gebhart/patrepeval huggingface dataset:
Gramicidin A Aggregation in Supported Gel State Phosphatidylcholine Bilayers (1996)

Using an atomic force microscope, supported bilayers of saturated phosphatidylcholine (in the gel state) containing various amounts of gramicidin A (gA) were imaged in aqueous solutions and at room temperature. gA clusters were directly observed for the first time under these conditions. It was found that, at a lower gA concentration, gA aggregated into domains, composed of small clusters along with a considerable amount of lipids. This basic aggregation unit, most likely a hexamer, remained the same for acyl chain lengths from 14 to 18 carbons. These small clusters were observed to form elongated aggregates (line type) but never into extended pure gA domains. When gA concentrations were increased, for bilayers with 16 carbons or less, gA aggregated into larger domains but the basic unit remained separated by lipid molecules. At about 5 mol % gA, a percolation-like transition occurred at which the line type aggregates were connected to each other. However, for bilayers with more than 16 carbons, multiple lamellar structures were formed at higher gA fractions and the top layer had a ripple-like surface morphology. The molecular mechanism for the formation of these peculiar structures remains to be elucidated.
Reg protein: a potential beta-cell-specific growth factor? (1996)

Beta-cell regeneration in adult pancreas is usually considered to be limited. However, various animal models suggest that this tissue is still capable of regeneration under certain conditions. Reg protein could be responsible for this replicative process. The reg gene codes for a 166 amino-acid protein usually synthesized and secreted by pancreatic acinar cells but expressed in islet beta cells during experimental regenerative processes in animals (90% pancreatectomy + nicotinamide, or insulinoma tumor removal in rats, or the "wrapping pancreas model" in the hamster). In addition, recombinant rat reg protein can stimulate beta-cell replication in vivo and in vitro. In animal models of Type 1 diabetes mellitus, reg gene overexpression occurs during active phases of diabetogenesis and could be a defence mechanism. During human pancreatic development, reg gene is expressed at an early stage but is not associated with the expression of other pancreatic genes. Conversely, gene expression for reg and insulin are correlated in adult pancreas. Accordingly, reg protein could be a beta-cell-specific growth factor implicated in the maintenance of beta-cell mass, especially in adult pancreas.
Ki-67 expression is a prognostic marker of prostate cancer recurrence after radical prostatectomy. (1996)

Proliferative activity as measured by the Ki-67 proliferative antigen, MIB 1, appears to be a prognostic marker of recurrent prostate cancer after radical prostatectomy.
Plasma D‐dimer levels and their relationship to serum fibrinogen/fibrin degradation products in hypercoagulable states (1989)

Plasma D-dimer was measured and compared with serum fibrinogen/fibrin degradation product levels (FDPs) in patients with disseminated intravascular coagulation (DIC) and other conditions associated with a hypercoagulable state. D-dimer (N less than 200 ng/ml) was elevated in all 43 patients with DIC, in 48 of 59 patients with liver disease, in 22 of 27 patients with acute leukaemia at presentation, in 17 of 23 patients with malignant disease, in 29 of 39 women in the third trimester of a complicated pregnancy, in 17 of 18 patients with deep venous thrombosis and in only four of 27 patients with acute myocardial infarction. There was a significant correlation between plasma D-dimer and serum FDP levels (P less than 0.01) as follows; DIC: r = 0.58, liver disease: r = 0.57, acute leukaemia: r = 0.84, malignancy: r = 0.87. The frequent elevation of D-dimer observed in liver disease, acute leukaemia, malignancy and complicated pregnancy indicates that a hypercoagulable state is a common occurrence in these conditions although in liver disease elevated levels resulting from a failure of normal clearance mechanisms cannot be excluded. The close relationship between D-dimer and FDP levels suggests that serum FDPs predominantly arise from the interaction of plasmin with crosslinked fibrin rather than with fibrinogen in the conditions in which these were compared.
The Metabolic Syndrome: A Global Public Health Problem and A New Definition (2005)

The constellation of metabolic abnormalities including centrally distributed obesity, decreased high-density lipoprotein cholesterol (HDL-C), elevated triglycerides, elevated blood pressure (BP), and hyperglycaemia is known as the metabolic syndrome. Associated with a 3 fold and 2 fold increase in type 2 diabetes and cardiovascular disease (CVD), respectively, it is thought to be a driver of the modern day epidemics of diabetes and CVD and has become a major public health challenge around the world. Since its initial description, several definitions of the syndrome have emerged. Each of these definitions used differing sets of criteria, which reflected contrasting views on pathogenic mechanisms and the need for clinical usefulness. The use of these definitions to conduct research into the metabolic syndrome in diverse populations resulted in wide ranging prevalence rates, inconsistencies and confusion, and spurred on the vigorous debate regarding how the metabolic syndrome should be defined. In response to this controversy, the International Diabetes Federation (IDF) has recently proposed a new definition, which is applicable to populations around the world. It is envisaged that the development of the new definition for the metabolic syndrome will help resolve the confusion caused by the number of earlier attempts to define this important entity.
Control of DNA Strand Displacement Kinetics Using Toehold Exchange (2009)

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.
Why Order Matters: Turing Equivalence in Automated Systems Administration (2002)

Hosts in a well-architected enterprise infrastructure are self-administered; they perform their own maintenance and upgrades. By definition, self-administered hosts execute self-modifying code. They do not behave according to simple state machine rules, but can incorporate complex feedback loops and evolutionary recursion.The implications of this behavior are of immediate concern to the reliability, security, and ownership costs of enterprise and mission-critical computing. In retrospect, it appears that the same concerns also apply to manually-administered machines, in which administrators use tools that execute in the context of the target disk to change the contents of the same disk. The self-modifying behavior of both manual and automatic administration techniques helps explain the difficulty and expense of maintaining high availability and security in conventionally-administered infrastructures.The practice of infrastructure architecture tool design exists to bring order to this self-referential chaos. Conventional systems administration can be greatly improved upon through discipline, culture, and adoption of practices better fitted to enterprise needs. Creating a low-cost maintenance strategy largely remains an art. What can we do to put this art into the hands of relatively junior administrators? We think that part of the answer includes adopting a well-proven strategy for maintenance tools, based in part upon the theoretical properties of computing.In this paper, we equate self-administered hosts to Turing machines in order to help build a theoretical foundation for understanding this behavior. We discuss some tools that provide mechanisms for reliably managing self-administered hosts, using deterministic ordering techniques.Based on our findings, it appears that no tool, written in any language, can predictably administer an enterprise infrastructure without maintaining a deterministic, repeatable order of changes on each host. The runtime environment for any tool always executes in the context of the target operating system; changes can affect the behavior of the tool itself, creating circular dependencies. The behavior of these changes may be difficult to predict in advance, so testing is necessary to validate changed hosts. Once changes have been validated in testing they must be replicated in production in the same order in which they were tested, due to these same circular dependencies.The least-cost method of managing multiple hosts also appears to be deterministic ordering. All other known management methods seem to include either more testing or higher risk for each host managed.This paper is a living document; revisions and discussion can be found at Infrastructures.Org, a project of TerraLuna, LLC.
Fungal pretreatment of aspen chips improves strength of refiner mechanical pulp (1988)

Pretreatment of wood chips with lignin-degrading fungi can improve the strength properties of unbleached refiner mechanical pulps. We studied the effect of two white-rot fungi (Phanerochaete chrysosporium and Dichomitus squalens) prior to refiner mechanical pulping. Strength and optical properties were compared in handsheets prepared from mechanical pulp of treated and untreated wood chips. Both fungal pretreatments resulted in handsheet strength properties better than the control when compared at an equivalent freeness. Fungal pretreatments decreased brightness and light-scattering coefficients but did not adversely affect opacity. Brightness of fungus pretreated pulps was restored to that of the control by use of hydrogen peroxide bleaching. Lignin content of the chips was reduced by the fungal pretreatments.
Functions of Invertebrate Hemoglobins with Special Reference to Adaptations to Environmental Hypoxia (1980)

The oxygen-binding properties and some associated structural features of invertebrate hemoglobins (Hb) are reviewed together with the environmental conditions (particularly in stressful habitats) that influence oxygen-binding functions in nature. Compared to the vertebrates invertebrate Hbs display a spectacular variation in functional properties, which is manifest within the major systematic groups of animals and within the different histological and molecular categories of the pigment. This variability is seen primarily to represent adaptations to the wide range of environmental conditions to which Hb-bearing invertebrates are subjected in nature but also to reflect certain organismic functions, which determine the internal conditions under which the Hbs work in life. These adaptations appear to be uniquely directed towards optimizing the transfer of oxygen from the environmental source to the mitochondrial combustion sites. The immense structural and functional complexity of invertebrate Hb systems may well compensate for a decreased organization at the organ level compared to that in vertebrates shifting more of the regulatory burden to the molecular level.
Automatic indexing and content-based retrieval of captioned images (1995)

The interaction of textual and photographic information in an integrated text/image database environment is being explored. Specifically, our research group has developed an automatic indexing system for captioned pictures of people; the indexing information and other textual information is subsequently used in a content-based image retrieval system. Our approach presents an alternative to traditional face identification systems; it goes beyond a superficial combination of existing text-based and image-based approaches to information retrieval. By understanding the caption accompanying a picture, we can extract information that is useful both for retrieving the picture and for identifying the faces shown. In designing a pictorial database system, two major issues are (1) the amount and type of processing required when inserting new pictures into the database and (2) efficient retrieval schemes for query processing. Our research has focused on developing a computational model for understanding pictures based on accompanying descriptive text. Understanding a picture can be informally defined as the process of identifying relevant people and objects. Several current vision systems employ the idea of top-down control in picture understanding. We carry the notion of top-down control one step further, exploiting not only general context but also picture-specific context.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunogenicity of osteogenic protein 1: results from a prospective, randomized, controlled, multicenter pivotal study of uninstrumented lumbar posterolateral fusion (2010)

Recombinant human OP-1 (bone morphogenetic protein 7), like many recombinant human proteins, induces an immune response following its use as a bone graft alternative. This response was transient and diminished over time, and there was no statistical evidence to suggest an association between Nab status and any of the efficacy or safety criteria that were examined.
Induction of Proinflammatory Cytokines in Primary Human Macrophages by Influenza A Virus (H5N1) Is Selectively Regulated by IFN Regulatory Factor 3 and p38 MAPK (2009)

The hyperinduction of proinflammatory cytokines and chemokines such as TNF-alpha, IFN-beta, and CCL2/MCP-1 in primary human macrophages and respiratory epithelial cells by the highly pathogenic avian influenza H5N1 is believed to contribute to the unusual severity of human H5N1 disease. Here we show that TNF-alpha, IFN-beta, and IFN-lambda1 are the key mediators directly induced by the H5N1 virus in primary human macrophages. In comparison with human influenza (H1N1), the H5N1 virus more strongly activated IFN regulatory factor 3 (IRF3). IRF3 knockdown and p38 kinase inhibition separately and in combination led to a substantial reduction of IFN-beta, IFN-lambda1, and MCP-1 but only to a partial reduction of TNF-alpha. IRF3 translocation was independent of p38 kinase activity, indicating that IRF3 and p38 kinase are distinct pathways leading to cytokine production by H5N1 virus. We conclude that IRF3 and p38 kinase separately and predominantly contribute to H5N1-mediated induction of IFN-beta, IFN-lambda1, and MCP-1 but only partly control TNF-alpha induction. A more precise identification of the differences in the regulation of TNF-alpha and IFN-beta could provide novel targets for the design of therapeutic strategies for severe human H5N1 influenza and also for treating other causes of acute respiratory distress syndrome.
A New Ultrasensitive Bioluminogenic Enzyme Substrate forβ-Galactosidase (1992)

A derivative of D-luciferin, D-luciferin-O-beta-galactoside, was synthesized and used as highly sensitive substrate for beta-galactosidase. The substrate was physicochemically characterized. Enzymatic cleavage of the new compound by beta-galactosidase was demonstrated and kinetic constants Km, Vmax, kcat and kcat/Km have been determined. The compound has been proved to be a highly sensitive substrate for beta-galactosidase, permitting a limit of detection of 3.7 x 10(-19) mol of enzyme per assay.
Adipose-Derived Stem Cells (2008)

Human adipose tissue has been shown to contain a population of cells that possesses extensive proliferative capacity and the ability to differentiate into multiple cell lineages. These cells are referred to as adipose tissue-derived stem cells (ADSCs) and are generally similar, though not identical, to mesenchymal stem cells (also referred to as marrow stromal cells). ADSCs for research are most conveniently extracted from tissue removed during an elective cosmetic liposuction procedure but may also be obtained from resected adipose tissue. This chapter describes surgical procedures associated with improved ADSC recovery and the processes by which aspirated adipose tissue is washed and digested with collagenase to yield a heterogeneous population from which ADSCs can be expanded. The large volume of tissue obtained from a liposuction procedure (average approximately 2 L), combined with the relatively high frequency of ADSC within the digestate, yields substantially more stem cells than can be realized from marrow without extensive expansion in culture.
Identification of the nonamer peptide from influenza A matrix protein and the role of pockets of HLA‐A2 in its recognition by cytotoxic T lymphocytes (1992)

Influenza matrix peptide 58-66 is shown to be the optimal nonamer for binding to HLA-A2 and presentation to cytotoxic T lymphocytes (CTL). If titered out to 2 x 10(-10) - 4 x 10(-10) M in CTL-mediated lysis assays and to 3 x 10(-9) M in an HLA-A2 assembly-stabilization assay in cell lysates. The peptide was shown to make probable contacts with its carboxy terminus close to residue 116 in the floor of the cleft of HLA-A2, close to the F pocket. The side chain of the amino-terminal amino acid was unimportant, but its free amino and carbonyl groups in the A pocket appeared important in optimizing peptide presentation. The B pocket probably accommodates the side chain of residue 2 (isoleucine) and was shown to be critical in peptide presentation.
Characterization of cis -Regulatory Elements and Nuclear Factors Conferring Th2-Specific Expression of the IL-5 Gene: A Role for a GATA-Binding Protein (1998)

Expression of the IL-5 gene is restricted to the Th2 subset of helper T cells. We have previously defined four cis-regulatory elements of the IL-5 promoter responding to PMA and cAMP in EL-4 cells. We now report that the 1.2-kb region of the IL-5 promoter directs expression of the IL-5 gene in a Th2 clone but not a Th1 clone, indicating that transcription from the IL-5 promoter is Th2 specific. For the functioning of the IL-5 promoter in a Th2 clone, IL-5C and IL-5CLE0 were critical. IL-5CLE0 interacted with both constitutive and inducible nuclear factors (designated NFIL-5CLE0), which existed in both Th1 and Th2 clones, whereas IL-5C interacted with a constitutive nuclear factor (designated NFIL-5C), which was found only in Th2 but not in Th1 clones. Th2 specificity of NFIL-5C was also confirmed using in vitro-differentiated Th1 and Th2 cells derived from TCR-transgenic mice. The sequence for NFIL-5C binding bears homology with GATA-binding sites. The NFIL-5C complex was supershifted by an anti-GATA-3 Ab and inhibited by an oligonucleotide containing GATA-binding sites. We showed preferential expression of GATA-3 in Th2 cells. Finally, we demonstrated that in vitro-translated GATA-3 bound to IL-5C and overexpression of GATA-3 augmented stimulation-dependent IL-5 promoter activity in EL-4 cells. Taken together, our results provide evidence that GATA-related factors may be involved in Th2-specific expression of the IL-5 gene.
Studies on the Damage Induced by Drilling Fluids in Limestone Cores (1999)

Abstract Well productivity can be seriously reduced by excessive fluid loss and solids invasion while drilling. If not adequately controlled, losses may push hydrocarbons very far from the hole and solids may plug the pores, increasing the time necessary for testing the well and distorting the evaluation of its productivity potential. Laboratory procedures for determining the damage of a mud system on rock samples are traditionally based on the return permeability test which provides an indication of both the damaging potential of mud and the efficiency of cleanup techniques. The non-destructive nuclear magnetic resonance (NMR) measurement is a new methodology for studying the influence of small scale geological heterogeneities on fluid flow and trapping. It permits to check the invasion of solids and filtrate present in the mud using different experimental set-ups. The main advantage is the possibility to have the spatial distribution of the invading phase inside the rock sample. Low frequency (2 MHz) nuclear magnetic resonance relaxation (NMRR) measurements were also used for following the effect of solid mud particulate invasion on the pore size distribution. These techniques provide fast and reliable analysis without the destruction of the sample. This paper reports the laboratory procedures and the results of a study aimed at determining the damage coming from the penetration of bentonite/mixed metal particle aggregates and polymers into low permeability carbonatic reservoirs. The results were compared with both traditional and innovative methods. Combined with spurt loss, non conventional rheological approaches, dynamic filtration and mud cake SEM (scanning electron microscopy) observations, nuclear magnetic resonance imaging (NMRI) provides precise and directly observable results to distinguish the severity of damage, the type and depth of invasion and, even more, the distribution of invaded particles in the matrix. The integration of conventional and advanced methods to study damage appears to be highly promising for selecting drilling fluids, with suitable components and particle size distribution appropriate to protect the reservoirs.
Single Molecule Fluorescence Spectroscopy at Ambient Temperature (1999)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSingle Molecule Fluorescence Spectroscopy at Ambient TemperatureW. Patrick Ambrose, Peter M. Goodwin, James H. Jett, Alan Van Orden, James H. Werner, and Richard A. KellerView Author Information Chemical Science and Technology Division and Life Sciences Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 Cite this: Chem. Rev. 1999, 99, 10, 2929–2956Publication Date (Web):September 23, 1999Publication History Received18 February 1999Revised16 July 1999Published online23 September 1999Published inissue 13 October 1999https://pubs.acs.org/doi/10.1021/cr980132zhttps://doi.org/10.1021/cr980132zresearch-articleACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views3566Altmetric-Citations272LEARN 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 SUBJECTS:Fluorescence,Fluorescence detection,Genetics,Lasers,Molecules Get e-Alerts