gebhart/patrepeval huggingface dataset:
Transforming Growth Factor β and Cyclosporin A Inhibit the Inducible Activity of the Interleukin-2 Gene in T Cells Through a Noncanonical Octamer-Binding Site (1993)

Transforming growth factor beta (TGF-beta) has a growth-inhibitory effect on numerous different cell types of the immune system, including T lymphocytes. We show in this study that the inhibitory action of TGF-beta on T lymphocytes is accompanied by a block of interleukin 2 (IL-2) gene expression which is mediated, at least in part, by inhibition of IL-2 promoter/enhancer activity. The functional analysis of cis-regulatory (proto-enhancer) elements of the IL-2 enhancer/promoter region showed that the most TGF-beta-responsive element maps to its so-called upstream promoter site. The proto-enhancer activity of the upstream promoter site element is also inhibited by cyclosporin A. The upstream promoter site DNA harbors two noncanonical, closely linked binding sequences for octamer and AP-1-like factors. Both sites are involved in the establishment of IL-2 enhancer activity. Since the activity of genuine octamer sites but not that of AP-1-binding sites is also impaired by TGF-beta and cyclosporin A in El4 T lymphoma cells, we conclude that both immunosuppressives interfere with the activity but not the DNA binding of octamer factors in T lymphocytes.
The primary structure of the α subunit of human elongation factor 1 (1986)

The primary structure of the alpha subunit of elongation factor 1 (EF-1 alpha) from human MOLT 4 cells was determined by cDNA sequencing. The data show that the conservation of the amino acid sequence is more than 80% when compared with yeast and Artemia EF-1 alpha. An inventory of amino acid sequences around the guanine-nucleotide-binding site in elongation factor Tu from Escherichia coli and homologous amino acid sequences in G proteins, initiation and elongation factors and proteins from the RAS family shows two regions containing conserved sequence elements. Region I has the sequence apolar-Xaa-Xaa-Xaa-Gly-Xaa-Xaa-Yaa-Xaa-Gly-LYs-Thr(Ser)- -Xaa-Xaa-Xaa-Xaa-X-apolar. Except for RAS proteins, Yaa is always an acidic amino acid residue. Region II is characterized by the invariant sequence apolar-apolar-Xaa-Xaa-Asn-Lys-Xaa-Asp. In order to facilitate sequence comparison we have used a graphic display, which is based on the hydrophilicity values of individual amino acids in a sequence.
Inhibition of platelet function by recombinant soluble ecto-ADPase/CD39. (1998)

Excessive platelet accumulation and recruitment, leading to vessel occlusion at sites of vascular injury, present major therapeutic challenges in cardiovascular medicine. Endothelial cell CD39, an ecto-enzyme with ADPase and ATPase activities, rapidly metabolizes ATP and ADP released from activated platelets, thereby abolishing recruitment. Therefore, a soluble form of CD39, retaining nucleotidase activities, would constitute a novel antithrombotic agent. We designed a recombinant, soluble form of human CD39, and isolated it from conditioned media from transiently transfected COS-1 cells and from stably transfected Chinese hamster ovary (CHO) cells. Conditioned medium from CHO cells grown under serum-free conditions was subjected to anti-CD39 immunoaffinity column chromatography, yielding a single approximately 66-kD protein with ATPase and ADPase activities. Purified soluble CD39 blocked ADP-induced platelet aggregation in vitro, and inhibited collagen-induced platelet reactivity. Kinetic analyses indicated that, while soluble CD39 had a Km for ADP of 5.9 microM and for ATP of 2.1 microM, the specificity constant kcat/Km was the same for both substrates. Intravenously administered soluble CD39 remained active in mice for an extended period of time, with an elimination phase half-life of almost 2 d. The data indicate that soluble CD39 is a potential therapeutic agent for inhibition of platelet-mediated thrombotic diatheses.
A Double-Inactivated Severe Acute Respiratory Syndrome Coronavirus Vaccine Provides Incomplete Protection in Mice and Induces Increased Eosinophilic Proinflammatory Pulmonary Response upon Challenge (2011)

Severe acute respiratory syndrome coronavirus (SARS-CoV) is an important emerging virus that is highly pathogenic in aged populations and is maintained with great diversity in zoonotic reservoirs. While a variety of vaccine platforms have shown efficacy in young-animal models and against homologous viral strains, vaccine efficacy has not been thoroughly evaluated using highly pathogenic variants that replicate the acute end stage lung disease phenotypes seen during the human epidemic. Using an adjuvanted and an unadjuvanted double-inactivated SARS-CoV (DIV) vaccine, we demonstrate an eosinophilic immunopathology in aged mice comparable to that seen in mice immunized with the SARS nucleocapsid protein, and poor protection against a nonlethal heterologous challenge. In young and 1-year-old animals, we demonstrate that adjuvanted DIV vaccine provides protection against lethal disease in young animals following homologous and heterologous challenge, although enhanced immune pathology and eosinophilia are evident following heterologous challenge. In the absence of alum, DIV vaccine performed poorly in young animals challenged with lethal homologous or heterologous strains. In contrast, DIV vaccines (both adjuvanted and unadjuvanted) performed poorly in aged-animal models. Importantly, aged animals displayed increased eosinophilic immune pathology in the lungs and were not protected against significant virus replication. These data raise significant concerns regarding DIV vaccine safety and highlight the need for additional studies of the molecular mechanisms governing DIV-induced eosinophilia and vaccine failure, especially in the more vulnerable aged-animal models of human disease.
Rapid quantitative detection of BCR-ABL transcripts in chronic myeloid leukemia patients by real-time reverse transcriptase polymerase-chain reaction using fluorescently labeled probes. (2000)

We may conclude that the TaqMan probe technology can be easily adapted to HybProbes with equivalent results. Besides, the results of BCR-ABL quantification in the follow-up of patients clearly confirm that real-time PCR with HybProbes is a reliable and sensitive method for monitoring minimal residual leukemia after HSCT in CML patients.
The polysaccharide fucoidan inhibits microvascular thrombus formation independently from P‐ and l‐selectin function in vivo (2000)

Taken together, our novel findings suggest that fucoidan effectively prevents microvascular thrombus formation induced by endothelial damage in arterioles and venules in vivo. This protective effect of fucoidan is not attributable to inhibition of P- and L-selectin function but may instead be related to the anticoagulative capacity of fucoidan.
Chemical Analysis of Inorganic and Organic Surfaces and Thin Films by Static Time‐of‐Flight Secondary Ion Mass Spectrometry (TOF‐SIMS) (1994)

Abstract By using mass spectrometry to analyze the atomic and molecular secondary ions that are emitted from a solid surface when bombarded with ions, one obtains detailed information about the chemical composition of the surface. A time‐of‐flight mass spectrometer is especially suitable for the analysis of secondary ions because of its high transmission, high mass resolution, and ability to detect ions of different masses simultaneously. By using a finely focused primary ion beam it is also possible to analyze microareas and generate surface images with a lateral resolution of 0.1 μm or less. Static time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) allows monolayer imaging and local analysis of monolayers with high sensitivity, a wide mass range, high mass resolution, and high lateral resolution. Besides information on elements and isotopes, the technique yields direct information on the molecular level and can also be used to analyze surface species of high molecular mass that are thermally unstable and cannot be vaporized. The method can be applied to practically all types of materials and sample forms, including insulators in particular. In this article the basic principles of TOF‐SIMS are explained, and its analytical capabilities for both large area and imaging applications are illustrated by examples. These include silicon surfaces (both uniform and structured), thermally unstable organic molecules on surfaces, synthetic polymers, and synthetically prepared molecular surface films, particles, and fibers. Emitted neutral particles can also be analyzed by postionization with a laser, and the possibilities of this technique are discussed.
Phylogeny of related functions: the case of polyamine biosynthetic enzymes (2000)

Genome annotation requires explicit identification of gene function. This task frequently uses protein sequence alignments with examples having a known function. Genetic drift, co-evolution of subunits in protein complexes and a variety of other constraints interfere with the relevance of alignments. Using a specific class of proteins, it is shown that a simple data analysis approach can help solve some of the problems posed. The origin of ureohydrolases has been explored by comparing sequence similarity trees, maximizing amino acid alignment conservation. The trees separate agmatinases from arginases but suggest the presence of unknown biases responsible for unexpected positions of some enzymes. Using factorial correspondence analysis, a distance tree between sequences was established, comparing regions with gaps in the alignments. The gap tree gives a consistent picture of functional kinship, perhaps reflecting some aspects of phylogeny, with a clear domain of enzymes encoding two types of ureohydrolases (agmatinases and arginases) and activities related to, but different from ureohydrolases. Several annotated genes appeared to correspond to a wrong assignment if the trees were significant. They were cloned and their products expressed and identified biochemically. This substantiated the validity of the gap tree. Its organization suggests a very ancient origin of ureohydrolases. Some enzymes of eukaryotic origin are spread throughout the arginase part of the trees: they might have been derived from the genes found in the early symbiotic bacteria that became the organelles. They were transferred to the nucleus when symbiotic genes had to escape Muller's ratchet. This work also shows that arginases and agmatinases share the same two manganese-ion-binding sites and exhibit only subtle differences that can be accounted for knowing the three-dimensional structure of arginases. In the absence of explicit biochemical data, extreme caution is needed when annotating genes having similarities to ureohydrolases.
Serum antibodies against p53 in relation to cancer risk and prognosis in breast cancer: a population-based epidemiological study (1999)

To perform an epidemiological evaluation of the predictive value of p53 autoantibodies in breast cancer, we measured antibodies against p53 in serum samples from 165 breast cancer patients in comparison with serum samples from 330 healthy controls, selected from the same population as the cases and matched for age, sex and specimen storage time. Median age of patients was 51 years (range 25–64 years). Presence of serum p53 autoantibodies was analysed by enzyme-linked immunosorbent assay (ELISA) and confirmed by Western blotting. The lower ELISA reactivities were similar for cases and controls, but presence of high-level reactivity was more common among cases than among controls [odds ratio (OR) 9.03, 95% confidence interval (CI) 2.40–50.43]. Presence of Western blot-detected p53 autoantibodies had a very similar association (OR 10.8, CI 3.0–59.4). Among the cases, we also studied whether there was any correlation between level of anti-p53 antibodies and stage of the disease or survival. There was no significant correlation between presence of antibodies and stage of the disease. There was a significant negative correlation between presence of p53 antibodies and survival (P= 0.003). A stepwise multivariate Cox regression analysis showed that T-stage, age and presence of anti-p53 antibodies were significant independent prognostic variables, with a dose-dependent negative effect on survival for all three variables. We conclude that presence of anti-p53 antibodies are of significance both for the risk of having breast cancer and the risk of dying from breast cancer.
The Evolving Relation between Humans andMycobacterium tuberculosis (1998)

Until the middle of this century, tuberculosis was, in Dickens's words, “a disease which medicine never cured, wealth warded off, or poverty could boast exemption from — which sometimes moves in giant strides, and sometimes at a tardy sluggish pace, but, slow or quick, is ever sure and certain.”1 Mycobacterium tuberculosis is an extremely successful pathogen that continues to thrive in developing countries and is reemerging in the industrialized world. Globally, it remains a more frequent cause of death than any other infectious agent.2 Approximately a third of the world's population is infected with M. tuberculosis, and the World Health . . .
Low threshold voltage vertical-cavity lasersfabricated by selective oxidation (1994)

Novel vertical-cavity surface emitting lasers fabricated using selective oxidation to form a current aperture under a top monolithic distributed Bragg reflector mirror are reported. Large cross-sectional area lasers (259 µm2) exhibit threshold current densities of 150 A/cm2 per quantum well and record low threshold voltage of 1.33 V. Smaller lasers (36 µm2) possess threshold currents of 900 µA with maximum output powers greater than 1 mW. The record performance of these oxidised vertical-cavity lasers arises from the low mirror series resistance and very efficient current injection into the active region.
The Purine Phosphoribosyltransferases of Crithidia fasciculata (1979)

The purine phosphoribosyltransferases of Crithidia fasciculata were identified and some of their properties described. The organism possesses three separate enzymes for the production of AMP, IMP, and GMP. The evidence for this comes from the observed differences in elution patterns from gel filtration columns, differences in heat sensitivity, and especially the clear separation of hypoxanthine phosphoribosyltransferase from guanine phosphoribosyltransferase by affinity chromatography on GMP-agarose. APRTase is activated most efficiently by Zn++, whereas HPRTase and GPRTase are activated most effectively by Co++. In no case did the product mononucleotides produce strong inhibition of the transferase activities.
Autoimmune Diseases: The Failure of Self Tolerance (1990)

The ability to discriminate between self and nonself antigens is vital to the functioning of the immune system as a specific defense against invading microorganisms. Failure of the immune system to "tolerate" self tissues can result in pathological autoimmune states leading to debilitating illness and sometimes death. The induction of autoimmunity involves genetic and environmental factors that have focused the attention of researchers on the trimolecular complex formed by major histocompatibility complex molecules, antigen, and T cell receptors. Detailed molecular characterization of these components points to potential strategies for disease intervention.
Analysis of short-chain acids from anaerobic bacteria by high-performance liquid chromatography (1982)

A standard mixture of 25 short-chain fatty acids was resolved by high-performance liquid chromatography, using an Aminex HPX-87 column. The acids produced in culture media by anaerobic bacteria were analyzed by high-performance liquid chromatography after extraction with ether and reextraction into a small volume of 0.1 N NaOH. The presence of fumaric acid in culture extracts of Peptostreptococcus anaerobius was confirmed by gas chromatography-mass spectrometry analysis of the trapped eluent fractions from the high-performance liquid chromatography column.
Coupled Iron Corrosion and Chromate Reduction: Mechanisms for Subsurface Remediation (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoupled Iron Corrosion and Chromate Reduction: Mechanisms for Subsurface RemediationRobert M. Powell, Robert W. Puls, Sharon K. Hightower, and David A. SabatiniCite this: Environ. Sci. Technol. 1995, 29, 8, 1913–1922Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/es00008a008https://doi.org/10.1021/es00008a008research-articleACS PublicationsRequest reuse permissionsArticle Views1435Altmetric-Citations341LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Novel Biphenyl Ether Lignans from the Rhizomes of Curcuma chuanyujin. (2000)

Three new biphenyl ether lignans, 1, 2 and 3, were isolated from the rhizomes of Curcuma chuanyujin along with curcuminoid compounds 4, 5 and 6 and their chemical structures were determined to be 1-feruloyloxy-2-methoxycinnamic acid, 1-feruloyloxy cinnamic acid and (1-p-hydroxycinnamoyl) cinnamic acid by means of spectral evidence. The latter three known substances showed antioxidant activity.
A Novel Random PWM Technique With Low Computational Overhead and Constant Sampling Frequency for High-Volume, Low-Cost Applications (2005)

A novel random pulse-width modulation (PWM) technique for three-phase voltage-source inverters, characterized by low computational overhead, a variable switching frequency, and a constant sampling frequency, is presented. The technique is based on two strategies: 1) the so-called arithmetic PWM (APWM), which yields the same switching patterns as the classic space-vector modulation, but with minimal computational effort and 2) randomization of switching periods by varying the delay of switching cycles with respect to corresponding sampling cycles. Simplicity of the technique, named a variable-delay random PWM (VDRPWM) method, allows its implementation in cheap, low-end processors. It makes the VDRPWM the best choice for high-volume, low-cost applications, such as domestic and automotive ac drives and UPSs. The random aspect of the technique has a mitigating effect on the acoustic and electromagnetic noise emitted by the supplied system. This feature has been confirmed by experiments with a 40-hp induction motor drive.
Heat shock proteins as novel therapeutic targets in cancer. (2008)

Heat shock proteins (HSPs) are evolutionarily conserved molecules synthesised by cells exposed to sub-lethal stresses. Acting as molecular chaperones, HSPs protect cells from environmental stress damage by assisting in proper folding and stabilisation of proteins. In addition, they help to sequester severely damaged proteins for degradation. Owing to the nature of their function, HSPs are often found to be overexpressed in a wide range of cancers. Members of the HSP family have been implicated in cancer growth as promoting tumour cell proliferation as well as inhibiting cellular death pathways. In recent years, several HSP90 client proteins have been validated as clinically important therapeutic targets for treatment of cancer, and inhibitors of HSP90 have emerged as potentially beneficial anticancer agents. This review explores the involvement of HSPs in cancer and the development of several anticancer agents with promising therapeutic applications.
How to store traceroute measurements and related metrics (2006)

This memo describes a standard way to store traceroute measurements
and related metrics. To better address the traceroute measurements
storing issue, the authors first of all give a definition of the
traceroute tool, describe the tool itself as well as its parameters
and the default values on the most common operating systems and the
output results that can be stored. Afterwards, the common information
model with the base elements of the traceroute measurement storing is
defined dividing the information elements in two semantically
separated groups (configuration elements and results ones). Moreover
an additional element is defined to relate configuration elements and
results ones by means of a common unique identifier. On the basis of
the information model a data model is then proposed in order to
actually store the traceroute measurements. Finally considerations on
how to extract relevant metrics related to traceroute measurements are
given.
Cell cycle and functional differences between CD34+/CD38hi and CD34+/38lo human marrow cells after in vitro cytokine exposure (1995)

The proliferation kinetics and clonogenic activity of CD34+/38hi (CD38hi) and CD34+/38lo (CD38lo) human marrow cells were measured before and after culturing the cells in vitro over a 6-day period in serum-deprived medium containing recombinant growth factors (interleukin-1 [IL-1], IL-3, IL-6, granulocyte colony-stimulating factor [G-CSF], granulocyte-macrophage [GM]-CSF, kit ligand, and erythropoietin). Before in vitro culture, 3% +/- 3% of the CD38lo and 13% +/- 2% of the CD38hi cells were in the S-phase of the cell cycle. The clonogenic activity of CD38hi cells was twofold greater than that of the CD38lo cells, as measured by colony-forming units (CFU) in short-term assays. However, CD38hi cells contained fewer pre-CFU than did the CD38lo cells, generating only 3 +/- 2 colonies per 1,000 cells after 4 weeks of culture on competent stromal layers, compared with 107 +/- 46 colonies per 1,000 cells from the CD38lo population. CD38hi and CD38lo cells exhibited distinctly different responses when cultured in serum-deprived medium supplemented with recombinant growth factors. After culturing cells for 24 hours, CD38lo cells essentially remained a noncycling population with only 5.1% +/- 3.0% of the cells cycling, whereas 44.2% +/- 6.9% of the CD38hi cells were in DNA synthesis. Gradually CD38lo cells were recruited into cycle, such that by 72 hours, approximately 28% of the CD38lo cells were in S-phase. However, during 6 days of culture, the percentage of cycling CD38lo cells never exceeded the proliferative response observed for CD38hi cells. Phenotype analysis conducted at day 6 indicated that 86% of the CD38hi population were no longer phenotypically CD34+/38hi, while 60% of CD38lo cells maintained a CD34+/38lo phenotype. Long-term cultures initiated with 6-day in vitro-expanded CD38lo cells showed approximately a twofold decrease in clonogenic activity attributable to a loss of erythroid precursors and a decrease in GM colonies. Thus, a proportion of CD38lo cells capable of generating CFU was maintained even after exposure to growth factors.
Issues associated with p-type band-edge effective work function metal electrodes: Fermi-level pinning and flatband roll-off (2007)

Issues associated with the integration of p-type band-edge (5.0~5.2 eV) effective work function (EWF) electrodes are identified and discussed. The Fermi-level (E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f</sub> ) pinning effect traditionally used to explain the lowering of p-MOS EWF is believed not to be an intrinsic limitation. However, a new described as the "flatband (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fb</sub> ,) rolloff effect" is shown to be the dominant factor.