gebhart/patrepeval huggingface dataset:
The adaptive immune response to sporadic cancer (2007)

Most of the current experimental cancer models do not reflect the pathophysiology of real-life cancer. Cancer usually occurs sporadically and is clonal in origin. Between tumor initiation and progression, clinically unapparent pre-malignant cells may persist for years or decades in humans. Recently, mouse models of sporadic cancer have been developed. The mouse germ-line can be engineered with high precision so that defined genes can be switched on and off in the adult organism in a targeted manner. Analysis of the immune response against sporadic tumors requires the knowledge of a tumor antigen. Ideally, a silent oncogene, for which the mice are not tolerant, is stochastically activated in individual cells. This approach offers the opportunity to analyze the adaptive immune response throughout the long process of malignant transformation and most closely resembles cancer in humans. In such a model with the highly immunogenic SV40 large T antigen as a dormant oncogene, we discovered that sporadic cancer is recognized by the adaptive immune system at the pre-malignant stage, concomitant with the induction of tumor antigen-specific tolerance. These results demonstrated that even highly immunogenic sporadic tumors are unable to induce functional cytotoxic T lymphocytes. Based on this model, we conclude that immunosurveillance plays little or no role against sporadic cancer and that tumors must not escape immune recognition or destruction.
Applied antisense oligonucleotide technology (1998)

CHEMISTRY, OLD AND NEW. Oligonucleoside Methylphosphonates: Synthesis and Properties (P. Miller). Oligo(Nucleoside Phosphorothioate)s (P. Guga, et al.). Modified Oligodeoxynucleotides as Antisense Therapeutics (P. Seeberger & M. Caruthers). Novel Chemistry (K. Altmann, et al.). OLIGONUCLEOTIDE INTERNALIZATION, MECHANISM OF ACTION, AND NON--SEQUENCE SPECIFICITY. Cellular Uptake and Biodistribution of Oligodeoxynucleotides (B. Hanss, et al.). Use of Cationic Lipid Complexes for Antisense Oligonucleotide Delivery (C. Bennett). Nonantisense Effects of Antisense Oligonucleotides (L. Neckers & K. Iyer). Ribonuclease H--Mediated Antisense Effects of Oligonucleotides and Controls for Antisense Experiments (D. Tidd). SEQUENCE--SPECIFIC INHIBITION OF GENE EXPRESSION. The Development of C--5 Propyne Oligonucleotides as Inhibitors of Gene Function (W. Flanagan & R. Wagner). The Use of Antisense Oligonucleotides to Inhibit Expression of Isozymes of Protein Kinase C (N. Dean, et al.). BCR--ABL as a Target for Antisense Intervention (S. O'Brien & T. Smetsers). The NF--kB Transcription Factor (R. Narayanan). Disruption of the Map Kinase Signaling Pathway Using Antisense Oligonucleotide Inhibitors Targeted to RAS and RAF Kinase (B. Monia). Protein Kinase A--Directed Antisense Blockade of Cancer Growth: Single Gene--Based Therapeutic Approach (Y. Cho--Chung). Use of Antisense Oligonucleotides in the Central Nervous System: Why Such Success? (M. McCarthy). APPLIED ANTISENSE OLIGONUCLEOTIDE THERAPEUTICS. Perturbing Hematopoietic Cell Gene Expression with Oligodeoxynucleotides: Research and Clinical Applications (A. Gewirtz & M. Ratajczak). BCL2 (B. Jansen & B. Brown). Biological Activity of Guanosine Quartet--Forming Oligonucleotides (R. Rando & M. Hogan). OLIGONUCLEOTIDES AS ANTI--HIV AGENTS. Perspectives on Antisense Technology Against HIV (J. Gee, et al.). In Vivo Pharmacokinetics of Oligonucleotides (S. Agrawal). Early Clinical Trails with Gem 91, A Systemic Oligodeoxynucleotide (R. Martin). THERAPEUTIC OLIGONUCLEOTIDE DATA BASE: PHARMACOKINETICS, IMMUNE STIMULATION, AND USE AS ANTIRESTENOTIC AGENTS. Antisense Therapy to Inhibit Angioplasty Restenosis (L. Rabbani & W. Wang). Pharmacokinetics of Oligonucleotides: A Review of Current Knowledge and Issues for the Future (T. Wallace & P. Cossum). Leukocyte Stimulation by Oligodeoxynucleotides (A. Krieg). SELECTED OLIGODEOXYNUCLEOTIDE DEVELOPMENTAL TOPICS: SPLICING AND TRIPLEXES. Modification of Alternative Splicing of Pre--mRNA by Antisense Oligonucleotides (R. Kole). Gene--Targeted Triple--Helix--Forming Oligonucleotides (F. Svinarchuk & C. Malvy). Triplex--Forming Oligonucleotides for Genetic Manipulation: An Alternative View (A. Faruqi & P. Glazer). A REVIEW OF RIBOZYME TECHNOLOGY. Therapeutic Ribozymes: Principles, Applications, and Problems (J. Rossi). Index.
Down-regulation of CXCR-4 and CCR-5 expression by interferon-γis associated with inhibition of chemotaxis and human immunodeficiency virus (HIV) replication but not HIV entry into human monocytes (2004)

Alterations in the expression of CXCR4 and CCR5, the co-receptors for HIV entry, may be associated with susceptibility of monocytic cells to HIV infection. Interferon (IFN)-gamma has been shown to inhibit HIV replication in monocytic cells, but the molecular mechanism involved is not well understood. To determine if IFN-gamma regulates HIV replication by altering CXCR-4/CCR-5 expression and hence virus entry into monocytic cells, we investigated the effects of IFN-gamma on CXCR-4 and CCR-5 expression and its biological implications with respect to HIV entry, replication and chemotaxis towards the CXCR-4 and CCR-5 ligands SDF-1 and MIP-1alpha, respectively. IFN-gamma decreased CXCR-4 and CCR-5 expression on monocytes derived from HIV-negative adults, HIV-positive adults and HIV-negative cord blood. This down-regulation of chemokine receptor expression did not result in a corresponding change in mRNA expression but was associated with elevated levels of the endogenously produced chemokines SDF-1 and RANTES. Furthermore, IFN-gamma inhibited chemotaxis in response to SDF-1 and MIP-1alpha, inhibited HIV replication, but failed to inhibit virus entry in monocytic cells. These results suggest that although IFN-gamma-induced down-regulation of CXCR-4 and CCR-5 expression is associated with an inhibition of SDF-1-/MIP-1alpha-mediated chemotaxis, IFN-gamma-induced inhibition of HIV replication may be mediated at levels subsequent to the virus entry.
Discovery and proof in attachment research (1984)

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Heteroepitaxial growth of BaTiO3 films on Si by pulsed laser deposition (1995)

Dielectric BaTiO3 films were heteroepitaxially grown on Si (100) substrates in cube-on-cube manner by employing a conductive TiN buffer layer. An epitaxial TiN film was grown by KrF pulsed excimer laser deposition. BaTiO3 film was grown epitaxially on the TiN film at a substrate temperature higher than 600 °C and in an oxygen pressure less than 1 mTorr. This epitaxial BaTiO3/TiN layer on Si was observed to have sharp interfaces and little interdiffusion of constituent atoms by secondary ion mass spectrometry. The surface of the BaTiO3 film had a root-mean-square roughness less than 1 nm as observed by atomic force microscopy. A TiN/BaTiO3/TiN trilayer structure was formed and the dielectric property was measured for this metal-insulator-metal type capacitor. The BaTiO3 film showed a high relative dielectric constant of 803 at the frequency of 1 MHz and a low leakage current less than 10−8 A/cm2 at 2 V.
The crystal structure of lithium hydrazinium fluoroberyllate (1973)

At r o o m tempera tu re crystals o f l i th ium h y d r a z i n i u m f luoroberyl la te , Li(NzHs)BeF4, are o r thorhombic , space g roup Pna2~, with a = 9 . 8 1 1 (4), b = 8.880 (8), and c = 5.139 (4) ,~, Z = 4 . The s t ructure was refined by least squares with X-ray d i f f rac tometer measurement s to give an R(we igh ted )=0 .039 . The * On leave from Laboratoire de Chimie Min6rale, E.R.A. 314, Chimie des Mat6tiaux, Facult6 des Sciences, Place Eug6ne Bataillon, 34060 Montpellier, France. l i th ium and bery l l ium a toms are 'at the centres of corner -shar ing f luorine te t rahedra . The hydraz in ium ions lie in channels in the resu l tan t f r amework so as to fo rm infinite h y d r o g e n b o n d e d chains a long the [001] screw axes. The average L i F and Be -F b o n d distances are 1.853 a n d 1.546 A respectively. Unl ike the co r re spond ing sulphate whose N H . . . O bonds are single, this s t ructure has single, b i furca ted and t r i furca ted N H . . F bonds. Table 1. Crystal data for Li(N2Hs)BeF4 and Li(N2Hs)SOa Estimated standard deviations are in parentheses. Li(N2Hs) BeF4 Li(N2Hs)SO4 Anderson & Brown This work Tedenac et al. (1971) (1972) System Orthorhombic Orthorhombic Orthorhombic Space group Pna2~ Pna2~ Pna2i a 9-811 (4) ,~ 9820 (5)/~ 9929 (5) A, b 8.880 (8) 8.896 (5) 8.973 (3) c 5139 (4) 5142 (5) 5181 (2) V 4477 (6) ,&s 4492 (8) A 3 4616 (6) A 3 D¢,1¢ 1854 g c m -3 1848 g cm -3 1.958 g cm -3 Z 4 4 4 Absorption coefficient for Mo K~ 2.50 cm -t 6.03 cm -1 Systematic absences Okl k + l=2n+ l hOl h = 2n + 1 Table 2. Parameters derived f rom the f inal least-squares refinement The expressions used for the temperature factors are: exp [ 2n2(Ullh2a *z + U22k2b .2 + Ua312c .2 + 2 Ua2hka*b* + 2 U23klb*c* + 2 Ulflhc*a*)] and exp[-2n2u(2Si2nO)2 ]. Estimated standard deviations are in parentheses.
Extending the duration of active oral contraceptive pills to manage hormone withdrawal symptoms (1997)

Experience in a series of 50 OC users with menstrual-related symptoms demonstrated that delaying menses by extending the number of consecutive days of active pills is well tolerated and efficacious. We believe that a large prospective study is warranted to further our knowledge in this area.
Low-voltage ULSI design (1993)

An overall view on low-voltage device and circuit design is presented, beginning with a discussion of the low-voltage limit. Low-voltage device design is then described. Low-voltage CMOS and BiCMOS logic circuits are discussed. Circuit techniques for the low-voltage DRAMs and SRAMs are presented. The low-voltage analog devices and circuits are considered. The future direction of the low-voltage and low-power ULSIs is discussed by comparing the switching energy of electronic devices and brain cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New Fluorescent 2-Phenylindolglyoxylamide Derivatives as Probes Targeting the Peripheral-Type Benzodiazepine Receptor:  Design, Synthesis, and Biological Evaluation (2006)

Fluorescent ligands for the peripheral-type benzodiazepine receptor (PBR) featuring the 7-nitrobenz-2-oxa-1,3-diazol-4-yl moiety were synthesized, based on N,N-dialkyl-2-phenylindol-3-ylglyoxylamides, a potent, selective class of PBR ligands previously described by us. All the new ligands are moderately to highly potent at the PBR, with a complete selectivity over the central benzodiazepine receptor. Results from fluorescence microscopy showed that these probes specifically labeled the PBR at the mitochondrial level in C6 glioma cells.
OpenGL Programming Guide: The Official Guide to Learning OpenGL, Versions 3.0 and 3.1 (2009)

OpenGL is a powerful software interface used to produce high-quality, computer-generated images and interactive applications using 2D and 3D objects, bitmaps, and color images. The OpenGLProgramming Guide, Seventh Edition, provides definitive and comprehensive information on OpenGL and the OpenGL Utility Library. The previous edition covered OpenGL through Version 2.1. This seventh edition of the best-selling red book describes the latest features of OpenGL Versions 3.0 and 3.1. You will find clear explanations of OpenGL functionality and many basic computer graphics techniques, such as building and rendering 3D models; interactively viewing objects from different perspective points; and using shading, lighting, and texturing effects for greater realism. In addition, this book provides in-depth coverage of advanced techniques, including texture mapping, antialiasing, fog and atmospheric effects, NURBS, image processing, and more. The text also explores other key topics such as enhancing performance, OpenGL extensions, and cross-platform techniques. This seventh edition has been updated to include the newest features of OpenGL Versions 3.0 and 3.1, including Using framebuffer objects for off-screen rendering and texture updates Examples of the various new buffer object types, including uniform-buffer objects, transform feedback buffers, and vertex array objects Using texture arrays to increase performance when using numerous textures Efficient rendering using primitive restart and conditional rendering Discussion of OpenGLs deprecation mechanism and how to verify your programs for future versions of OpenGL This edition continues the discussion of the OpenGL Shading Language (GLSL) and explains the mechanics of using this language to create complex graphics effects and boost the computational power of OpenGL. The OpenGL Technical Library provides tutorial and reference books for OpenGL. The Library enables programmers to gain a practical understanding of OpenGL and shows them how to unlock its full potential. Originally developed by SGI, the Library continues to evolve under the auspices of the Khronos OpenGL ARB Working Group, an industry consortium responsible for guiding the evolution of OpenGL and related technologies.
A robotic system for crystallizing membrane and soluble proteins in lipidic mesophases (2004)

A high-throughput robotic system has been developed for crystallizing membrane proteins using lipidic mesophases. It incorporates commercially available components and is relatively inexpensive. The crystallization robot uses standard automated liquid-handlers and a specially built device for accurately and reproducibly delivering nanolitre volumes of highly viscous protein/lipid mesophases. Under standard conditions, the robot uses just 20 nl protein solution, 30 nl lipid and 1 microl precipitant solution. 96 wells can be set up using the robot in 13 min. Trials are performed in specially designed 96-well glass plates. The slim (<2 mm high) plates have exquisite optical properties and are well suited for the detection of microcrystals and for birefringence-free imaging between crossed polarizers. Quantitative evaluation of the crystallization progress is performed using an automated imaging system. The optics, in combination with the slim crystallization plates, enables in-focus imaging of the entire well volume in a single shot such that a 96-well plate can be imaged in just 4.5 min. The performance characteristics of the robotic system and the versatility of the crystallization robot in performing vapor-diffusion, microbatch and bicelle crystallizations of membrane and soluble proteins are described.
Design and Control of Concentric-Tube Robots (2010)

A novel approach toward construction of robots is based on a concentric combination of precurved elastic tubes. By rotation and extension of the tubes with respect to each other, their curvatures interact elastically to position and orient the robot's tip, as well as to control the robot's shape along its length. In this approach, the flexible tubes comprise both the links and the joints of the robot. Since the actuators attach to the tubes at their proximal ends, the robot itself forms a slender curve that is well suited for minimally invasive medical procedures. This paper demonstrates the potential of this technology. Design principles are presented and a general kinematic model incorporating tube bending and torsion is derived. Experimental demonstration of real-time position control using this model is also described.
Physical Randomness Extractors: Generating Random Numbers with Minimal Assumptions (2014)

How to generate provably true randomness with minimal assumptions? This question is important not only for the efficiency and the security of information processing, but also for understanding how extremely unpredictable events are possible in Nature. All current solutions require special structures in the initial source of randomness, or a certain independence relation among two or more sources. Both types of assumptions are impossible to test and difficult to guarantee in practice. Here we show how this fundamental limit can be circumvented by extractors that base security on the validity of physical laws and extract randomness from untrusted quantum devices. In conjunction with the recent work of Miller and Shi (arXiv:1402:0489), our physical randomness extractor uses just a single and general weak source, produces an arbitrarily long and near-uniform output, with a close-to-optimal error, secure against all-powerful quantum adversaries, and tolerating a constant level of implementation imprecision. The source necessarily needs to be unpredictable to the devices, but otherwise can even be known to the adversary. Our central technical contribution, the Equivalence Lemma, provides a general principle for proving composition security of untrusted-device protocols. It implies that unbounded randomness expansion can be achieved simply by cross-feeding any two expansion protocols. In particular, such an unbounded expansion can be made robust, which is known for the first time. Another significant implication is, it enables the secure randomness generation and key distribution using public randomness, such as that broadcast by NIST's Randomness Beacon. Our protocol also provides a method for refuting local hidden variable theories under a weak assumption on the available randomness for choosing the measurement settings.
A DOUBLE‐BLIND CONTROLLED CLINICAL TRIAL OF MASTIC AND PLACEBO IN THE TREATMENT OF DUODENAL ULCER (1984)

A double-blind clinical trial was carried out on thirty-eight patients with symptomatic and endoscopically proven duodenal ulcer to compare the therapeutic responses to mastic (1 g daily, twenty patients) and placebo (lactose, 1 g daily, eighteen patients) given orally over a period of 2 weeks. Symptomatic relief was obtained in sixteen (80%) patients on mastic and in nine (50%) patients on placebo, while endoscopically proven healing occurred in fourteen (70%) patients on mastic and four (22%) patients on placebo. The differences between treatments were highly significant (P less than 0.01). Mastic was well tolerated and did not produce side effects. It is concluded that mastic has an ulcer healing effect, but further studies are needed to establish its role in treating peptic ulcer.
Refractive-Index Profiling of Buried Planar Waveguides by an Inverse Wentzel–Kramer–Brillouin Method (2008)

We propose an inverse Wentzel-Kramer-Brillouin (WKB) method for the construction of the refractive-index profiles of buried graded-index planar waveguides from the measured effective indexes of the guided modes. Our method involves experimental determination of the location of the peak index in the buried profile, measurement of the effective indexes in air, and an index-matching liquid, and application of a searching algorithm to find the best-fit profile through inverting the WKB equations. We present numerical examples and experimental results to demonstrate the performance of the method.
The Cysteine-Rich Domain of the Macrophage Mannose Receptor Is a Multispecific Lectin That Recognizes Chondroitin Sulfates a and B and Sulfated Oligosaccharides of Blood Group Lewisa and Lewisx Types in Addition to the Sulfated N-Glycans of Lutropin (2000)

The mannose receptor (MR) is an endocytic protein on macrophages and dendritic cells, as well as on hepatic endothelial, kidney mesangial, tracheal smooth muscle, and retinal pigment epithelial cells. The extracellular portion contains two types of carbohydrate-recognition domain (CRD): eight membrane-proximal C-type CRDs and a membrane-distal cysteine-rich domain (Cys-MR). The former bind mannose-, N-acetylglucosamine-, and fucose-terminating oligosaccharides, and may be important in innate immunity towards microbial pathogens, and in antigen trapping for processing and presentation in adaptive immunity. Cys-MR binds to the sulfated carbohydrate chains of pituitary hormones and may have a role in hormonal clearance. A second feature of Cys-MR is binding to macrophages in marginal zones of the spleen, and to B cell areas in germinal centers which may help direct MR-bearing cells toward germinal centers during the immune response. Here we describe two novel classes of carbohydrate ligand for Cys-MR: chondroitin-4 sulfate chains of the type found on proteoglycans produced by cells of the immune system, and sulfated blood group chains. We further demonstrate that Cys-MR interacts with cells in the spleen via the binding site for sulfated carbohydrates. Our data suggest that the three classes of sulfated carbohydrate ligands may variously regulate the trafficking and function of MR-bearing cells.
Determination of SMN1 and SMN2 copy number using TaqMan™ technology (2003)

Infantile spinal muscular atrophy (SMA) is a neuromuscular disease caused by homozygous deletion of the SMN1 gene in more than 90% of patients. Identification of carriers for the SMN1 deletion is important for diagnostic purposes and for genetic counseling. The current practical implications of SMN2 copy number determination are limited but may be important, for example, for future drug trials. Here we present a new rapid and reliable approach to determine the copy numbers of the SMN1 and SMN2 genes: For differentiation of the two genes, we developed a quantitative test on the basis of TaqMan technology using minor groove binder (MGB) probes. To evaluate the approach in respect to detection of SMN1 deletion carriers, we tested 40 putative carriers as well as 100 controls. We confirmed the carrier status in all individuals; furthermore, the distribution of SMN1 and SMN2 copies in the control cohort corresponded to that published previously. In total, a clear-cut differentiation between the different copy number ranges could be observed for both genes. This distinct differentiation is based on the exact specificity of MGB probes and the parallel analysis of an external reference locus that circumvents the problem of unavoidable deviations in DNA concentrations. The simplicity and reproducibility of the TaqMan assay presented here should facilitate its establishment in molecular diagnostic laboratories. Nevertheless, the applicability of quantitative analyses of SMN copy numbers requires knowledge about its options and limitations, based on the complex nature of the SMN region and the clinical variability of SMA. Therefore, determination of SMN1 and SMN2 copy numbers should only be offered after careful consideration in each case.
ARB: a hardware mechanism for dynamic reordering of memory references (1996)

To exploit instruction level parallelism, it is important not only to execute multiple memory references per cycle, but also to reorder memory references-especially to execute loads before stores that precede them in the sequential instruction stream. To guarantee correctness of execution in such situations, memory reference addresses have to be disambiguated. This paper presents a novel hardware mechanism, called an Address Resolution Buffer (ARB), for performing dynamic reordering of memory references. The ARB supports the following features: (1) dynamic memory disambiguation in a decentralized manner, (2) multiple memory references per cycle, (3) out-of-order execution of memory references, (4) unresolved loads and stores, (5) speculative loads and stores, and (6) memory renaming. The paper presents the results of a simulation study that we conducted to verify the efficacy of the ARB for a superscalar processor. The paper also shows the ARB's application in a multiscalar processor.