor-backed CPW delay line is among the best in terms of the widest resonance-free band (2-18 GHz), low insertion loss (0.06 dB/ns at 60 K and 10 GHz), small ripple (<1 dB up until 16 GHz), and small dispersion (<2 ns in the variation of group delay between 2-18 GHz). This is also the first coplanar delay line successfully demonstrated without using wire bonding. The reflecting elements in the delay lines were identified through time-domain measurements. Full-wave simulations were performed to compare the double-spiral meander-line structure with conventional double-spiral line, and to identify the geometric factors restricting the bandwidth of the double-spiral meander line.
Air pollution and respiratory health. (1983)

Air pollution is frequently incriminated as a risk factor in the development of chronic lung impairment and in the aggravation of existing disease. The federal government has set primary air quality standards to protect public health and secondary standards to protect public welfare (eg, to preserve vegetation and buildings). Much of the debate surrounding the development and evaluation of air standards focuses on the diseases of patients with whom the respiratory care practitioner has daily contact. We review the legislative efforts to protect the public from the effects of air pollution and provide insight into some of the scientific and medical dilemmas involved in this current public health issue.
A toll-like receptor agonist mimicking microbial signal to generate tumor-suppressive macrophages (2019)

Switching macrophages from a pro-tumor type to an anti-tumor state is a promising strategy for cancer immunotherapy. Existing agents, many derived from bacterial components, have safety or specificity concerns. Here, we postulate that the structures of the bacterial signals can be mimicked by using non-toxic biomolecules of simple design. Based on bioactivity screening, we devise a glucomannan polysaccharide with acetyl modification at a degree of 1.8 (acGM-1.8), which specifically activates toll-like receptor 2 (TLR2) signaling and consequently induces macrophages into an anti-tumor phenotype. For acGM-1.8, the degree of acetyl modification, glucomannan pattern, and acetylation-induced assembly are three crucial factors for its bioactivity. In mice, intratumoral injection of acGM-1.8 suppresses the growth of two tumor models, and this polysaccharide demonstrates higher safety than four classical TLR agonists. In summary, we report the design of a new, safe, and specific TLR2 agonist that can generate macrophages with strong anti-tumor potential in mice.
Novel Terpenoids from the West Indian Sea Whip <i>Pseudopterogorgia elisabethae</i> (Bayer). Elisapterosins A and B:  Rearranged Diterpenes Possessing an Unprecedented Cagelike Framework<sup>1</sup> (2000)

Four diterpenes and a nor-diterpenoid, all of which possess unusual carbocyclic skeletons, were isolated from the hexane solubles of the West Indian gorgonian Pseudopterogorgia elisabethae. The structures and relative configurations of novel metabolites elisabethin D (2), elisabethin D acetate (3), 3-epi-elisabanolide (5), elisapterosin A (6), and elisapterosin B (7) were elucidated by interpretation of overall spectral data, which included 2D NMR correlation methods, IR, UV, and accurate mass measurements (HREI-MS and HRFAB-MS), chemical reactions, and X-ray diffraction analyses. The tetracyclic carbon skeleton of the elisapterosins is undescribed and constitutes a new class of C(20) rearranged diterpenes. Elisapterosin B displays strong in vitro anti-tuberculosis activity.