gebhart/patrepeval huggingface dataset:
NITRIC OXIDE GENERATION (1994)

The L-arginine:nitric oxide (NO) biosynthetic pathway has been proposed as an important mediator in host defense mechanisms and may therefore play a role in the acute allograft response. We have studied NO generation in liver allograft rejection and determined its value in immunological monitoring. Stable end products of this pathway have been determined serially in 50 primary liver recipients and compared with 2 known mediators and markers of acute allograft rejection (IL-2R positive lymphocytes and circulating TNF alpha). Plasma concentrations of acid-labile nitrosocompounds (NOx), which increased during acute allograft rejection (P < 0.0001), correlated with rejection severity and were reduced after administration of supplemental high dose glucocorticoids. Concentrations were significantly lower in nonrejection graft complications but were elevated during episodes of sepsis. Correlations between plasma NOx levels and circulating TNF-alpha (r = 0.451, P < 0.001) and IL-2R-positive lymphocytes in peripheral blood (r = 0.781, P < 0.001) were demonstrated. In a logistic analysis of these variables, plasma NOx was the most predictive parameter of an episode of acute cellular rejection. Nitric oxide generation in FK506-treated patients was lower compared with patients receiving a CsA-based immunosuppression regimen and was associated with a reduced frequency of acute rejection in the FK506 group. These data are consistent with a role for NO in the cellular alloantigen immune response and indicate that monitoring of plasma levels of NOx may be useful in the detection of acute allograft rejection.
Therapeutic peptidomimetic strategies for autoimmune diseases: costimulation blockade* (2005)

Cognate interactions between immune effector cells and antigen-presenting cells (APCs) govern immune responses. Specific signals occur between the T-cell receptor peptide and APCs and nonspecific signals between pairs of costimulatory molecules. Costimulation signals are required for full T-cell activation and are assumed to regulate T-cell responses as well as other aspects of the immune system. As new discoveries are made, it is becoming clear how important these costimulation interactions are for immune responses. Costimulation requirements for T-cell regulation have been extensively studied as a way to control many autoimmune diseases and downregulate inflammatory reactions. The CD28:B7 and the CD40:CD40L families of molecules are considered to be critical costimulatory molecules and have been studied extensively. Blocking the interaction between these molecules results in a state of immune unresponsiveness termed 'anergy'. Several different strategies for blockade of these interactions are explored including monoclonal antibodies (mAbs), Fab fragments, chimeric, and/or fusion proteins. We developed novel, immune-specific approaches that interfere with these interactions. Using experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis mediated by central nervous system (CNS)-specific T-cells, we developed a multi-targeted approach that utilizes peptides for blockade of costimulatory molecules. We designed blocking peptide mimics that retain the functional binding area of the parent protein while reducing the overall size and are thus capable of blocking signal transduction. In this paper, we review the role of costimulatory molecules in autoimmune diseases, two of the most well-studied costimulatory pathways (CD28/CTLA-4:B7 and CD40:CD40L), and the advantages of peptidomimetic approaches. We present data showing the ability of peptide mimics of costimulatory molecules to suppress autoimmune disease and propose a mechanism for disease suppression.
Segmented genome and nucleocapsid of La Crosse virus (1976)

La Crosse (LAC) virions purified by velocity and equilibrium gradient centrifugation contained three single-stranded RNA species. The three segments had sedimentation coefficients of 31S, 25S, and 12S by sodium dodecyl sulfate-sucrose gradient centrifugation. By comparison with other viral and cellular RNA species, the LAC viral RNAs had molecular weights of 2.9 x 10(6), 1.8 x 10(6), and 0.4 x 10(6). Phenol-sodium dodecyl sulfate-extracted LAC virion RNA was not infectious for BHK-21 cell cultures under conditions in which Sindbis viral RNA was infectious. Treatment of LAC virus with the nonionic detergent Triton X-100 and salt released three nucleocapsid structures, each containing one species of virion RNA. The nucleocapsids had sedimenation coefficients of 115S, 90S, and 65S. Negative-contrast electron microscopy of the nucleocapsids indicated that they were convoluted, supercoiled, and apparently circular. They had a mean diameter of 10 to 12 nm and modal lengths of 200, 510, and 700 nm (some were even longer). By chemical and enzymatic analysis of purified viral RNA, one type of 5' nucleotide (pppAp) present in the proportion of one per RNA segment was identified. After periodate oxidation, each virion RNA species was labeled by reduction with [3H]sodium borohydride. Taken together, these results suggest that although the nucleocapsids appear as closed loops, the viral RNA has free 5' and 3' ends and is, therefore, not circular.
Isolation and Identification of Flavonoids in Licorice and a Study of Their Inhibitory Effects on Tyrosinase (2005)

Five different flavonoids were isolated from licorice after multistep chromatographic fractionation. The aim was to identify and characterize active components in licorice responsible for antibrowning activities and to seek new tyrosinase inhibitors for applications as antibrowning and depigmenting agents in the food and cosmetic industries. The isolated flavonoids were identified as liquiritin, licuraside, isoliquiritin, liquiritigenin (from Glycyrrhiza uralensis Fisch.), and licochalcone A (from Glycyrrhiza inflate Bat.) by UV, MS, (1)H NMR, and (13)C NMR analyses. The inhibitory potencies and capacities of these flavonoids toward monophenolase activity of mushroom tyrosinase were investigated. The IC(50) values of licuraside, isoliquiritin, and licochalcone A for monophenolase activity were 0.072, 0.038, and 0.0258 mM, respectively. A study of the mechanisms of monophenolase inhibition by these flavonoids indicated that they are all competitive inhibitors. Different from the above flavonoids, no inhibitory activity was observed for liquiritin, whereas liquiritigenin activated the monophenolase activity as a cofactor. The inhibitory effect of licuraside, isoliquiritin, and licochalcone A on diphenolase activity with l-DOPA as the substrate was much lower than those with l-tyrosine. Results suggest that licuraside, isoliquiritin, and licochalcone A have the high potential to be further developed into effective antibrowning and depigmenting agents.
Mutations in the SLC3A1 transporter gene in cystinuria. (1995)

Cystinuria is an autosomal recessive disease characterized by the development of kidney stones. Guided by the identification of the SLC3A1 amino acid-transport gene on chromosome 2, we recently established genetic linkage of cystinuria to chromosome 2p in 17 families, without evidence for locus heterogeneity. Other authors have independently identified missense mutations in SLC3A1 in cystinuria patients. In this report we describe four additional cystinuria-associated mutations in this gene: a frameshift, a deletion, a transversion inducing a critical amino acid change, and a nonsense mutation. The latter stop codon was found in all of eight Ashkenazi Jewish carrier chromosomes examined. This report brings the number of disease-associated mutations in this gene to 10. We also assess the frequency of these mutations in our 17 cystinuria families.
Diffusion of the Interspecies Electron Carriers H 2 and Formate in Methanogenic Ecosystems and Its Implications in the Measurement of K m for H 2 or Formate Uptake (1989)

We calculated the potential H(2) and formate diffusion between microbes and found that at H(2) concentrations commonly found in nature, H(2) could not diffuse rapidly enough to dispersed methanogenic cells to account for the rate of methane synthesis but formate could. Our calculations were based on individual organisms dispersed in the medium, as supported by microscopic observations of butyrate-degrading cocultures. We isolated an axenic culture of Syntrophomonas wolfei and cultivated it on butyrate in syntrophic coculture with Methanobacterium formicicum; during growth the H(2) concentration was 63 nM (10.6 Pa). S. wolfei contained formate dehydrogenase activity (as does M. formicicum), which would allow interspecies formate transfer in that coculture. Thus, interspecies formate transfer may be the predominant mechanism of syntrophy. Our diffusion calculations also indicated that H(2) concentration at the cell surface of H(2)-consuming organisms was low but increased to approximately the bulk-fluid concentration at a distance of about 10 mum from the surface. Thus, routine estimation of kinetic parameters would greatly overestimate the K(m) for H(2) or formate.
Nanoheterogeneous Multilayer Films with Perfluorinated Domains Fabricated Using the Layer-by-Layer Method (2010)

Nanoheterogenous ultrathin films containing perfluorinated domains were prepared via the layer-by-layer (LbL) electrostatic self-assembly method. The films are constructed from the amphiphilic cationic copolymer with perfluorinated side chains and poly(sodium styrenesulfonate) (PSS). The LbL process was optimized by the application of sonication which allowed linear growth of the film. The resulting film exhibited micellar structure with isolated fluorocarbon hydrophobic domains. The remarkable features of the films were their switchable wettability and friction properties. The obtained water-processable films can find a number of potential applications, e.g., as smart and low friction coatings.
Fractionation of Mastic Gum in Relation to Antimicrobial Activity (2009)

Mastic gum is a viscous light-green liquid obtained from the bark of Pistacia lentiscus var. chia. which belongs to the Anacardiaceae family. The gum has been fractionated to investigate the antimicrobial activity of the whole gum and its fractions against various strains of Helicobacter pylori. The polymeric gum fraction was separated from the essential oil and the resin (trunk exudates without essential oil) to assess and compare the anti-H. pylori activity of the polymer fraction against lower molecular weight fractions, the gum itself and masticated gum. The polymer fraction was also oxidized and assessed for antimicrobial activity.
Analysis of a highly immunodominant epitope in the human immunodeficiency virus type 1 transmembrane glycoprotein, gp41, defined by a human monoclonal antibody (1990)

A human monoclonal antibody, 41-7 [immunoglobulin G1(kappa)], directed against the transmembrane glycoprotein gp41 of the human immunodeficiency virus type 1 (HIV-1) has been produced by direct fusion of lymph node cells from an HIV-1-infected individual with a human B-lymphoblastoid cell line. The minimal essential epitope for 41-7 was mapped to a conserved seven-amino acid sequence, N-CSGKLIC-C, located within the N-terminal part of gp41. Antibodies blocking the binding of 41-7 could be detected in the serum of all HIV-1-infected individuals tested, irrespective of the stage of the infection. The epitope is located externally to the plasma membrane, and it is accessible to antibody in the native conformation of the glycoprotein. Despite this, no neutralizing activity of 41-7 could be demonstrated in vitro. These data indicate, directly and indirectly, that this immunodominant epitope on gp41, although exposed on the viral surface, elicits antibodies lacking antiviral activity and, hence, should be avoided in future vaccine candidates.
FORESEE: Fully Outsourced secuRe gEnome Study basEd on homomorphic Encryption (2015)

Unlike many existing HME based studies, in which final results need to be computed by the data owner due to the lack of the secure division operation, the proposed FORESEE framework support complete outsourcing to the cloud and output the final encrypted chi-square statistics.
T cell receptor repertoire of infiltrating T cells in lips of Sjögren's syndrome patients. (1992)

Infiltrating T cells around salivary glands in the lips of Sjögren's syndrome (SjS) patients are crucial in the pathogenesis of this disease. To analyze the nature of infiltrating T cells, their T cell receptor repertoire was examined with quantitative polymerase chain reaction. The repertoire of V beta transcripts in lips of SjS was not restricted; however, the V beta 2 and V beta 13 genes were predominantly expressed on the T cells of lip specimens in six and four of seven lips, respectively. Predominance of these genes was specific in lips because no predominant V beta transcripts were found in lips from healthy subjects and PBLs from SjS patients. These results indicated that the V beta 2- and V beta 13-positive T cells expanded specifically and preferentially in SjS lips, thereby suggesting the possible role in triggering the autoimmunity of this disease.
Accelerated Walkthroughs of Virtual Environments Based on Visibility Preprocessing and Simplification (1998)

This paper proposes a new preprocessing method for interactive rendering of complex polygonal virtual environments. The approach divides the space that observer can reach into many rectangular viewpoint regions. For each region, an outer rectangular volume (ORV) is established to surround it. By adaptively partitioning the boundary of the ORV together with the viewpoint region, all the rays that originate from the viewpoint region are divided into the beams whose potentially visible polygon number is less than a preset threshold. If a resultant beam is the smallest and intersects many potentially visible polygons, the beam is simplified as a fixed number of rays and the averaged color of the hit polygons is recorded. For other beams, their potentially visible sets (PVS) of polygons are stored respectively. During an interactive walkthrough, the visual information related to the current viewpoint is retrieved from the storage. The view volume clipping, visibility culling and detail simplification are efficiently supported by these stored data. The rendering time is independent of the scene complexity.
Metabolism of Neurohypophysial Hormonesa (1993)

Over the past decade several new routes of neurohypophysial hormone metabolism have been identified. These include nonhepatic splanchnic clearance and renal clearance in addition to filtration that appears to be receptor mediated. The intraluminal degradation of VP in the proximal tubule, and distal tubular secretion, at least in one species, has been identified. The brain has been identified as a site for VP and OT metabolism, and the amniotic sac may be a major site for VP clearance in the guinea pig fetus. There have been generalized findings regarding VP and OT metabolism. First, VP metabolism in the whole body and in the amniotic sac appears to increase with increasing concentrations of hormone; this does not appear to be the case with OT. Also, evidence has been presented that suggests a potential for the formation of biologically active metabolites. There have been several associations of pathophysiological states with altered VP or OT metabolism, sometimes with plasma levels remaining unchanged. Lastly, caution is emphasized when measuring these hormones by RIA, and differences in specificities of antisera toward hormone metabolites must be considered.
Multimodal Convolutional Neural Networks for Matching Image and Sentence (2015)

In this paper, we propose multimodal convolutional neural networks (m-CNNs) for matching image and sentence. Our m-CNN provides an end-to-end framework with convolutional architectures to exploit image representation, word composition, and the matching relations between the two modalities. More specifically, it consists of one image CNN encoding the image content and one matching CNN modeling the joint representation of image and sentence. The matching CNN composes different semantic fragments from words and learns the inter-modal relations between image and the composed fragments at different levels, thus fully exploit the matching relations between image and sentence. Experimental results demonstrate that the proposed m-CNNs can effectively capture the information necessary for image and sentence matching. More specifically, our proposed m-CNNs significantly outperform the state-of-the-art approaches for bidirectional image and sentence retrieval on the Flickr8K and Flickr30K datasets.
Anomaly Intrusion Detection Systems: Handling Temporal Relations Between Events. (1999)

Lately, many approaches have been developed to discover computer abuse. Some of them use data mining techniques to discover anomalous behavior in audit trail, considering this behavior as an intrusive one. This paper discusses a temporal knowledge representation of users&amp;apos; behavior that is used by data mining tools to construct behavior patterns. These are used to decide whether current behavior follows a certain normal pattern or differs from all known users&amp;apos; behavior patterns. The representation uses Allen&amp;apos;s temporal interval algebra to describe the temporal relations between events caused by the user. Also we discuss how our representation is used to help in the concept drift when the set of training samples is reduced by removing old data which is no more used for classification.
An Introduction to Topological Data Analysis: Fundamental and Practical Aspects for Data Scientists (2021)

With the recent explosion in the amount, the variety, and the dimensionality of available data, identifying, extracting, and exploiting their underlying structure has become a problem of fundamental importance for data analysis and statistical learning. Topological data analysis (tda) is a recent and fast-growing field providing a set of new topological and geometric tools to infer relevant features for possibly complex data. It proposes new well-founded mathematical theories and computational tools that can be used independently or in combination with other data analysis and statistical learning techniques. This article is a brief introduction, through a few selected topics, to basic fundamental and practical aspects of tda for nonexperts.
Optimization of the helper-dependent adenovirus system for production and potency in vivo (2000)

Helper-dependent (HD) adenoviral vectors devoid of all viral coding sequences provide for safe and highly efficient gene transfer with long-lasting transgene expression. High titer stocks of HD vectors can be generated by using the cre-recombinase system. However, we have encountered difficulties with this system, including rearranged HD vectors and variable efficiency of HD vector rescue. These problems represent a major hindrance, particularly with regard to large-scale production. To overcome these limitations, we have modified the system in two ways: We constructed a new helper virus with a modified packaging signal and enhanced growth characteristics. We also redesigned the vector backbones by including noncoding adenovirus sequences adjacent to the right inverted terminal repeat and by incorporated a number of different segments of noncoding DNA of human origin as "stuffer." Comparison of these vectors showed that the nature of the stuffer sequence affects replication of the HD vector. Optimization of the system resulted in a more robust and consistent production of HD vectors with low helper contamination and high in vivo potency.
Tumor Necrosis Factor-α Develops Late Anaphylactic Reaction through Cytosolic Phospholipase A<sub>2</sub> Activation (2008)

TNF-alpha-induces cPLA(2) activation through the pathway involving p38 MAPK and ERK activation and appears to be the key mechanism leading to the development of late-phase anaphylaxis.
Automotive FM Diversity Systems, Part II: Analog Systems (2007)

&lt;div class="htmlview paragraph"&gt;This paper represents Part II of a three part series on automotive FM diversity systems. Part I (2007-01-1731) focuses on a review of propagation channel modeling and multipath fading. Part II deals with analog diversity systems which have been developed to combat the effects of this fading in an FM broadcast signal. Part III (2007-01-1734) discusses new FM diversity system designs that have been implemented in digital signal processors (DSP's).&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Analog automotive diversity systems have been in production for more than 20 years. The main purpose of a diversity system is to reduce the degraded reception performance caused by multipath propagation, mainly, the flat (amplitude) fading of the carrier. This is often accomplished by the use of two or more uncorrelated receiving antennas. This paper investigates the performance of analog implementations of Phase Aligning Systems (PAS) and Switched Antenna diversity systems in flat fading conditions and frequency selective multipath (long-delay) situation.&lt;/div&gt;
EmailValet: Learning Email Preferences for Wireless Platforms (1999)

this paper is the break-even point of a method. This method attempts to find a point where precision and recall are roughly equal. The precision of a classification method is the proportion of data that is labeled positive that really is positive, and the recall of a classification method is the proportion of all truly positive data that is labeled as positive. By varying the parameters to some classifiers, it is possible to get different pairs of these values, giving a curve of trade-offs between the two. The break-even point attempts to find the point on this curve where the two values are roughly equal. 2.5 Results
Expression of N -Acetylglucosaminyltransferase V Is Associated with Prognosis and Histology in Non-Small Cell Lung Cancers (2004)

GnT-V expression is associated with histology in NSCLCs. Low GnT-V expression is associated with shorter survival and poor prognosis in pStage I overall NSCLCs and non-squamous cell carcinomas.
Relation of Gestation Time to Brain Weight for Placental Mammals: Implications for the Theory of Vertebrate Growth (1974)

Duration of gestation in homothermic placental mammals has a much more precise alaxensis relation to neonatal brain size than to neonatal body size or any of three other neonatal or maternal dimensions. This was shown by a multivariate analysis of data on gestation time, neonatal and adult brain and body weight, and litter size for 91 species. These results can be explained by a theory of kinetics of fetal growth based on three hypotheses: (1) the brain is the slowest-growing organ in the fetal mammal; (2) it is also the pacemaker for growth of other tissues, which are held to its rate of growth; and (3) brain growth proceeds at the maximum rate allowed by its intrinsic growth law, so that the growth of all mammalian brains is governed in great degree by a single functional relation of attained size and time. The invariant rate constant for mammalian brain growth could be due to nutritional limitations or to the existence of an upper limit on rate of information flow during development.
Palladium‐Catalyzed Borylation of Aryl Chlorides: Scope, Applications, and Computational Studies (2007)

Von Chlorid zu Boronat: Biarylmonophosphan-Palladium-Katalysatoren zeichnen sich durch hohe Aktivität bei der Borylierung von Aryl- und Heteroarylchloriden aus (siehe Schema). Symmetrische und unsymmetrische Biaryle können auch direkt aus zwei Arylchloriden hergestellt werden, ohne dass die Boronatester-Zwischenprodukte isoliert werden müssen. Rechnungen geben Einblicke in die Rolle des Biarylphosphan-Liganden und der Base KOAc im Katalysezyklus. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z701551_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.