gebhart/patrepeval huggingface dataset:
Three Protein Cocktails Mediate Delayed-Type Hypersensitivity Responses Indistinguishable from That Elicited by Purified Protein Derivative in the Guinea Pig Model of<i>Mycobacterium tuberculosis</i>Infection (2010)

Purified protein derivative (PPD) is a widely used reagent for the diagnosis of Mycobacterium tuberculosis infection. Recently, the molecular composition of PPD was defined, with hundreds of mycobacterial protein representatives making up PPD. Which, if any, of these specific products drive the potency of PPD remains in question. In this study, two proteins (DnaK and GroEL2) previously identified as dominant proteins in PPD were tested for the capacity to induce delayed-type hypersensitivity (DTH) responses in H37Rv-infected or BCG-vaccinated guinea pigs. These two proteins were used in pull-down assays to identify interacting PPD products. Six proteins were identified as interacting partners with DnaK and GroEL2, i.e., Rv0009, Rv0475, Rv0569, Rv0685, Rv2626c, and Rv2632c. These six proteins were tested alone and in combination with DnaK and GroEL2 for the capacity to induce a DTH response in the guinea pig model. From these studies, two cocktails, DnaK/GroEL2/Rv0009 and DnaK/GroEL2/Rv0685, were found to induce DTH responses in H37Rv-infected or BCG-vaccinated guinea pigs that were indistinguishable from DTH responses driven by a PPD injection. The mechanism by which DTH responses were induced was elucidated by histologic examination, analysis of activated CD4(+)/CD8(+) T cells, and cytokine mRNA expression at the site of the DTH response. PPD and the protein cocktails tested induced strong DTH responses in H37Rv-infected guinea pigs. Ex vivo phenotyping of T cells at the DTH site indicated that this response is mediated by activated CD4(+) and CD8(+) T cells, with increases in gamma interferon and tumor necrosis factor alpha, but not interleukin-10, at the site of the DTH response. Our results demonstrate for the first time that the PPD response can be mimicked at the molecular level with defined protein cocktails. The use of this defined product will allow a more thorough understanding of the DTH response and may provide a platform for more rapid and sensitive second-generation skin test reagents for the diagnosis of M. tuberculosis infection.
Mechanism of Action and Clinical Application of Tafamidis in Hereditary Transthyretin Amyloidosis (2016)

Transthyretin (TTR) transports the retinol-binding protein-vitamin A complex and is a minor transporter of thyroxine in blood. Its tetrameric structure undergoes rate-limiting dissociation and monomer misfolding, enabling TTR to aggregate or to become amyloidogenic. Mutations in the TTR gene generally destabilize the tetramer and/or accelerate tetramer dissociation, promoting amyloidogenesis. TTR-related amyloidoses are rare, fatal, protein-misfolding disorders, characterized by formation of soluble aggregates of variable structure and tissue deposition of amyloid. The TTR amyloidoses present with a spectrum of manifestations, encompassing progressive neuropathy and/or cardiomyopathy. Until recently, the only accepted treatment to halt progression of hereditary TTR amyloidosis was liver transplantation, which replaces the hepatic source of mutant TTR with the less amyloidogenic wild-type TTR. Tafamidis meglumine is a rationally designed, non-NSAID benzoxazole derivative that binds with high affinity and selectivity to TTR and kinetically stabilizes the tetramer, slowing monomer formation, misfolding, and amyloidogenesis. Tafamidis is the first pharmacotherapy approved to slow the progression of peripheral neurologic impairment in TTR familial amyloid polyneuropathy. Here we describe the mechanism of action of tafamidis and review the clinical data, demonstrating that tafamidis treatment slows neurologic deterioration and preserves nutritional status, as well as quality of life in patients with early-stage Val30Met amyloidosis.
Methodischer Teil (1963)

ZusammenfassungDie Umesterung von Fetten in Lösung wurde im wesentlichen unter den gleichen Bedingungen durchgeführt, wie sie bereits in der Literatur ohne Verwendung eines inerten Lösungsmittels beschrieben sind. Als Lösungsmittel diente Petroläther, der mit metalli schem Natrium getrocknet und durch Destillation gereinigt wurde. Durchweg benutzte ich die Fraktion zwischen 60 und 85° C, die einem Gemisch aus Hexan und Heptan entspricht. Dies ist auch das Lösungsmittel, das bei der Extraktion von Ölsaaten in der Industrie vorwiegend verwendet wird. Zur Umesterung dienten raffinierte Fette, Öle und Fettmischungen, die durch zwei- bis dreistündiges Erhitzen auf 200–250° C im Vakuum unter Verwendung von Stickstoff als Schutzgas getrocknet wurden. Diese Fette fanden in Konzentrationen von 10, 20 bzw. 30% Verwendung, die den technisch anfallenden Miszellen entsprechen.
Tolerance to Maternal Immunoglobulins: Resilience of the Specific T Cell Repertoire in Spite of Long-Lasting Perturbations (1999)

T cell tolerance is established and maintained through various mechanisms, the critical component being the persistence of the specific Ag. However, at the molecular level, the nature of the recovering TCR repertoire following breakdown of tolerance is unknown. We address this important question by following kappa light chain constant region (C kappa)-specific CD4+ T cells of kappa light chain knock-out (kappa-/-) mice born to kappa+/- mothers. These cells, which were in contact with maternal kappa+ Igs from early ontogeny until weaning, were strongly tolerized. Tolerance was reversible and waned with the disappearance of peptide C kappa 134-148 presentation in lymphoid organs, including the thymus. Whereas three specific V beta-J beta rearrangements emerged in the peptide C kappa 134-148-specific CD4+ T cell response of all regular kappa-/- mice, soon after breakdown of tolerance only one of these rearrangements was detected. The two others displayed a significant delay in reappearance and were still rare at 26 wk of age, while the control proliferative response had already recovered 3 mo earlier. At 52 wk of age, a complete recovery of the three canonical V beta-J beta rearrangements was observed. Thus, although profoundly perturbed for several months, the T cell repertoire returns to equilibrium, highlighting the resilient nature of this system.
A suffix array approach to video copy detection in video sharing social networks (2009)

To address the multiplicity and copyright issues on file sharing social networks, we propose a fast video copy detection algorithm using the suffix array data structure in this work. The proposed algorithm consists of two steps. In the first step, we extract robust features which are discriminative yet insensitive to various attacks. Specifically, we develop a compact one-dimensional signature based on the shot change position of video files. Unlike images and audio, the size of a video file is usually large, which makes it computationally expensive to match two long signature sequences. Thus, in the second step, we adopt an efficient matching technique based on the suffix array data structure. The proposed system can perform the sequence matching in linear time while the complexity of conventional duplicate video detection algorithms grows at least quadratically with the video length.
Multi-channel image deblurring using coded flashes (2021)

Motion blur is easily observable in an image having moving objects, and the coded exposure photography is one of the well-known solutions to its removal. In this paper, we propose a novel coded exposure photography technique to capture images of moving objects using coded flashes. Noting that the camera acquires a multi-channel image at once by using a color filter array, we modulate each channel image differently by using multi-band coded flashes. By modulating the point spread function of the acquired channel image to have a jointly invertible point spread function, its deconvolution performance is significantly improved compared to the existing single image coded exposure photography. We prove the effectiveness of the proposed method through experiments using synthetic and real data.
Focusing of an Atomic Beam and Imaging of Atomic Sources by Means of a Laser Lens Based on Resonance-radiation Pressure (1988)

Abstract We propose and realize a laser lens capable of focusing an atomic beam by means of spontaneous-resonance radiation pressure. The focal length, resolution and aberrations of the laser lens are derived. An image from two atomic-beam sources has been obtained and the influence of chromatic aberration investigated.
Design and Optimization Strategies for Muscle-Like Direct Drive Linear Permanent Magnet Motors (2010)

We report a new approach to the design of directdrive linear permanent magnet motors for use in general-purpose robotic actuation, with particular attention to applications in bird-scale flapping-wing robots. We show a simple, quantitative analytical modeling framework for this class of actuators, and demonstrate inherent scaling properties that allow the production of motors with force densities and efficiencies comparable to those of biological muscles. We will show how this model leads to a set of practical design specifications for muscle-like motors, and examine the resulting trade-off between thermal management and motor fabrication complexity.
Production of a TEM-24 Plasmid-Mediated Extended-Spectrum β-Lactamase by a Clinical Isolate of <i>Pseudomonas aeruginosa</i> (2000)

Several Pseudomonas aeruginosa strains, including one urinary isolate producing an extended-spectrum beta-lactamase TEM-24, were isolated from a long-term-hospitalized woman. Three TEM-24-producing enterobacterial species (Enterobacter aerogenes, Escherichia coli, and Proteus mirabilis) were isolated from the same patient. TEM-24 and the resistance markers for aminoglycosides, chloramphenicol, and sulfonamide were encoded by a 180-kb plasmid transferred by conjugation into E. coli HB101.
Robot arm dynamic model reduction for control (1983)

General methods are described by which the mathematical complexities of explicit and exact state equations of robot arms can be reduced to a simplified and compact state equation representation without introducing significant errors into the robot arm dynamic model. The model reduction methods are based on homogeneous coordinates and on the Lagrangian algorithm for robot arm dynamics, and utilize matrix, vector and numeric analysis techniques. The derivation of differential vector representation of centripetal and Coriolis forces which has not yet been established in the literature is presented.
Design Considerations of Gas Chromatography System Employing High Efficiency Golay Columns (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDesign Considerations of Gas Chromatography System Employing High Efficiency Golay ColumnsR. D. CondonCite this: Anal. Chem. 1959, 31, 10, 1717–1722Publication Date (Print):October 1, 1959Publication History Published online1 May 2002Published inissue 1 October 1959https://doi.org/10.1021/ac60154a054Request reuse permissionsArticle Views99Altmetric-Citations40LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
Scalable Knowledge Graph Construction over Text using Deep Learning based Predicate Mapping (2019)

Automatic extraction of information from text and its transformation into a structured format is an important goal in both Semantic Web Research and computational linguistics. Knowledge Graphs (KG) serve as an intuitive way to provide structure to unstructured text. A fact in a KG is expressed in the form of a triple which captures entities and their interrelationships (predicates). Multiple triples extracted from text can be semantically identical but they may have a vocabulary gap which could lead to an explosion in the number of redundant triples. Hence, to get rid of this vocabulary gap, there is a need to map triples to a homogeneous namespace. In this work, we present an end-to-end KG construction system, which identifies and extracts entities and relationships from text and maps them to the homogenous DBpedia namespace. For Predicate Mapping, we propose a Deep Learning architecture to model semantic similarity. This mapping step is computation heavy, owing to the large number of triples in DBpedia. We identify and prune unnecessary comparisons to make this step scalable. Our experiments show that the proposed approach is able to construct a richer KG at a significantly lower computation cost with respect to previous work.
How Software Works (2015)

To the uninitiated, information security can sometimes seem like a dark art. Indeed, even to those in the business, certain aspects – not least encryption – have the distinct whiff of witchcraft about them.
Effect of roughness in nondiffusive regions within diffusive media (2001)

Recently it has been shown that clear regions within diffusive media can be accurately modeled within the diffusion approximation by means of a novel boundary condition [J. Opt. Soc. Am. A17, 1671 (2000)] or by an approximation to it [Phys. Med. Biol.41, 767 (1996); Med. Phys.27, 252 (2000)]. This can be directly applied to the study of light propagation in brain tissue, in which there exist clear regions, and in particular in the cerebrospinal fluid (CSF) layer under the skull. In this work we present the effect that roughness in the boundary of nondiffusive regions has on the measured average intensity, since, in practice, the CSF layer is quite rough. The same conclusions can be extended to any diffusive medium that encloses rough nondiffusive regions. We will demonstrate with numerical calculations that the roughness statistics of the interfaces (although not their actual profiles) must be known a priori to correctly predict the shape of the average intensity. We show that as the roughness increases, the effect of the nondiffusive region diminishes until it disappears, thus yielding data similar to those of a fully diffusive region. We also present a numerical study of the diffuse light scattered in the presence of both diffusive and nondiffusive regions and the interaction between the two, showing that when the nondiffusive region is rough, the spatial-intensity distribution produced by the two regions can be very similar.
Safety design of an Assisting Robotic Arm for minimally invasive thoracic surgery (2009)

Based on the analysis of the first prototype of an assisting robotic arm (ARA) for minimally invasive thoracic surgery, an improved design is presented. A self-gravity compensation mechanism is developed to resist joint torques caused by the weight of the robot and to reduce the force exerted on the end-effector by the surgeon. With a motor built into the arm, the design of the ball-socket-joint is modified to widen the surgeon's field of view. The current pedal brake is replaced with an operating pushbutton to avoid maloperation. A control system for the improved ARA is developed. The experimental results show that the workspace and the locking torque can satisfy the basic requirements of a surgery.
A hardware logic simulation system (1990)

Multiple-delay logic simulation algorithms developed for the microprogrammable accelerator for rapid simulations (MARS) hardware simulator are discussed. In particular, timing-analysis algorithms for event cancellations, spike and race analyses, and oscillation detection are described. It is shown how a reconfigurable set of processors, called processing elements (PEs), can be arranged in a pipelined configuration to implement these algorithms. The algorithms operate within the partitioned-memory, message-passing architecture of MARS. Three logic simulators-two multiple delay and one unit delay-have been implemented using slightly different configuration of the available PEs. In these simulators, VLSI chips are modeled at the gate level with accurate rise/fall delays assigned to each logic primitive. On-chip memory blocks are modeled functionally and are integrated into the simulation framework. The MARS hardware simulator has been tested on many VLSI chip designs and has demonstrated a speed improvement of about 50 times that of an Amdahl 5870 system running a production-quality software simulator while retaining the accuracy of simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Theoretical and Experimental Study of Counteracting Chromatographic Electrophoresis (1989)

Abstract Counteracting chromatographic electrophoresis (CACE) is a separation process that combines gel chromatography with electrophoresis. This process, originally developed by O'Farrell1, may be used for protein separation by causing a specific protein to accumulate at the interface between two bed packings of different internal porosity. In this paper a theoretical model for CACE has been developed. This model gives an accumulation criterion that specifies the operating conditions (i.e. applied field and flow rates), and the bed and protein parameters (i.e. external bed porosity, internal particle porosity, protein free mobility, and the ratio of the protein mobility in the get to that in free solution) that lead to accumulation in the column. This accumulation criterion was tested with experimental data for the accumulation of the colored proteins ferritin, myoglobin, and cytochrome-c. This data fit the criterion fairly well for all three proteins. The theoretical model was extended to consider the transient accumulation at the interface between the packings in the column for the batch process where no product was removed from the interface, and for the continuous process where product was continuously removed from this interface. A critical value of the operating parameter lμl (i.e. the ratio of the electrical migration to the convective flow) was found to give the fastest approach to steady-state for the continuous process.
Molecular programming of steady‐state dendritic cells: impact on autoimmunity and tumor immune surveillance (2013)

Dendritic cells are master regulators of immunity. Immature dendritic cells are essential for maintaining self-tolerance, while mature dendritic cells initiate a variety of specialized immune responses. Dendritic cell quiescence is often viewed as a default state that requires exogenous stimuli to induce maturation. However, recent studies have identified dendritic cell quiescence factors that actively program dendritic cells to an immature state. In the absence of these factors, dendritic cells spontaneously become immunogenic and can induce autoimmune responses. Herein we discuss two such factors, NF-κB1 and A20, that preserve dendritic cell immaturity through their regulation of NF-κB signaling. Loss of either of these factors increases dendritic cell immunogenicity, suggesting that they may be important targets for enhancing dendritic cell-based cancer immunotherapies. Alternatively, defects in molecules critical for maintaining steady-state DCs may provide novel biomarkers that identify patients who have enhanced natural antitumor immunity or that correlate with better responses to various immunotherapies.
State-space model of freely vibrating and surface-coupled cantilever dynamics in atomic force microscopy (2004)

The dynamics of the microcantilever in atomic force microscopy (AFM) is represented by a multiple-degrees-of-freedom state-space model and is discussed within the framework of system theory. The cantilever dynamics is modeled as a linear time-invariant system with a nonlinear output feedback due to the tip-sample interaction. This allows one to use the same model to analyze different aspects of atomic force microscopy such as the dynamics of contact-mode or the dynamics of tapping-mode AFM. The state-space approach to the dynamic response of the AFM cantilever allows for numerically efficient simulations. We show that not only the eigenfrequency but also the modal damping of a cantilever interacting with a surface strongly depends on the contact stiffness. This is important for a quantitative characterization of elastic sample properties. Additionally, our model shows the presence of higher harmonics in tapping-mode AFM. The excitation of higher eigenmodes can strongly distort the system response. The results illustrate that higher eigenmodes have to be considered in the analysis of dynamic AFM.
Evidence of the Existence of an He3+ Ion (1968)

An ion-mobility apparatus was used to study the chemistry of helium ions in helium at gas pressures of 1–30 torr and temperatures of 300°–76°K. At temperatures below 200°K, the He2+ ion was observed to convert to an ion believed to be He3+. Identification of the He3+ was based upon observations of its behavior under varied experimental conditions. At 76°K, the rate of formation of He3+ from He2+ was faster than the three-body formation of He2+ from He+. The rate coefficient of the latter reaction was found to be 1.7 ± 0.4 × 10− 31 cm6/sec at 76°K. Between the temperatures of 135° and 200°K, He2+ and He3+ were present in equilibrium. A He3+ dissociation energy of 0.17 ± 0.03 was determined from measurements of the equilibrium constant as a function of temperature.
Seesoft-a tool for visualizing line oriented software statistics (1992)

The Seesoft software visualization system allows one to analyze up to 50000 lines of code simultaneously by mapping each line of code into a thin row. The color of each row indicates a statistic of interest, e.g., red rows are those most recently changed, and blue are those least recently changed. Seesoft displays data derived from a variety of sources, such as version control systems that track the age, programmer, and purpose of the code (e.g., control ISDN lamps, fix bug in call forwarding); static analyses, (e.g., locations where functions are called); and dynamic analyses (e.g., profiling). By means of direct manipulation and high interaction graphics, the user can manipulate this reduced representation of the code in order to find interesting patterns. Further insight is obtained by using additional windows to display the actual code. Potential applications for Seesoft include discovery, project management, code tuning, and analysis of development methodologies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>