gebhart/patrepeval huggingface dataset:
Directed Arbuzov-type reactions of 2-cyano-1,1-dimethylethyl deoxynucleoside phosphites (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDirected Arbuzov-type reactions of 2-cyano-1,1-dimethylethyl deoxynucleoside phosphitesJohn. Nielsen and Marvin H. CaruthersCite this: J. Am. Chem. Soc. 1988, 110, 18, 6275–6276Publication Date (Print):August 1, 1988Publication History Published online1 May 2002Published inissue 1 August 1988https://pubs.acs.org/doi/10.1021/ja00226a069https://doi.org/10.1021/ja00226a069research-articleACS PublicationsRequest reuse permissionsArticle Views842Altmetric-Citations62LEARN 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
Enzyme-Linked Immunosorbent Assays for Lyme Disease: Reactivity of Subunits of Borrelia burgdorferi (1989)

We prepared fractions of Borrelia burgdorferi, the etiologic agent of Lyme disease, from cultured spirochetes and used them as antigen in an enzyme-linked immunosorbent assay (ELISA) for IgG antibody. Polystyrene plates coated with an extract containing major proteins with apparent molecular masses of 34, 39, 59, and 68 kilodaltons had comparable sensitivity but greater specificity than plates coated with whole cells. Of the 33 serum specimens from individuals with Lyme disease that reacted with whole cells of B. burgdorferi in the class-specific ELISA, 30 (91%) remained positive when this extract was used. Cross-reactivity was minimal with antibody to treponemes. Use of subunit antigens may improve serological diagnosis of Lyme disease.
Regulation of wound healing from a connective tissue perspective (1996)

Tissue injury resulting in irreversible tissue loss initiates the repair process. The restoration of dermal loss is by scarring, where a new cell population resides in a new connective tissue matrix. The chemical composition of a scar is similar to normal dermis, but the organization of that tissue is altered. The inability of the organism to reassemble collagen into a normal dermal pattern is an attribute of a scar, but in most cases it restores normal function. With impaired scarring, wound dehiscence or chronic wounds arise, whereas the overproduction of scar tissue results in keloid or hypertrophic scarring. In both situations a catastrophic end point occurs. The volume of scar tissue deposited, as well as its organization, is critical for determining the scar's integrity, stability, and restoration of function. The maturation of scar depends on the character of its resident cell populations, the quality of deposited connective tissue, and the interactions between those components. In this Perspective article, the focus will be on the repair process in terms of collagen fiber organization. As our knowledge of cell-cell and cell-matrix interactions in the repair process increases, we may be able to direct the pattern of scar collagen fibers to resemble that of dermis and thereby provide better wound care to the patient of the future.
Proteases and protease receptors in modulation of leukocyte effector functions (1995)

Cellular immune responses depend on regulated pathways of intracellular signal transduction and leukocyte activation. Although these mechanisms are coordinated by a variety of leukocyte-restricted effector molecules, recent observations have uncovered a novel role of proteases in transducing outside-in signals of leukocyte activation. Through regulated, receptor-mediated recognitions, coagulation and fibrinolytic enzymes or effector cell granular proteases influence monocyte motility and chemotaxis, modulate pleiotropic cytokine responses, contribute to mononuclear cell proliferation, or induce target cell apoptosis. Overall, these mechanisms define a novel interface between general inflammatory reactions, invariably characterized by activation of blood protease cascades, and specialized aspects of cellular immune functions.
NewsTime--a graphical user interface to audio news (1993)

Thesis (M.S.)--Massachusetts Institute of Technology, Program in Media Arts & Sciences, 1993.
Surface Plasmon Resonance Imaging Studies of Protein-Carbohydrate Interactions (2003)

Carbohydrate arrays fabricated on gold films were used to study carbohydrate-protein interactions with surface plasmon resonance (SPR) imaging. An immobilization scheme consisting of the formation of a surface disulfide bond was used to attach thiol-modified carbohydrates onto gold films and to fabricate carbohydrate arrays. The carbohydrate attachment steps were characterized using polarization modulation Fourier transform infrared reflection absorption spectroscopy; and poly(dimethylsiloxane) microchannels were used to immobilize probe compounds at discrete locations on a gold film. The binding of the carbohydrate-binding proteins concanavalin A (ConA) and jacalin to arrays composed of the monosaccharides mannose and galactose was monitored with SPR imaging. SPR imaging measurements were employed to accomplish the following: (i) construct adsorption isotherms for the interactions of ConA and jacalin to the carbohydrate surfaces, (ii) monitor protein binding to surfaces presenting different compositions of the immobilized carbohydrates, and (iii) measure the solution equilibrium dissociation constants for ConA and jacalin toward mannose and galactose, respectively. Adsorption coefficients (KADS) of 2.2 ± 0.8 × 107 M-1 and 5.6 ± 1.7 × 106 M-1 were obtained for jacalin adsorbing to a galactose surface and ConA adsorbing to a mannose surface, respectively. The solution equilibrium dissociation (KD) constant for the interaction of jacalin and galactose was found to be 16 ± 5 μM, and for ConA and mannose was found to be 200 ± 50 μM.
IRAK4 kinase activity controls Toll-like receptor–induced inflammation through the transcription factor IRF5 in primary human monocytes (2017)

Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a critical role in innate immune signaling by Toll-like receptors (TLRs), and loss of IRAK4 activity in mice and humans increases susceptibility to bacterial infections and causes defects in TLR and IL1 ligand sensing. However, the mechanism by which IRAK4 activity regulates the production of downstream inflammatory cytokines is unclear. Using transcriptomic and biochemical analyses of human monocytes treated with a highly potent and selective inhibitor of IRAK4, we show that IRAK4 kinase activity controls the activation of interferon regulatory factor 5 (IRF5), a transcription factor implicated in the pathogenesis of multiple autoimmune diseases. Following TLR7/8 stimulation by its agonist R848, chemical inhibition of IRAK4 abolished IRF5 translocation to the nucleus and thus prevented IRF5 binding to and activation of the promoters of inflammatory cytokines in human monocytes. We also found that IKKβ, an upstream IRF5 activator, is phosphorylated in response to the agonist-induced TLR signaling. Of note, IRAK4 inhibition blocked IKKβ phosphorylation but did not block the nuclear translocation of NFκB, which was surprising, given the canonical role of IKKβ in phosphorylating IκB to allow NFκB activation. Moreover, pharmacological inhibition of either IKKβ or the serine/threonine protein kinase TAK1 in monocytes blocked TLR-induced cytokine production and IRF5 translocation to the nucleus, but not nuclear translocation of NFκB. Taken together, our data suggest a mechanism by which IRAK4 activity regulates TAK1 and IKKβ activation, leading to the nuclear translocation of IRF5 and induction of inflammatory cytokines in human monocytes.
Strategic Security Intelligence — Embedded Security (2002)

Networks dominate today’s computing landscape, yet commercial technical protection is lagging behind attack technology. As a result, protection programme success depends more on prudent management decisions than on the selection of technical safeguards. Managing Network Security takes a management view of protection and seeks to reconcile the need for security with the limitations of technology.
Mechanisms of Cancer Chemoprevention by Hop Bitter Acids (Beer Aroma) through Induction of Apoptosis Mediated by Fas and Caspase Cascades (2003)

The bitter acids of hops (Humulus lupulus L.) mainly consist of alpha-acids, beta-acids, and their oxidation products that contribute the unique aroma of the beer beverage. Hop bitter acids displayed a strong growth inhibitory effect against human leukemia HL-60 cells, with an estimated IC(50) value of 8.67 microg/mL, but were less effective against human histolytic lymphoma U937 cells. Induction of apoptosis was confirmed in HL-60 cells by DNA fragmentation and the appearance of a sub-G1 DNA peak, which were preceded by dissipation of mitochondrial membrane potential, cytochrome c release, and subsequent induction of pro-caspase-9 and -3 processing. Cleavages of PARP and DFF-45 were accompanied with activation of caspase-9 and -3 triggered by hop bitter acids in HL-60 cells. The change in the expression of Bcl-2, Bcl-X(L), and Bax in response to hop bitter acids was studied, and the Bcl-2 protein level slightly decreased; however, the Bcl-X(L) protein level was obviously decreased, whereas the Bax protein level was dramatically increased, indicating that the control of Bcl-2 family proteins by hop bitter acids might participate in the disruption of mitochondrial integrity. In addition, the results showed that hop bitter acids promoted the up-regulation of Fas and FasL prior to the processing and activation of pro-caspase-8 and cleavage of Bid, suggesting the involvement of a Fas-mediated pathway in hop bitter acids-induced cells. Taken together, these findings suggest that a certain intimate link might exist between receptor- and mitochondria-mediated death signalings that committed to cell death induced by hop bitter acids. The induction of apoptosis by hop bitter acids may offer a pivotal mechanism for their chemopreventive action.
Multiple hematopoietic lineages develop from embryonic stem (ES) cells in culture (1991)

When embryonic stem cells are cultured directly in semisolid media (methyl cellulose), they proliferate and differentiate to generate colonies known as embryoid bodies (EBs). These EBs consist of differentiated cells from a number of lineages including those of the hematopoietic system. Following 10 days of culture in the presence of 10% fetal calf serum, more than 40% of all EBs from three different ES cell lines, CCEG2, D3 and SQ1.2S8 contained visible erythropoietic cells (i.e. red with hemoglobin). Beta H1 (z globin) mRNA is detectable in EBs within 5 days of differentiation, whilst beta(maj)-globin RNA appears by day 6. In the presence of erythropoietin (Epo), the frequency of EBs with erythropoietic activity increases to greater than 60%; Epo also prolongs this erythropoietic activity. Interleukin-3 (IL-3) does not significantly increase the frequency of EBs that contain erythroid cells, but increases slightly the number of erythropoietic cells associated with them. In the presence of IL-3, in addition to cells of the erythroid lineage, macrophages, mast cells and in some instances neutrophils are found within differentiating EBs. The development of macrophages is significantly enhanced by the addition of IL-3 alone or in combination with IL-1 and M-CSF or GM-CSF. When well-differentiated EBs are allowed to attach onto tissue-culture plates and grown in the presence of IL-3, a long-term output of cells from the mast cell lineage is observed.(ABSTRACT TRUNCATED AT 250 WORDS)
Optimizing Waterflood Management in a Giant UAE Carbonate Oil Field Using Simulation-Based Streamlines (2014)

Abstract Streamlines have been acknowledged as a powerful tool for modeling and optimizing waterfloods in oil reservoirs. Streamlines provide visualization of reservoir fluid flow and a unique way to conceptualize and quantify injector-producer well connectivity. Well allocation factors (WAFs) between injectors and producers as well as injection efficiency can be calculated and used to optimize water injection and reduce injection water cycling while focusing on maximizing oil recovery. The objective of this study was to develop a methodology, tool, and workflow for optimizing pattern waterflood management and to demonstrate application in a giant offshore carbonate reservoir. This methodology utilizes history-matched simulation models to generate streamlines from the pressure field and fluxes computed by a finite-difference reservoir simulator, EMpower. A finite-difference simulator is more rigorous than streamline simulators in terms of its ability to model complex fluid flow, and therefore, provides a more realistic solution. The streamlines thus obtained take into account the detailed geology, well locations, phase behavior, and flow behavior of the history-matched models. This methodology utilizes the concept of pair "injection efficiency" (IE) and pair "voidage replacement ratio" (VRR) which was necessary for the subject giant oil field and is equally applicable to other fields. The optimization process is started by generating streamlines and associated WAFs at the current time using the simulation model. The injection efficiency is calculated and injector-producer well pairs are identified with high and low IE. New producer rates are then calculated by increasing producer rates in high IE well pairs and decreasing rates in low IE well pairs based on a weight factor. The injector rates are then calculated by applying a target VRR to each individual well pair. This results in redistribution of injection and production rates in a more balanced/optimal manner. The process is repeated at regular intervals (e.g., yearly or quarterly) while simulation is run in the prediction mode. Results show higher total oil production rates or lower water production and water injection rates. The WOR versus cumulative oil production clearly demonstrates that the overall injection efficiency increases as the optimization process is progressed.
MR imaging of lung parenchyma: a solution to susceptibility. (1992)

The authors have developed a pulse sequence for imaging lung parenchyma with projection reconstruction magnetic resonance (MR) imaging that reduces the effects of motion and susceptibility. In this study, the projection reconstruction technique was further modified by optimizing MR signal frequencies for reconstructing the images. This was done by means of one of two methods. With the first method, a susceptibility map was derived from the raw image data and this map was used to indicate the optimal frequencies for reconstructing the images. The second method of susceptibility correction was a postprocessing technique in which the optimal reconstruction frequencies were selected with use of specific focusing criteria to generate the least blurred image. The effect of using susceptibility map correction on a phantom was demonstrated, and both of these methods were used to improve the visibility of pulmonary structures on images of subjects with normal and abnormal lungs.
Analysis of human bone marrow with monoclonal antibodies. (1985)

In order to study the antigenic phenotype of different hemopoietic cells, we used a series of monoclonal antibodies to investigate normal bone marrow in a standard immunofluorescence assay. The antibodies detected the following antigens: HLA-ABC, beta 2-microglobulin (beta 2m), HLA-DR (Ia), a lymphocyte subset and specific antigen (T and B) HuLy-m2, m3, T lymphocyte antigen (HuLy-m1), lymphocyte T200 antigen (HuLy-m4), a viral-associated antigen (HuLy-m5), and platelet-specific glycoproteins IIb-IIIa (HuPl-m1). The following results were obtained: (a) normoblasts were weakly HLA-ABC+, beta 2m+ and Ia-; all other lymphocyte and platelet antigens were not detected. (b) Myeloid cells at all stages of differentiation (promyelocytes, myelocytes, metamyelocytes, and neutrophils) were HLA-ABC+; beta 2m+; HuLy-m1-, m2-, m3+/- (20%), m4+, m5+/- (20%); HuPl-m1-; in addition, promyelocytes and myelocytes were Ia+ but neutrophils and metamyelocytes were Ia-. (c) Lymphocytes were HLA-ABC+, beta 2m+, Ia+/- (20-30%), HuLy-m1+/- (40-50%), m2+/- (60-70%), m3+, m4+, m5+; Pl-m1-. (d) Platelets and megakaryocytes were HLA-ABC+; beta 2m+; Ia-; HuLy-m1+-, m2-, m3-, m4-, m5-, HuPl-m1+, and the putative "megakaryocyte precursors" were HuPl-m1+, Ia-, HuLy-m1-. The different cell types in bone marrow could readily be distinguished, particularly cells of the myeloid series (Ia and HuLy-m4, m5), lymphocytes (Ia and HuLy-m1, m2, m3), and platelets and their precursor cells (HuPl-m1). This simple method of defining cellular phenotypes in bone marrow has demonstrated the practicality of using monoclonal antibodies to identify marrow cells and should be of diagnostic value.
Effects of extracellular magnesium and beta adrenergic stimulation on contractile force and magnesium mobilization in the isolated rat heart. (1994)

This study investigates the metabolism of the divalent cation, magnesium (Mg2+) in the isolated perfused Langendorff's rat heart and ventricular slices in the absence and presence of catecholamines including isoprenaline, noradrenaline and adrenaline. Perfusion of the isolated rat heart with a physiological salt solution containing elevated extracellular Mg2+ [Mg2+]o (2.4 mM-6.0 mM) resulted in a marked and progressive decrease in the amplitude of contraction compared to control [Mg2+]o (1.2 mM). In contrast, perfusion of hearts with low (0-0.6 mM) [Mg2+]o caused a small transient increase in the amplitude of contraction which was often accompanied by arrhythmic activity. Perfusion of the heart with a nominally Mg2+ free medium resulted in a time-dependent net efflux of Mg2+ reaching a steady state after approximately 40-50 min of perfusion. This release of Mg2+ was associated with a concurrent decrease in total heart Mg2+. Stimulation of the heart with the beta adrenergic agonist, isoprenaline (10(-7) M) caused large increases in net Mg2+ efflux which was associated with marked increased in both rate and the amplitude of contraction. Similar effects on Mg2+ efflux were also observed during perfusion of the heart with the adenylate cyclase activator, forskolin (10(-5) M). Superfusion of paced ventricular segments with either isoprenaline, adrenaline or noradrenaline (all 10(-6) M) also resulted in a marked transient net efflux of Mg2+. Pre-treatment of segments with the beta adrenergic antagonist, propranolol (10(-5) M) competitively blocked the Mg2+ efflux evoked by the catecholamines. Similarly, pre-treatment of segments with the calcium (Ca2+) channel blocker, verapamil (10(-5) M) caused a significant (P < 0.05) decrease in net Mg2+ efflux evoked by isoprenaline. The results of this study indicate that (1) the perturbation of [Mg2+]o has an important influence on myocardial contractility and (2) the mobilization of Mg2+ in the heart is associated with beta adrenergic stimulation possibly via an elevation in intracellular adenosine 3.5 cyclic monophosphate (cyclic AMP).
Selecting neural network architectures via the prediction risk: application to corporate bond rating prediction (2002)

The notion of generalization can be defined precisely as the prediction risk, the expected performance of an estimator on new observations. The authors propose the prediction risk as a measure of the generalization ability of multi-layer perceptron networks and use it to select the optimal network architecture. The prediction risk must be estimated from the available data. The authors approximate the prediction risk by v-fold cross-validation and asymptotic estimates of generalized cross-validation or H. Akaike's (1970) final prediction error. They apply the technique to the problem of predicting corporate bond ratings. This problem is very attractive as a case study, since it is characterized by the limited availability of the data and by the lack of complete a priori information that could be used to impose a structure to the network architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Agrobacterium rhizogenes -mediated hairy root production in tea leaves (Camellia sinensis (L.) O. Kuntze) (2009)

Leaves of tea [Camellia sinensis (L.) O. Kuntze] plants were transformed with Agrobacterium rhizogenes strain (MTCC 532) and hairy roots were induced. Among the different concentrations of acetosyringeone tested, 300 µ M/L was found to enhance the transformation frequency upto 70%. Murashige and Skoog (MS) medium supplemented with 30 g/L maltose and indole-3-acetic acid (IAA) at 5 mg/L was found suitable for hairy-root culture and accumulation of phenolic compounds. Confirmatory studies were carried out by PCR analysis using rol C gene primer for transformation. Amplification of the specific gene was noted in the transformant at 540 bp. High performance liquid chromatography (HPLC) analysis confirmed the higher levels of catechins and their fractions in roots arising from the transformed tissues. Catechin fractions, viz ., EC, ECG, EGC and EGCG were detected both in untransformed leaves and hairy roots produced by Agrobacterium infected cells.
Anatomy of a New B-Cell-Specific Enhancer (1989)

The major histocompatibility complex class II molecules, like the immunoglobulins, are prominent B-lymphocyte markers. Herein, we describe a B-cell-specific enhancer associated with the murine class II gene, Ek alpha. This enhancer has a complex anatomy that suggests interactions between remotely spaced elements. Of particular interest is the finding that two CCAAT boxes spaced one kilobase apart are important for enhancer activity. Somewhat surprisingly, the E alpha and immunoglobulin enhancers seem to show little resemblance.
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression (2007)

We introduce a method that considers target genes of a transcription factor, and searches for transcription factor binding sites (TFBSs) of secondary factors responsible for differential responses among these targets. Based on the distance difference matrix concept, the method simultaneously integrates statistical overrepresentation and co-occurrence of TFBSs. Our approach is validated on datasets of differentially regulated human genes and is shown to be highly effective in detecting TFBSs responsible for the observed differential gene expression.