gebhart/patrepeval huggingface dataset:
Detection of multiple 'Ebnotypes' in individual Epstein-Barr virus carriers following lymphocyte transformation by virus derived from peripheral blood and oropharynx (1994)

Transformation of a B lymphocyte into a lymphoblastoid cell line (LCL) by Epstein-Barr virus (EBV) results in the expression of EBV nuclear antigens (EBNAs) of which the size spectrum ('Ebnotype') is characteristic for the transforming virion. Ebnotyping has been used as an epidemiological tool for studies of EBV infection. We compared the occurrence of a single and of multiple Ebnotypes, as defined by EBNAs 1, 2 and 6, in healthy and diseased EBV carriers. Cases from which two or more LCLs could be established from peripheral blood or oropharyngeal cultures were considered informative. The frequency of multiple Ebnotypes was relatively low in healthy individuals and in patients with infectious mononucleosis or with haematological diseases who were awaiting a bone marrow transplant [blood, 11 of 74 patients (15%); oropharynx, 12 of 49 patients (24%)], whereas it was relatively high in recipients of bone marrow or cardiac allografts and one patient with AIDS [blood, 12 of 34 patients (35%); oropharynx, 11 of 16 patients (69%)]. Three patterns of the simultaneous presence of multiple Ebnotypes were distinguished. The first, most frequent, pattern observed predominantly in oropharyngeal cultures of all groups consisted of minority Ebnotypes differing from the majority type by only a single EBNA protein (usually EBNA 1). The second, less frequent, pattern observed in the healthy carriers and the (candidate) transplant recipients consisted of minority Ebnotypes differing from the majority type by two EBNA proteins (mostly EBNAs 1 and 6). The third pattern, characterized by the simultaneous presence of totally different Ebnotypes, was restricted to the (candidate) transplant recipients and the AIDS patient and was more frequently observed in the blood than in the oropharynx. We suggest that the first two patterns result from heterologous recombinations occurring during viral replication at repeat sequences within the EBNA coding regions, whereas the third pattern reflects multiple infections with exogenous viruses.
Factor VIII Is Synthesized in Human Endothelial Cells, Packaged in Weibel-Palade Bodies and Secreted Bound to ULVWF Strings (2015)

The cellular synthesis site and ensuing storage location for human factor VIII (FVIII), the coagulation protein deficient in hemophilia A, has been elusive. FVIII stability and half-life is dependent on non-covalent complex formation with von Willebrand factor (VWF) to avoid proteolysis and clearance. VWF is synthesized in megakaryocytes and endothelial cells, and is stored and secreted from platelet alpha granules and Weibel-Palade bodies of endothelial cells. In this paper we provide direct evidence for FVIII synthesis in 2 types of primary human endothelial cells: glomerular microvascular endothelial cells (GMVECs) and umbilical vein endothelial cells (HUVECs). Gene expression quantified by real time PCR revealed that levels of F8 and VWF are similar in GMVECs and HUVECs. Previous clinical studies have shown that stimulation of vasopressin V2 receptors causes parallel secretion of both proteins. In this study, we found that both endothelial cell types express AVPR2 (vasopressin V2 receptor gene) and that AVPR2 mRNA levels are 5-fold higher in GMVECs than HUVECs. FVIII and VWF proteins were detected by fluorescent microscopy in Weibel-Palade bodies within GMVECs and HUVECs using antibodies proven to be target specific. Visual presence of FVIII and VWF in Weibel-Palade bodies was confirmed by correlation measurements. The high extent of correlation was compared with negative correlation values obtained from FVIII detection with cytoplasmic proteins, β-actin and Factor H. FVIII activity was positive in GMVEC and HUVEC cell lysates. Stimulated GMVECs and HUVECs were found to secrete cell-anchored ultra-large VWF strings covered with bound FVIII.
Platelet Phagocytosis and Processing of β-Amyloid Precursor Protein as a Mechanism of Macrophage Activation in Atherosclerosis (2002)

In human occluded saphenous vein grafts, we previously demonstrated cytotoxic foam cells, presumably derived from macrophages engulfing platelets. In the present study, we investigated whether platelet phagocytosis occurs in human atherosclerotic plaques, whether this activates macrophages, and whether the platelet constituent, amyloid precursor protein (APP), was involved. Immunohistochemistry documented the presence of APP, β-amyloid peptide (Aβ, cleaved from APP), and platelets (CD9), along with inducible NO synthase (iNOS) and cyclooxygenase-2, two markers of macrophage activation, around microvessels in advanced human carotid artery plaques (n=18). Aβ colocalized with iNOS-expressing macrophages that were often surrounded by platelets. In vitro, murine J774 and human THP-1 macrophages were incubated with or without washed human platelets. Coincubation of macrophages and platelets led to platelet phagocytosis (electron and confocal microscopy) and formation of lipid-, APP-, and Aβ-containing foam cells. These expressed iNOS mRNA (reverse transcription–polymerase chain reaction) and protein and produced nitrite and tumor necrosis factor-α (ELISA). Macrophage pretreatment with 4-(2-aminoethyl)benzenesulfonyl fluoride, a protease inhibitor, reduced APP processing and inhibited NO biosynthesis induced by platelet phagocytosis but not by lipopolysaccharides. Human atherosclerotic plaques and J774 and THP-1 macrophages contained mRNA of the APP-cleaving enzyme β-secretase. This is the first demonstration of Aβ, a peptide extensively studied in Alzheimer’s disease, in human atherosclerotic plaques. It was present in activated iNOS-expressing perivascular macrophages that had phagocytized platelets. In vitro studies indicate that platelet phagocytosis leads to macrophage activation and suggest that platelet-derived APP is proteolytically processed to Aβ, resulting in iNOS induction. This represents a novel mechanism for macrophage activation in atherosclerosis.
Eco‐friendly Crosslinking Agent for Acid Functional Acrylic Resin (2008)

Oil from J. multifida was extracted and it was first converted into N,N ‐bis(2‐hydroxyethyl) Jatropha fatty amide (HEJFA). HEJFA has been synthesized by reaction between Jatropha oil and diethanol amine in presence of zinc oxide as a catalyst. The reaction is relatively rapid and proceeded to high yield at 200±5 O C. The resulting HEJFA was used to formulate thermosetting coating compositions. Films were cured at ambient (air drying) and elevated (stove drying) temperatures using N, N ‐bis(2‐hydroxyethyl) Jatropha fatty amide (HEJFA) as eco‐friendly crosslinking agent for acrylic resin. The coating performance of the various compositions was tested by measurement of scratch hardness, impact strength and chemical resistance. The results show better performance of the HEJFA based compositions compared to butylated melamine formaldehyde (MF) based compositions.
Co‐administration of IGF‐I and glycosaminoglycans greatly delays motor neurone disease and affects IGF‐I expression in the <i>wobbler</i> mouse: a long‐term study (2002)

The study on wobbler mouse has shown that the combined treatment with low doses of glycosaminoglycans (GAGs) and insulin-like growth factor-I (IGF-I) fully prevented motor neurone death and forelimb impairment up to 9-12 weeks of a mouse's life. The effect was accompanied by the prevention of the early hypertrophy of wobbler neurones, an effect likely due to the promotion of neuronal survival. At the 18th week, wobbler mice treated with IGF-I + GAGs still showed significantly improved forelimb function, reduced muscle atrophy and a higher number of cervical motor neurones. IGF-I alone and GAGs alone were active up to the 3rd week of treatment; thereafter the beneficial effects of single treatments decreased drastically. GAGs and IGF-I treatments also affected IGF-I plasma and muscle levels. In wobbler mice there was a progressive reduction in IGF-I plasma levels that was prevented by IGF-I or GAGs alone and greatly increased, even above heterozygote levels, by the combination treatment. Such a powerful increase was correlated by a small enhancement in insulin-like growth factor binding protein-3 (IGFBP-3) plasma levels, while treatment with IGF-I alone affected very significantly both IGFBP-1 and IGFBP-3. Co-treatment also prevented the decrease in IGF-I content observed in vehicle-treated wobbler mice forelimb muscles.
Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal–Organic Frameworks: The Effect of Lateral Interactions for Methane/CPO-27-Mg (2012)

A hybrid method that combines density functional theory for periodic structures with wave function-based electron correlation methods for finite-size models of adsorption sites is employed to calculate energies for adsorption of CH(4) onto different sites in the metal-organic framework (MOF) CPO-27-Mg (Mg-MOF-74) with chemical accuracy. The adsorption energies for the Mg(2+), linker, second layer sites are -27.8, -18.3, and -15.1 kJ/mol. Adsorbate-adsorbate interactions increase the average CH(4) adsorption energy by about 10% (2.4 kJ/mol). The free rotor-harmonic oscillator-ideal gas model is applied to calculate free energies/equilibrium constants for adsorption on the individual sites. This information is used in a multisite Langmuir model, augmented with a Bragg-Williams model for lateral interactions, to calculate adsorption isotherms. This ab initio approach yields the contributions of the individual sites to the final isotherms and also of the lateral interactions that contribute about 15% to the maximum excess adsorption capacity. Isotherms are calculated for both absolute amounts, for calculation of isosteric heats of adsorption as function of coverage, and excess amounts, for comparison with measured isotherms. Agreement with observed excess isotherms is reached if the experimentally determined limited accessibility of adsorption sites (78%) is taken into account.
Low overhead Clifford gates from joint measurements in surface, color, and hyperbolic codes (2018)

One of the most promising routes towards fault-tolerant quantum computation utilizes topological quantum error correcting codes, such as the ${\mathbb{Z}}_{2}$ surface code. Logical qubits can be encoded in a variety of ways in the surface code, based on either boundary defects, holes, or bulk twist defects. However, proposed fault-tolerant implementations of the Clifford group in these schemes are limited and often require unnecessary overhead. For example, the Clifford phase gate in certain planar and hole encodings has been proposed to be implemented using costly state injection and distillation protocols. In this paper, we show that within any encoding scheme for the logical qubits, we can fault tolerantly implement the full Clifford group by using joint measurements involving a single appropriately encoded logical ancilla. This allows us to provide low overhead implementations of the full Clifford group in surface and color codes. It also provides the first proposed implementations of the full Clifford group in hyperbolic codes. We further use our methods to propose state-of-the art encoding schemes for small numbers of logical qubits; for example, for code distances $d=3,5,7$, we propose a scheme using $60,160,308$ (respectively) physical data qubits, which allow for the full logical Clifford group to be implemented on two logical qubits. To our knowledge, this is the optimal proposal to date, and thus may be useful for demonstration of fault-tolerant logical gates in small near-term quantum computers.
Virtual/Real Transfer in a Large-Scale Environment: Impact of Active Navigation as a Function of the Viewpoint Displacement Effect and Recall Tasks (2013)

The purpose of this study was to examine the effect of navigation mode (passive versus active) on the virtual/real transfer of spatial learning, according to viewpoint displacement (ground: 1 m 75 versus aerial: 4 m) and as a function of the recall tasks used. We hypothesize that active navigation during learning can enhance performances when route strategy is favored by egocentric match between learning (ground-level viewpoint) and recall (egocentric frame-based tasks). Sixty-four subjects (32 men and 32 women) participated in the experiment. Spatial learning consisted of route learning in a virtual district (four conditions: passive/ground, passive/aerial, active/ground, or active/aerial), evaluated by three tasks: wayfinding , sketch-mapping, and picture-sorting . In the wayfinding task , subjects who were assigned the ground-level viewpoint in the virtual environment (VE) performed better than those with the aerial-level viewpoint, especially in combination with active navigation. In the sketch-mapping task , aerial-level learning in the VE resulted in better performance than the ground-level condition, while active navigation was only beneficial in the ground-level condition. The best performance in the picture-sorting task was obtained with the ground-level viewpoint, especially with active navigation. This study confirmed the expected results that the benefit of active navigation was linked with egocentric frame-based situations.
Amphiphilic Resin‐Supported Ruthenium(II) Complexes as Recyclable Catalysts for the Hydrogenation of Supercritical Carbon Dioxide (2003)

Abstract Dichloro‐ and dihydridoruthenium(II) catalysts attached to an amphiphilic resin (PS−PEG) were prepared and tested for hydrogenation of supercritical carbon dioxide (scCO 2 ) in the presence of dimethylamine leading to N , N ‐dimethylformamide (DMF). The supported catalysts were successfully recyclable with only moderate loss of activity.
Epithelial Ovarian Cancer:  Disease Etiology, Treatment, Detection, and Investigational Gene, Metabolite, and Protein Biomarkers (2007)

Cancer research in recent years has immensely benefited from the development of novel technologies that enable scientists to perform detailed investigations of genomes, transcriptomes, proteomes, and metabolomes. This has invariably furthered knowledge of tumorigenesis and etiology of cancer. The resulting information can, in the foreseeable future, effect a significant change in the pace of cancer research, thereby producing improvements in patient care. Ovarian cancer in particular has received the interest of the scientific community, being the most frequent cause of death from gynecological cancers, characterized by few early symptoms, diagnosis at an advanced stage, as well as poor prognosis. Ovarian cancer is a malignancy in which normal ovarian cells begin to grow in an uncontrolled, abnormal manner and produce tumors in one or both ovaries. Epithelial cancers, the most common ovarian cancers (>80%), develop from cells lining the ovarian surface. Most ovarian cancer research is primarily focused on the early detection and treatment of epithelial ovarian cancer, the more common ovarian malignancy. This review offers an introduction to ovarian cancer, with particular emphasis on human epithelial ovarian cancer. Current methods of detection and therapy are discussed. A survey of promising new protein, gene, and metabolite biomarkers on the horizon is provided. Future prospects for improved diagnosis are offered.
Calculation of the wave propagation angle in complex media: application to turning wave simulations (2009)

The wave propagation angle is one of the key factors in seismic processing methods. For the dual-domain propagators, it is sometimes necessary to acquire the wave propagation angle in the space-frequency domain instead of the wavenumber domain or the angle domain. We propose a method dealing with this problem, in which the wavefield gradient is used for the calculation of the wave propagation angle. The wavefield gradient can be directly obtained by either the finite difference approximation or the marching expression of the propagator. This method is not applicable in the case of extremely low frequency due to the comparability between the wavelength and the grid interval. Combined with the superwide-angle one-way propagator, this approach is instrumental in simulating the turning wave, which is hard to be handled by the traditional one-way propagator. Numerical examples show the good performance of the superwide-angle one-way propagator with our approach involved. The turning wave is modelled accurately; as a result, a high-quality image of the overhanging salt flank can be obtained.
<i>PiggyBac</i> Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice (2010)

Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon-transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed that PiggyBac is capable of genome-wide mutagenesis. The PiggyBac screen uncovered many cancer genes not identified in previous retroviral or Sleeping Beauty transposon screens, including Spic, which encodes a PU.1-related transcription factor, and Hdac7, a histone deacetylase gene. PiggyBac and Sleeping Beauty have different integration preferences. To maximize the utility of the tool, we engineered 21 mouse lines to be compatible with both transposon systems in constitutive, tissue- or temporal-specific mutagenesis. Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability.
Location Accuracy of INS/Gravity-Integrated Navigation System on the Basis of Ocean Experiment and Simulation (2017)

An experiment comparing the location accuracy of gravity matching-aided navigation in the ocean and simulation is very important to evaluate the feasibility and the performance of an INS/gravity-integrated navigation system (IGNS) in underwater navigation. Based on a 1' × 1' marine gravity anomaly reference map and multi-model adaptive Kalman filtering algorithm, a matching location experiment of IGNS was conducted using data obtained using marine gravimeter. The location accuracy under actual ocean conditions was 2.83 nautical miles (n miles). Several groups of simulated data of marine gravity anomalies were obtained by establishing normally distributed random error N ( u , σ 2 ) with varying mean u and noise variance σ 2 . Thereafter, the matching location of IGNS was simulated. The results show that the changes in u had little effect on the location accuracy. However, an increase in σ 2 resulted in a significant decrease in the location accuracy. A comparison between the actual ocean experiment and the simulation along the same route demonstrated the effectiveness of the proposed simulation method and quantitative analysis results. In addition, given the gravimeter (1-2 mGal accuracy) and the reference map (resolution 1' × 1'; accuracy 3-8 mGal), location accuracy of IGNS was up to reach ~1.0-3.0 n miles in the South China Sea.
Is Forced Expiratory Volume in One Second the Best Measure of Severity in Childhood Asthma? (2004)

This essay focuses on whether FEV1 is the best measure of asthma severity in childhood asthma. For better or worse, FEV1 has become the gold standard lung function measurement in asthma, as it can be easily and quickly measured with relatively simple equipment. The current asthma guidelines use FEV1 in addition to daytime and nighttime symptoms in judging asthma severity (1, 2). Patients with mild persistent asthma are said to have FEV1 values of more than 80% of predicted, patients with moderate persistent asthma have values of 60 to 80% of predicted, whereas those with severe persistent asthma have values of less than 60% of predicted (1, 2). Despite widespread acceptance, neither are these criteria evidence-based nor is the basis of criteria described. FEV1 is also the outcome variable favored by the U.S. Food and Drug Administration to judge efficacy of asthma-controller medications. Thus, nearly all studies evaluating response to medications in asthma require subjects to have FEV1 values of 60 to 80% of predicted as essential entry criteria. Although this approach provides objective data to evaluate efficacy, it may not be the best measure for children with asthma. This is in large part because children with asthma are likely to have FEV1 values within the normal range when clinically stable.
Polymer semiconductor crystals (2010)

One of the long-standing challenges in the field of polymer semiconductors is to figure out how long interpenetrating and entangled polymer chains self-assemble into single crystals from the solution phase or melt. The ability to produce these crystalline solids has fascinated scientists from a broad range of backgrounds including physicists, chemists, and engineers. Scientists are still on the hunt for determining the mechanism of crystallization in these information-rich materials. Understanding the theory and concept of crystallization of polymer semiconductors will undoubtedly transform this area from an art to an area that will host a bandwagon of scientists and engineers. In this article we describe the basic concept of crystallization and highlight some of the advances in polymer crystallization from crystals to nanocrystalline fibers.
Use of monoclonal antibody to immunochemically characterize variant-specific surface coat glycoprotein from <i>Trypanosoma rhodesiense</i>. (1981)

Monoclonal antibodies were employed to study the molecular basis for charge heterogeneity in variant-specific surface coat glycoprotein prepared from clone CP3B4 of the Wellcome strain of Trypanosoma rhodesiense. Thirteen hybridomas secreting monoclonal antibodies specific for CP3B4 were obtained by fusing murine plasmacytoma cells to spleen cells from mice immunized with purified surface coat glycoprotein. The clone population of CP3B4 trypanosomes was shown to be homogeneous by means of immunofluorescent assays using culture supernatants from each of the 13 hybridomas. No cross-reactivity was found with other variant antigenic types of the same serodeme. Ascitic fluids were generated from 4 of the hybridomas and th molecular and epitopic specificities of the fluids or their IgG fractions were determined isoelectrofocusing of immunoprecipitates of radioiodinated glycoprotein antigen followed by autoradiography revealed that all 3 major components of the charge heterogeneous CP3B4 surface-coat glycoprotein were immunoprecipitated by each of the 4 monoclonal IgG fractions. Immunofluorescent staining of live trypanosomes was obtained with only one of the 4 ascitic fluids. The results show that charge heterogeneity does not derive from a heterogeneous population of parasites. Furthermore, the data indicate that there are at least 2 different epitopic specificities exhibited by the monoclonal antibodies tested and that each of the 3 charge heterogeneous components of the surface coat glycoprotein contains these epitopes. Charge heterogeneity of CP3B4 surface coat glycoprotein may be attributed to post-translational modification or to limited proteolysis.
The Risk of Cancer among Patients with Cystic Fibrosis (1995)

Although the overall risk of cancer in patients with cystic fibrosis is similar to that of the general population, there is an increased risk of digestive tract cancers. Persistent or unexplained gastrointestinal symptoms in these patients should be carefully investigated.