gebhart/patrepeval huggingface dataset:
Epstein-Barr Virus (EBV)-associated Gastric Carcinoma (2012)

The ubiquitous Epstein-Barr virus (EBV) is associated with several human tumors, which include lymphoid and epithelial malignancies. It is known that EBV persistently infects the memory B cell pool of healthy individuals by activating growth and survival signaling pathways that can contribute to B cell lymphomagenesis. Although the monoclonal proliferation of EBV-infected cells can be observed in epithelial tumors, such as nasopharyngeal carcinoma and EBV-associated gastric carcinoma, the precise role of EBV in the carcinogenic progress is not fully understood. This review features characteristics and current understanding of EBV-associated gastric carcinoma. EBV-associated gastric carcinoma comprises almost 10% of all gastric carcinoma cases and expresses restricted EBV latent genes (Latency I). Firstly, definition, epidemiology, and clinical features are discussed. Then, the route of infection and carcinogenic role of viral genes are presented. Of particular interest, the association with frequent genomic CpG methylation and role of miRNA for carcinogenesis are topically discussed. Finally, the possibility of therapies targeting EBV-associated gastric carcinoma is proposed.
Fatigue Behavior of Polymers (2002)

Abstract Polymers and polymer‐based composites are increasingly displacing more traditional materials in a wide variety of engineering applications, and as such characterization of their fatigue behavior is of utmost importance. This article presents a general overview of the fatigue behavior of polymers. After a brief introduction that includes general terminology, the effects of test conditions (sample geometry, loading frequency, etc) are discussed. The effects of these conditions are also discussed in relevance to both the high cycle and low cycle fatigue behavior. Current models for predicting fatigue life are also reviewed, including cumulative damage theories and fatigue crack propagation models. Morphological and environmental effects are then discussed over a broad range of semicrystalline, amorphous, and modified polymer systems.
Purification and characterization of <i>Robinia pseudoacacia</i> seed lectins. A re-investigation (1986)

Two lectins, RPA 1 and RPA 3, were purified from Robinia pseudoacacia seeds. These two lectins differ in their physicochemical and biological properties. By analytical ultracentrifugation the Mr values of RPA 1 and RPA 3 were estimated to be 59,000 and 105,000 respectively. From SDS/polyacrylamide-gel-electrophoresis data it was estimated that RPA 1 consisted of two subunits of Mr 34,000, and RPA 3 of two types of subunits (Mr 30,500 and 29,000). RPA 1 and RPA 3 were found to be glycoproteins of comparable amino acid composition. RPA 1 was the more highly glycosylated molecule (11.6% versus 4.3%). The carbohydrate-specificity of RPA 1 appears to be complex. RPA 3 was inhibited by N-acetyl-D-galactosamine and human alpha-glycoproteins. Both lectins exerted a mitogenic effect on human peripheral-blood lymphocytes. Concentrations between 0.5 and 1 microgram of RPA 3/ml gave optimal proliferative responses, whereas for RPA 1 concentrations higher than 10 micrograms/ml were needed for these responses.
Asymmetric design of semiconductor laser diodes: thin p-clad and low divergence InGaAs/AlGaAs/GaAs devices (2003)

The asymmetric design of a semiconductor laser structure presented in this paper is based on the extension of the near field in the vertical direction (growth direction) preferentially on the n-side of the structure. P-type layers show lower mobility and higher optical losses than n-type layers. Thus the series resistance of the device and the internal losses would benefit from this approach. The vertical spot size is 0.8 /spl mu/m, making the structures also suitable for high power operation. We give the refractive index profile and optical field distribution in the asymmetric structures.
GAUSSIAN PROCESSES FOR MACHINE LEARNING (2004)

Gaussian processes (GPs) are natural generalisations of multivariate Gaussian random variables to infinite (countably or continuous) index sets. GPs have been applied in a large number of fields to a diverse range of ends, and very many deep theoretical analyses of various properties are available. This paper gives an introduction to Gaussian processes on a fairly elementary level with special emphasis on characteristics relevant in machine learning. It draws explicit connections to branches such as spline smoothing models and support vector machines in which similar ideas have been investigated. Gaussian process models are routinely used to solve hard machine learning problems. They are attractive because of their flexible non-parametric nature and computational simplicity. Treated within a Bayesian framework, very powerful statistical methods can be implemented which offer valid estimates of uncertainties in our predictions and generic model selection procedures cast as nonlinear optimization problems. Their main drawback of heavy computational scaling has recently been alleviated by the introduction of generic sparse approximations.13,78,31 The mathematical literature on GPs is large and often uses deep concepts which are not required to fully understand most machine learning applications. In this tutorial paper, we aim to present characteristics of GPs relevant to machine learning and to show up precise connections to other "kernel machines" popular in the community. Our focus is on a simple presentation, but references to more detailed sources are provided.
MRG15 Activates the B-myb Promoter through Formation of a Nuclear Complex with the Retinoblastoma Protein and the Novel Protein PAM14 (2001)

The MORF4-Related Gene on chromosome 15 (MRG15) is a member of a novel family of genes originally identified in studies to reveal cell senescence-inducing factors. MRG15 contains several predicted protein motifs, including a nuclear localization signal, a helix-loop-helix region, a leucine zipper, and a chromodomain. These motifs are commonly associated with transcription factors, suggesting that MRG15 may likewise function as a transcriptional regulator. To examine the potential function(s) of MRG15, we sought to identify cellular factors associated with this MRG family member. In this regard, we have found that both the retinoblastoma tumor suppressor (Rb) and a novel nuclear protein PAM14 (Protein Associated with MRG, 14 kDa) specifically associate with MRG15. We have further demonstrated that these interactions require the helix-loop-helix and leucine zipper domains of MRG15. Interestingly we have found all three proteins present in a multiprotein complex, suggesting that at least some of their functions may be interdependent. Although the functions of PAM14 have yet to be elucidated, Rb has several well characterized activities, including repression of E2F-activated promoters such as that of B-myb. Significantly we have demonstrated that MRG15 blocks the Rb-induced repression of this promoter, leading to B-myb promoter activation. Collectively these results suggest that MRG15 regulates transcription through interactions with a cellular protein complex containing Rb and PAM14.
Real-Time Collaborative Solid Shape Design (RCSSD) on the Internet (2002)

The Internet and the World-Wide Web created a new infrastructure and new possibilities for concurrent engineering. In order to support real-time (synchronous) collaborative solid shape design, however, some major issues still have to be resolved. These involved deployment of solid modeling software on the Web, shared access to common solid models, communication and control of the design actions among designers, and efficient representation of the many different but related design versions of the product. This paper discusses the development of a real-time collaborative solid modeling system that addresses these issues. The prototype system has been implemented in a client-server environment in Java, using the Java Remote Method Invocation package for networking support.
Molecular Cloning and Characterization of a Dermatan-specific N-Acetylgalactosamine 4-O-Sulfotransferase (2001)

We have identified and characterized an N-acetylgalactosamine-4-O-sulfotransferase designated dermatan-4-sulfotransferase-1 (D4ST-1) (GenBank(TM) accession number AF401222) based on its homology to HNK-1 sulfotransferase. The cDNA predicts an open reading frame encoding a type II membrane protein of 376 amino acids with a 43-amino acid cytoplasmic domain and a 316-amino acid luminal domain containing two potential N-linked glycosylation sites. D4ST-1 has significant amino acid identity with HNK-1 sulfotransferase (21.4%), N-acetylgalactosamine-4-O-sulfotransferase 1 (GalNAc-4-ST1) (24.7%), N-acetylgalactosamine-4-O-sulfotransferase 2 (GalNAc-4-ST2) (21.0%), chondroitin-4-O-sulfotransferase 1 (27.3%), and chondroitin-4-O-sulfotransferase 2 (22.8%). D4ST-1 transfers sulfate to the C-4 hydroxyl of beta1,4-linked GalNAc that is substituted with an alpha-linked iduronic acid (IdoUA) at the C-3 hydroxyl. D4ST-1 shows a strong preference in vitro for sulfate transfer to IdoUAalpha1,3GalNAcbeta1,4 that is flanked by GlcUAbeta1,3GalNAcbeta1,4 as compared with IdoUAalpha1,3GalNAcbeta1,4 flanked by IdoUAalpha1,3GalNAcbeta1,4. The specificity of D4ST-1 when assayed in vitro suggests that the addition of sulfate to GalNAc occurs immediately after epimerization of GlcUA to IdoUA. The open reading frame of D4ST-1 is encoded by a single exon located on human chromosome 15q14. Northern blot analysis reveals a single 2.4-kilobase transcript. D4ST-1 message is expressed in virtually all tissues at some level but is most highly expressed in pituitary, placenta, uterus, and thyroid. The properties of D4ST-1 indicate that sulfation of the GalNAc moieties in dermatan is mediated by a distinct GalNAc-4-O-sulfotransferase and occurs following epimerization of GlcUA to IdoUA.
Building and Manipulating Three-Dimensional and Linked Two-Dimensional Structures of Nanoparticles Using Scanning Force Microscopy (1998)

Manipulation of nanoparticles with the scanning force microscope (SFM) has been limited until now to clearing areas on a surface or to moving single particles sequentially to create two-dimensional patterns. The research reported here uses a previously described setup for nanomanipulation with the SFM to (i) build a simple three-dimensional pyramidal structure by pushing a nanoparticle on top of two others and (ii) rotate and translate a linked two-particle structure. The experiments are conducted in air and at room temperature with gold nanoparticles deposited on silicon previously coated with a silane layer.
Aqueous Phase Synthesis of Au–Ag Core–Shell Nanocrystals with Tunable Shapes and Their Optical and Catalytic Properties (2013)

In this study, rhombic dodecahedral gold nanocrystals were used as cores for the generation of Au-Ag core-shell nanocrystals with cubic, truncated cubic, cuboctahedral, truncated octahedral, and octahedral structures. Gold nanocrystals were added to an aqueous mixture of cetyltrimethylammonium chloride (CTAC) surfactant, AgNO3, ascorbic acid, and NaOH to form the core-shell nanocrystals. The nanocrystals are highly uniform in size and shape, and can readily self-assemble into ordered packing structures on substrates. Results from observation of solution color changes and variation in the reaction temperature suggest octahedra are produced at a higher growth rate, while slower growth favors cube formation. The major localized surface plasmon resonance (LSPR) band positions for these nanocrystals are red-shifted compared to those for pristine silver particles with similar dimensions due to the LSPR effect from the gold cores. By increasing the concentrations of reagents, Au-Ag core-shell cubes and octahedra with tunable sizes were obtained. Au-Ag cubes with body diagonals of 130, 144, and 161 nm and octahedra with body diagonals of 113, 126, and 143 nm have been prepared, allowing the investigation of size effect on their optical properties. Au-Ag octahedra with thinner Ag shells (12-16.5 nm) exhibit a blue-shifted major LSPR band relative to the LSPR band at 538 nm for the gold cores. For Au-Ag octahedra and cubes with thicker shells (22.5-37 nm), the major LSPR band is progressively red-shifted from that of the gold cores with increasing shell thickness and particle size. The Au-Ag octahedra show higher catalytic activity than cubes toward reduction of 2-amino-5-nitrophenol by NaBH4 at 30 °C, but both particle shapes display significantly enhanced catalytic efficiency at 40 °C.
1.2 Å crystal structure of the <i>S. pneumoniae</i> PhtA histidine triad domain a novel zinc binding fold (2005)

The recently described pneumococcal histidine triad protein family has been shown to be highly conserved within the pneumococcus. As part of our structural genomics effort on proteins from Streptococcus pneumoniae, we have expressed, crystallised and solved the structure of PhtA-166-220 at 1.2 Angstroms using remote SAD with zinc. The structure of PhtA-166-220 shows no similarity to any protein structure. The overall fold contains 3beta-strands and a single short alpha-helix. The structure appears to contain a novel zinc binding motif. The remaining 4 histidine triad repeats from PhtA have been modelled based on the crystal structure of the PhtA histidine triad repeat 2. From this modelling work, we speculate that only three of the five histidine triad repeats contain the residues in the correct geometry to allow the binding of a zinc ion.
Relationship between mitochondria and oxygen consumption in isolated cat muscles. (1987)

1. Oxygen consumption, mitochondrial content and composition, intracellular lipid stores and fibre size were studied in isolated cat muscles: predominantly glycolytic gracilis, purely oxidative soleus and gracilis transformed into an oxidative muscle by chronic low-frequency (10 Hz) electrical stimulation. 2. Oxygen consumption in control gracilis at rest (0.303 +/- 0.050 ml O2 min-1 100 g-1; mean +/- S.E. of mean) was three to five times lower than in either stimulated gracilis (1.16 +/- 0.40) or soleus (1.57 +/- 0.56); it was about two times lower during maximal contractions in control gracilis (5.15 +/- 0.24) than in either stimulated gracilis (11.6 +/- 2.0) or soleus (9.34 +/- 0.78). 3. The volume density of mitochondria in control gracilis (2.75 +/- 0.12%) was half that of soleus (6.23 +/- 0.76) and only one-third that of stimulated gracilis (8.35 +/- 0.71). Subsarcolemmal mitochondria represented a significantly smaller fraction of the total mitochondrial volume in control gracilis than in either soleus or stimulated gracilis. 4. The surface area of inner and outer mitochondrial membranes per unit volume of mitochondria ranged from 23.4 to 26.1 and from 14.0 to 16.5 m2 cm-3, respectively. Mean values of these variables were not significantly different among experimental groups. 5. The volume density of the intracellular lipid stores in control gracilis (0.232 +/- 0.041%) was one-fourth of that in stimulated gracilis (0.860 +/- 0.12) and one-fifth of that in soleus (1.17 +/- 0.27). 6. The fibre cross-sectional area was 1670 +/- 260 micron 2 in control gracilis, 2250 +/- 280 in stimulated gracilis and 2390 +/- 110 in soleus. The difference was statistically significant only between control gracilis and soleus. 7. There was a significant correlation between the volume density of mitochondria and maximal oxygen consumption for all three muscles combined. 8. It was found that mitochondrial structure was similar in muscles with different oxidative capacities and that equal amounts of mitochondria consumed equal amounts of oxygen under limiting conditions of maximal in vivo respiration.
The eaeB gene of enteropathogenic Escherichia coli is necessary for signal transduction in epithelial cells (1994)

An enteropathogenic Escherichia coli mutant carrying an internal deletion in the eaeB gene (UMD864) was unable to activate epithelial cell signals, including tyrosine phosphorylation, cytoskeletal rearrangements, and the release of inositol phosphates, indicating that the eaeB locus encodes a product that is involved in stimulating signals in epithelial cells.
Induction of Mating in <i>Candida albicans</i> by Construction of <i>MTL</i> a and <i>MTL</i> α Strains (2000)

Although the diploid fungus Candida albicans, a human pathogen, has been thought to have no sexual cycle, it normally possesses mating-type-like orthologs (MTL) of both of the Saccharomyces cerevisiae mating-type genes (MAT) a and alpha. When strains containing only MTLa or MTLalpha were constructed by the loss of one homolog of chromosome 5, the site of the MTL loci, MTLa and MTLalpha strains mated, but like mating types did not. Evidence for mating included formation of stable prototrophs from strains with complementing auxotrophic markers; these contained both MTL alleles and molecular markers from both parents and were tetraploid in DNA content and mononucleate.
Calibration service for spectral responsivity of laser and optical-fiber power meters at wavelengths between 0.4µm and 1.8 µm (1999)

rhe National Institute of Standards and Technology was established in 1988 by Congress to "
Deletion of MyD88 markedly attenuates sepsis-induced T and B lymphocyte apoptosis but worsens survival (2008)

Sepsis induces widespread lymphocyte apoptosis, resulting in impaired immune defenses and increased morbidity and mortality. There are multiple potential triggers or signaling molecules involved in mediating death signals. Elucidating the specific signaling pathways that are involved in mediating lymphocyte apoptosis may lead to improved therapies of this lethal disorder. We investigated a number of key cellular receptors and intracellular signaling pathways that may be responsible for apoptotic cell death. Specifically, we investigated the role of pathogen-associated molecular patterns (TLR2, TLR4, and IL-1R), intracellular signaling proteins (MyD88 and TRIF), cytoplasmic transcription factors (STAT1 and STAT4), and the MAPK pathway (JNK1) in sepsis-induced lymphocyte apoptosis. Studies were performed in the cecal ligation and puncture (CLP) model of sepsis using specific gene-targeted deletions. CLP-induced lymphocyte apoptosis was evaluated 20 h post-operation by active caspase-3 and TUNEL staining. Surprisingly, the only genetic construct that ameliorated T and B lymphocyte sepsis-induced apoptosis ( approximately 80% and 85%, respectively) occurred in MyD88(-/-) mice. Despite the marked decrease in sepsis-induced apoptosis, MyD88(-/-) mice had a worsened survival. In conclusion, lymphocyte death in sepsis likely involves multiple pathogen-sensing receptors and redundant signaling pathways. MyD88 was effective in blocking apoptosis, as it is essential in mediating most pathogen recognition pathways; however, MyD88 is also critical for host survival in a model of severe peritonitis.
Sunlight-Driven Dehydrogenative Oxidation Photocatalysis by a Mononuclear Complex Acting as both Chromophore and Catalyst (2020)

Under simulated solar irradiation in the visible spectral region, the catalytically active Ru IV -oxo species [Ru(O)(bpy)(tppz)] 2+ (tppz = tetrapyridylpyrazine, a strongly -accepting tridentate N,N,N-ligand) is produced directly from a single metal-to-ligand charge-transfer (MLCT) photoexcitation of the resting Ru II -aquo complex [Ru(H 2 O)(bpy)(tppz)] 2+ in aqueous media containing an electron acceptor. This photoinduced path to 2-electron/2-proton activation of a mononuclear catalyst (i.e., without a paired chromophoric unit) is enabled by the thermodynamic instability of the intermediate Ru III -hydroxo species [Ru(OH)(bpy)(tppz)] 2+ , which promptly disproportionates into the Ru IV -oxo and Ru II -aquo states as electrochemically observed by cyclic and pulse voltammetries in a wide range of pH. The proton-coupled multielectron photocatalytic capability of the complex in neutral aqueous solutions, at room conditions, was demonstrated through the dehydrogenative oxidation of benzyl alcohol into benzaldehyde with a product selectivity of about 100%. The performance of this mononuclear complex acting as chromophore/catalyst is comparable to that of the previously reported dinuclear complex [(tpy)Ru(tppz)Ru(H x O)(bpy)] 4+ . In addition to the characterization of redox and spectroscopic properties for the [Ru(L)(bpy)(tppz)] n+ derivatives with L = Cl -or H x O, structural analysis of the precursor chloro complex [RuCl(bpy)(tppz)](PF 6 ) was also performed by single-crystal X-ray diffraction in this work.
Understanding International Relations (2019)

This concise introductory text for students approaching the subject of international relations for the first time takes as its starting point the main theoretical approaches which have been adopted historically and shows how these can be applied to understanding the central questions of war and peace, poverty and wealth, economic management and global governance confronting the world today. The second edition has been revised and updated throughout with increased coverage of globalization and of the emerging 21st-century world order.
[The dynamic of biochemical stress reaction inductors in various tactics for surgical treatment of patients with a combined trauma of cranium and lower limbs ]. (2000)

In 31 patients after a craniocerebral trauma combined with a trauma of locomotor system (CCCT), and in 28 patients with only a limb fractures a time course (1, 3, 7, and 14 days) of biochemical stress reaction inductors (cortisol, serotonin, histamine, lipid peroxidation products) in various tactics of surgical treatment was studied. It was established that CCCT in a significantly stronger degree increases cortisol and lipid peroxidation products' levels than an isolated locomotor system trauma. An early postponed surgical intervention in lower extremities in CCCT results in the same increase in the biochemical stress reaction inductors as a late postpone surgical intervention in the lower extremities. In an early postponed osteosynthesis in CCCT patients, a mean term of hospital stay was 67 days, and in a late postponed one 117 days. The disability period was correspondingly 200 vs 315 days.
Low jitter FBAR based chip scale precision oscillator (2014)

We present a FBAR oscillator that operates at 628MHz, achieves low jitter <;50fs and good frequency stability all while fitting in a small package of 1.1 × 0.9 × 0.25 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> . The chip-scale oscillator employs a feedback circuitry in the encapsulating lid of a FBAR resonator and makes use of a differential Colpitts oscillator design fabricated in 0.6μm CMOS technology. To achieve the frequency precision required for a reference oscillator, we demonstrate the ability to tune the oscillator over 700ppm using a switched capacitor scheme to compensate for manufacturing tolerances. For achieving frequency stability over temperature and packaging stress, the FBAR resonators used in these oscillators employ silicon dioxide layer temperature compensation and a stress relieved structure respectively. The measured integrated jitter (12kHz to 20MHz) for the oscillators with a supply voltage of 3.3V across a wafer is 33fs with a far from carrier phase noise of -170dBc/Hz .The median current draw from the supply is 16.5mA and the output power measured at a 50ohm load using a balun is 0dBm.These oscillators are suitable for co-integration as reference clocks in high speed communication ICs where size and performance are paramount.
Selective Functionalization of 2-Fluoropyridine, 2,3-Difluoropyridine, and 2,5-Difluoropyridine at Each Vacant Position (2005)

The concept of "regioexhaustive substitution" has been successfully applied to 2-fluoro-, 2,3-difluoro-, and 2,5-difluoropyridine. All vacant positions were amenable to regioselective metalation and subsequent carboxylation by employing either chlorine as a neighboring site activating protective group or trimethylsilyl as a neighboring site screening protective group. In this way, approximately half a dozen fluorinated pyridinecarboxylic acids were derived from each starting material.