gebhart/patrepeval huggingface dataset:
Catheter Ablation of Pulmonary Vein Foci for Atrial Fibrillation (1999)

While experimental and human mapping studies have documented multiple wavelet reentry as the electrophysiological mechanism maintaining atrial fibrillation, recent evidence shows that nearly all paroxysms of atrial fibrillation are initiated by trains of rapid discharges from the pulmonary veins. Radiofrequency catheter ablation targeting these initiating triggers has resulted in an overall 69% freedom from atrial fibrillation at a follow-up of 8 +/- 4 months in a population of 110 patients with paroxysmal atrial fibrillation. Six of the targeted pulmonary veins (4%) developed pulmonary vein stenosis; none requiring specific treatment. Catheter ablation of pulmonary vein foci initiating atrial fibrillation is therefore an effective curative modality for paroxysmal atrial fibrillation.
Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analog 3,4-dihydrouridine and contribution of the 4-hydroxyl group to its binding affinity (1989)

Cytidine deaminase, purified to homogeneity from constitutive mutants of Escherichia coli, was found to bind the competitive inhibitors pyrimidin-2-one ribonucleoside (apparent Ki = 3.6 x 10(-7) M) and 5-fluoropyrimidin-2-one ribonucleoside (apparent Ki = 3.5 x 10(-8) M). Enzyme binding resulted in a change of the lambda max of pyrimidin-2-one ribonucleoside from 303 nm for the free species to 239 nm for the bound species. The value for the bound species was identical with that of an oxygen adduct formed by combination of hydroxide ion with 1,3-dimethyl-2-oxopyrimidinium (239 nm), but lower than that of a sulfur adduct formed by combination of the thiolate anion of N-acetylcysteamine with 1,3-dimethyl-2-oxopyrimidinium (259 nm). The results suggest that pyrimidin-2-one ribonucleoside is bound by cytidine deaminase as an oxygen adduct, probably the covalent hydrate 3,4-dihydrouridine, rather than intact or as an adduct involving a thiol group of the enzyme. In dilute solution at 25 degrees C, the equilibrium constant for formation of a single diastereomer of 3,4-dihydrouridine from pyrimidin-2-one ribonucleoside was estimated as approximately 4.7 x 10(-6), from equilibria of dissociation of water, protonation of 1-methylpyrimidin-2-one, and combination of the 1,3-dimethylpyrimidinium cation with the hydroxide ion.(ABSTRACT TRUNCATED AT 250 WORDS)
Effects of Leukotriene D on the Airways in Asthma (1983)

One characteristic of patients with asthma is that their airways are exquisitely sensitive to a variety of inhaled stimulants. For example, their airways regularly become obstructed after inhalation of bronchoconstrictor substances at 1/100 to 1/300 of the concentration required to produce a similar response in normal persons.1 2 3 4 This airway hyperresponsiveness is nonspecific: patients react to low concentrations of agents of different chemical classes as well as to substances that are not smooth-muscle constrictors.5 The recent identification of a new family of bronchoconstrictors, the sulfidopeptide leukotrienes C, D, and E (previously termed slow-reacting substance of anaphylaxis, or SRS-A),6 7 8 allows further study . . .
A Strong Candidate for the Breast and Ovarian Cancer Susceptibility Gene BRCA1 (1994)

A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods. Probable predisposing mutations have been detected in five of eight kindreds presumed to segregate BRCA1 susceptibility alleles. The mutations include an 11-base pair deletion, a 1-base pair insertion, a stop codon, a missense substitution, and an inferred regulatory mutation. The BRCA1 gene is expressed in numerous tissues, including breast and ovary, and encodes a predicted protein of 1863 amino acids. This protein contains a zinc finger domain in its amino-terminal region, but is otherwise unrelated to previously described proteins. Identification of BRCA1 should facilitate early diagnosis of breast and ovarian cancer susceptibility in some individuals as well as a better understanding of breast cancer biology.
Binding of IL-1 alpha , IL-1 beta , and IL-1 receptor antagonist by soluble IL-1 receptors and levels of soluble IL-1 receptors in synovial fluids. (1994)

These studies have examined the binding of the three IL-1 ligands, IL-1 alpha, IL-1 beta, and IL-1 receptor antagonist (IL-1 ra), to soluble forms of types I and II IL-1Rs (sIL-1RI and sIL-1RII). This interaction was measured in direct binding experiments, in which the ligands bound to immobilized sIL-1R, and in inhibition experiments, in which sIL-1R in solution inhibited the binding of IL-1 ligands to immobilized sIL-1R. In addition, the effects of sIL-1R on the detection of IL-1 ligands by ELISA were examined. Finally, levels of sIL-1R in synovial fluid samples were determined, and their effects on measurement of IL-1 in these samples were estimated. IL-1 beta bound more avidly to sIL-1RII than IL-1 alpha or IL-1ra, primarily because of a slow dissociation rate. In contrast, IL-1 ra bound more avidly than IL-1 alpha or IL-1 beta to sIL-1RI, again because of a slow dissociation rate. sIL-1RII and sIL-1RI inhibited the detection of IL-1 beta and IL-1ra, respectively, by ELISA. Low levels of sIL-1RI (approximately 1.0-2.5 ng/ml) were present in all synovial fluids, irrespective of the degree of inflammation, and were correlated inversely with the levels of measured IL-1ra. In contrast, higher levels of sIL-1RII (approximately 10-20 ng/ml) were found in inflammatory synovial fluids and were not correlated with IL-1ra levels. IL-1 beta could not be detected in any synovial fluid. These results suggest that some IL-1 beta and IL-1ra may be bound in vivo to sIL-1RII and sIL-1RI, respectively, leading to underestimations of cytokine concentrations in body fluids when measured by ELISA.
Novel pathways for implantation and establishment and maintenance of pregnancy in mammals (2009)

Uterine receptivity to implantation varies among species, and involves changes in expression of genes that are coordinate with attachment of trophectoderm to uterine lumenal and superficial glandular epithelia, modification of phenotype of uterine stromal cells, silencing of receptors for progesterone and estrogen, suppression of genes for immune recognition, alterations in membrane permeability to enhance conceptus-maternal exchange of factors, angiogenesis and vasculogenesis, increased vascularity of the endometrium, activation of genes for transport of nutrients into the uterine lumen, and enhanced signaling for pregnancy recognition. Differential expression of genes by uterine epithelial and stromal cells in response to progesterone, glucocorticoids, prostaglandins and interferons may influence uterine receptivity to implantation in mammals. Uterine receptivity to implantation is progesterone-dependent; however, implantation is preceded by loss of expression of receptors for progesterone (PGR) so that progesterone most likely acts via PGR-positive stromal cells throughout pregnancy. Endogenous retroviruses expressed by the uterus and/or blastocyst also affect implantation and placentation in various species. Understanding the roles of the variety of hormones, growth factors and endogenous retroviral proteins in uterine receptivity for implantation is essential to enhancing reproductive health and fertility in humans and domestic animals.
Iago attacks (2013)

In recent years, researchers have proposed systems for running trusted code on an untrusted operating system. Protection mechanisms deployed by such systems keep a malicious kernel from directly manipulating a trusted application's state. Under such systems, the application and kernel are, conceptually, peers, and the system call API defines an RPC interface between them. We introduce Iago attacks , attacks that a malicious kernel can mount in this model. We show how a carefully chosen sequence of integer return values to Linux system calls can lead a supposedly protected process to act against its interests, and even to undertake arbitrary computation at the malicious kernel's behest. Iago attacks are evidence that protecting applications from malicious kernels is more difficult than previously realized.
Recyclable and repolymerizable thiol–X photopolymers (2018)

Truly recyclable and repolymerizable photopolymers were achieved by utilizing thiol–ene polymerization and thiol–thioester exchange reactions.
The TSIMMIS project: Integration of heterogeneous information sources (1994)

The goal of the Tsimmis Project is to develop tools that facilitate the rapid integration of heterogeneous information sources that may include both structured and unstructured data. This paper gives an overview of the project, describ-ing components that extract properties from unstructured objects, that translate information into a common object model, that combine information from several sources, that allow browsing of information, and that manage constraints across heterogeneous sites. Tsimmis is a joint project be-tween Stanford and the IBM Almaden Research Center. 1
siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells (2003)

RNA interference has emerged as a powerful tool for the silencing of gene expression in animals and plants. It was reported recently that 21 nt synthetic small interfering RNAs (siRNAs) specifically suppressed the expression of endogenous genes in several lines of mammalian cells. However, the efficacy of siRNAs is dependent on the presence of a specific target site within the target mRNA and it remains very difficult to predict the best or most effective target site. In this study, we demonstrate that siRNAs that have been generated in vitro by recombinant human Dicer (re-hDicer) significantly suppress not only the exogenous expression of a puromycin-resistance gene but also the endogenous expression of H-ras, c-jun and c-fos. In our system, selection of a target site is not necessary in the design of siRNAs. However, it is important to avoid homologous sequences within a target mRNA in a given protein family. Our diced siRNA system should be a powerful tool for the inactivation of genes in mammalian cells.
A novel polarization smart antenna (2002)

The wave propagating through the mobile channel becomes partially depolarised by polarization-dependent scattering. Measurements of the amount of depolarization (XPD-cross polarization discrimination) for linear polarizations reveal an energy transfer of -8 to -15 dB to the orthogonal polarization in outdoor propagation, indicating that the wave is essentially polarized. The independent fading of the wave components are commonly interpreted as being randomly polarized but the histogram of the incident wave appears to be bounded by an eccentric ellipse-like shape with an axial-ratio equal to the value of XPD. Moreover, the measured projection of the averaged-in-time polarization of the incident wave is found to be highly correlated over a wide frequency bandwidth. This observation serves as the foundation for a new polarization-matching algorithm, whereby the time-average polarization of the incident wave serves to adjust the polarization of the transmission back to each individual mobile station (MS). This process recovers a substantial portion of the polarization-induced transmission losses that may exceed 10 dB, and serves to reduce the forward power control variations, and the average transmit power of the base-transceiver-station (BTS), as well as the induced interference. The paper presents the proof-of-concept polarization matching trial, and the analysis of the results. A novel polarization-matching smart-antenna system architecture is described.
Effect of precise mechanical loading on fibroblast populated collagen lattices: Morphological changes (1998)

The contraction of a collagen lattice by resident fibroblasts causes strains to be developed within that lattice. These strains can be increased or decreased by altering the aspect ratio (ratio of length/width/thickness) of the fibroblast populated collagen lattice, as the cross-sectional area resisting the strain is changed and by the application of an external load. The fibroblasts align themselves with the direction of the maximum principle strain; in effect, these cells are "hiding" from the perceived strain. The direction of the maximum principle strain can be predetermined by the use of a computational finite element analysis. Using the tensioning-Culture Force Monitor to apply pre-determined loading patterns of known repeatable magnitudes, as calculated by the finite element analysis, we have succeeded in aligning fibroblasts into a deliberate predicted orientation. This study has shown that the resident fibroblast population will respond to changes in strain resulting from the most subtle of mechanical loads. This may be an important mechanism in development and repair of connective tissue.
In Pursuit of Carbohydrate‐Based HIV Vaccines, Part 1: The Total Synthesis of Hybrid‐Type gp120 Fragments (2004)

Schlüsselschritte in der erfolgreichen Synthese von hybriden gp120-Fragmenten (siehe Bild) umfassen β-Mannosylierungen zum Aufbau des Trisaccharidkerns und eine Fragmentkupplung zur Einführung der „oberen“ High-Mannose-Einheiten. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2004/z53625_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.
Two-step affinity purification of U7 small nuclear ribonucleoprotein particles using complementary biotinylated 2'-O-methyl oligoribonucleotides. (1991)

U7 snRNP is a low-abundance small nuclear ribonucleoprotein particle essential for 3' processing of replication-dependent histone pre-mRNA. We have developed a two-step purification of the particle from TB21 mouse mastocytoma cell nuclear extracts, with about a 20% overall yield, using affinity binding to 2'-O-methyl oligoribonucleotides. The purified particle is homogeneous with respect to RNA content. SDS/PAGE of the U7 snRNP proteins revealed a full complement of the standard core proteins (B, DD', E, F, and G) found in the majority of snRNPs. In addition, two U7-specific polypeptides of 14 kDa and 50 kDa were identified. Summation of the molecular masses of the identified components of the U7 particle yields a particle mass of 249 kDa, in approximate agreement with estimates from sucrose gradient sedimentation (261 kDa) and nondenaturing gradient PAGE (217 kDa).
Domain Substructure of HPV E6 Oncoprotein:  Biophysical Characterization of the E6 C-Terminal DNA-Binding Domain (2003)

E6 is a viral oncoprotein implicated in cervical cancers, produced by high-risk human papillomaviruses (HPVs). Structural data concerning this protein are scarce due to the difficulty of producing recombinant E6. Recently, we described the expression and purification of a stable, folded, and biologically active HPV16 E6 mutant called E6 6C/6S. Here, we analyzed the domain substructure of this mutated E6. Nonspecific proteolysis of full-length E6 6C/6S (158 residues) yielded N-terminal and C-terminal fragments encompassing residues 7-83 and 87-158, respectively. The C-terminal fragment of residues 87-158 was cloned, overexpressed, and purified at concentrations as high as 1 mM. The purified domain retains the selective four-way DNA junction recognition activity of the full-length E6 protein. Using UV absorption, UV fluorescence, circular dichroism, and nuclear magnetic resonance, we show that the peptide is primarily monomeric and folded with equal proportions of alpha-helix and beta-sheet secondary structure.
Generalized Potential of Adult Neural Stem Cells (2000)

The differentiation potential of stem cells in tissues of the adult has been thought to be limited to cell lineages present in the organ from which they were derived, but there is evidence that some stem cells may have a broader differentiation repertoire. We show here that neural stem cells from the adult mouse brain can contribute to the formation of chimeric chick and mouse embryos and give rise to cells of all germ layers. This demonstrates that an adult neural stem cell has a very broad developmental capacity and may potentially be used to generate a variety of cell types for transplantation in different diseases.
Human papillomavirus DNA in normal, metaplastic, preneoplastic and neoplastic epithelia of the cervix uteri (1988)

Colposcopically directed cervical punch biopsies from 362 patients were screened by Southern blot hybridization for the presence of DNA of human papillomavirus (HPV) 6, 10, 11, 16, 18, 31 and 33. The biopsies represented original squamous epithelium, epithelium of metaplastic origin, different stages of cervical intraepithelial neoplasia (CIN) and invasive carcinomas. HPV6/11, 16, 18 and 31 were detected in 2.9% to 13.7% of histologically normal epithelia. HPV6/11 prevailed in CIN I. HPV16 was clearly more abundant than other HPV types in high-grade CIN and invasive cancers (50%-60%), compared with healthy epithelium. Restriction enzyme cleavage analysis of DNA from primary cancers and corresponding metastases proved the stable association of HPV16 DNA with invasive tumor cells. Preliminary follow-up studies of CIN II patients suggested that HPV16-associated lesions are relatively more likely to persist or to progress. Taken together, the data support the notion of a higher oncogenic potential of HPV16.
Whisker growth induced by implantation of cultured vibrissa dermal papilla cells in the adult rat (1986)

Retention of the capacity to induce the growth of hair by cultured adult rat vibrissa dermal papilla cells has been investigated. Small pellets of serially cultured papilla cells were implanted into the bases of the exposed follicular epidermis of amputated adult rat vibrissa follicles. Amputated follicles that received no cell implants or implants of cultured dorsal skin fibroblasts were used as controls. Over 50% of follicles implanted with cultured papilla cells in the passage range 1-3 grew hairs. In contrast none of the follicles that received late passage cells (range 6-15) produced hairs; and spontaneous regeneration of hair occurred in only 3% of the control follicles. These results demonstrate that cultured papilla cells of early passage numbers retain their ability to induce hair growth. Histological examination confirmed that the implanted papilla cells interacted with follicular epidermis to organize the development of new, hair-producing bulbs, each containing a discrete dermal papilla. An important observation was that aggregative behaviour leading to papilla formation was only manifested by early passage papilla cell implants. This persisting embryonic characteristic appears to be an essential functional component of papilla cell activity which operates to regulate the profound morphogenetic changes that occur during the hair growth cycle.
Control of intestinal inflammation by regulatory T cells (2001)

Summary: Transfer of CD4 + T cells to immune‐deficient mice in the absence of the CD25 + subset leads to the development of colitis, indicating that regulatory cells capable of controlling a bacteria‐driven inflammatory response are present in normal mice. Cells with this function are present in the thymus as well as in the periphery of germ‐free mice, suggesting they may be reactive with self‐antigen. These cells resemble CD4 + CD25 + cells that inhibit organ‐specific autoimmunity, suggesting that a similar subset of regulatory T cells may control responses to self and foreign antigens. Development of colitis is dependent on accumulation of activated CD134L + dendritic cells (DC) in the mesenteric lymph nodes, which is inhibited by CD4 + CD25 + cells, indicating that regulatory T cells may control DC activation in vivo . Whilst inhibition of T‐cell activation in vitro by CD4 + CD25 + cells does not involve interleukin‐10 and transforming growth factor‐β, these cytokines are required for the suppression of colitis. It may be that control of responses that activate the innate immune system requires multiple mechanisms of immune suppression. Recently, we identified CD4 + CD25 + cells with immune suppressive activity in the thymus and peripheral blood of humans, raising the possibility that dysfunction in this mechanism of immune regulation may be involved in the development of autoimmune and inflammatory diseases.
Yellow fever 17D as a vaccine vector for microbial CTL epitopes (2005)

The yellow fever vaccine 17D (17D) is safe, and after a single immunizing dose, elicits long-lasting, perhaps lifelong protective immunity. One of the major challenges facing delivery of human vaccines in underdeveloped countries is the need for multiple injections to achieve full efficacy. To examine 17D as a vector for microbial T cell epitopes, we inserted the H-2K(d)-restricted CTL epitope of the circumsporozoite protein (CS) of Plasmodium yoelii between 17D nonstructural proteins NS2B and NS3. The recombinant virus, 17D-Py, was replication competent and stable in vitro and in vivo. A single subcutaneous injection of 10(5) PFU diminished the parasite burden in the liver by approximately 70%. The high level of protection lasted between 4 and 8 wk after immunization, but a significant effect was documented even 24 wk afterwards. Thus, the immunogenicity of a foreign T cell epitope inserted into 17D mimics some of the remarkable properties of the human vaccine. Priming with 17D-Py followed by boosting with irradiated sporozoites conferred sterile immunity to 90% of the mice. This finding indicates that the immune response of vaccine-primed individuals living in endemic areas could be sustained and magnified by the bite of infected mosquitoes.
Role of Individual T-Cell Epitopes of Theiler’s Virus in the Pathogenesis of Demyelination Correlates with the Ability To Induce a Th1 Response (1998)

Intracerebral inoculation of susceptible strains of mice with Theiler's murine encephalomyelitis virus (TMEV) results in immune-mediated demyelination. Three major T-cell epitopes have previously been identified within the VP1 (VP1233-250), VP2 (VP274-86), and VP3 (VP324-37) capsid proteins in virus-infected SJL/J mice. These epitopes appear to account for the majority ( approximately 90%) of major histocompatibility complex class II-restricted T-cell responses to TMEV. Interestingly, the effect of immunization with synthetic peptides bearing the predominant T-cell epitopes on the course of TMEV-induced demyelination indicates that T cells reactive to the VP1 and VP2 epitopes, but not VP3, accelerate the pathogenesis of demyelination. The predominant pathogenic role of the T cells is verified by similar immunization with the fusion proteins containing the entire individual capsid proteins. The order of appearance and level of T cells specific for the individual epitopes during the course of demyelination are similar to each other. However, cytokine profiles of T cells from virus-infected mice indicate that T cells specific for the VP1 (and perhaps the VP2) epitope are Th1, whereas T cells reactive to VP3 are primarily Th2. These results suggest that Th1-type cells specific for VP1 and VP2 are involved in the pathogenesis of viral demyelination induced by TMEV. Thus, a predominance of Th1-inducing viral epitopes is likely critical for the pathogenesis of demyelination.
ChemInform Abstract: THERMAL LACTONIZATION OF BROMINATED ALKYLIDENEMALONATES‐ SYNTHESIS OF 2‐BUTEN‐4‐OLIDES (1978)

Abstract Von den nach bekanntem Schema aus (I) über (II) erhaltenen Verbindungen (III) reagieren (IIIa), (IIIb) und (IIId) bei Erhitzen in siedenen Xylol zu den Butenoljden (1V)‐ Bromierung von (IIe) führt schon bei Raumtemp. direkt zu (IVe).