gebhart/patrepeval huggingface dataset:
Changes in infectivity and plasmid profile of the Lyme disease spirochete, Borrelia burgdorferi, as a result of in vitro cultivation (1988)

In vitro cultivation of Borrelia burgdorferi, the etiologic agent of Lyme spirochetosis, allows for the isolation and growth of this bacterium from infected tissues. However, continuous cultivation in modified Kelly medium causes a reduction in the number of detectable plasmids and the loss of infectivity in the white-footed mouse, Peromyscus leucopus. In an unpassaged culture of B. burgdorferi, nine plasmids were present, including seven linear plasmids ranging in size from 49 to 16 kilobases (kb) and two circular plasmids of 27 and 7.6 kb. The 7.6-kb circular and 22-kb linear plasmids were no longer detectable in spirochetes noninfective in white-footed mice, suggesting that a gene(s) encoding for factors responsible for infection may be present on one or more of these extrachromosomal elements. Furthermore, changes in spirochetal proteins and lipopolysaccharide-like material were observed also during early cultivation and may be related to loss of infectivity.
Expression of growth factors, growth inhibiting factors, and their receptors in invasive breast cancer. I: An inventory in search of autocrine and paracrine loops (1998)

The aim of the present study was to investigate which growth factors, receptors, and growth inhibiting factors are expressed in invasive breast cancer. Five (angiogenic) growth factors and their receptors: platelet-derived growth factor A chain (PDGF-AA) and PDGF receptor alpha (PDGF alpha R), PDGF-BB and PDGF beta receptor, transforming growth factor alpha (TGF alpha) and its receptor epidermal growth factor receptor (EGFR), and vascular endothelial growth factor (VEGF) and its receptors vascular endothelial growth factor receptor I (Flt-1) and vascular endothelial growth factor receptor II (Flk-1/KDR); two growth inhibiting factors: transforming growth factor-beta-1 (TGF beta 1) and (TGF beta 2) and their receptor couple transforming growth factor beta receptor I (TGF beta R-I) and TGF beta R-II; and basic fibroblast growth factor (bFGF) were stained by standard immunohistochemistry on frozen sections in 45 cases of invasive carcinoma of the breast. Staining was scored as negative or positive in tumour epithelium, stroma, and blood vessels. TGF beta 1 and TGF beta 2 were expressed in the tumour cells in 67 per cent and 76 per cent of cases, respectively, whereas PDG beta R and TGF beta R-II were expressed in 0 per cent and 2 per cent, respectively. The other factors showed variable expression in tumour cells. All factors were expressed in the stroma in most cases, except Flt-1, Flk-1/KDR, TGF beta 2, and TGF beta R-II, which showed variable expression, and EGFR, which showed no expression. The endothelium was in most cases positive for bFGF, PDGF-AA, PDGF-BB, VEGF, PDGF alpha R, PDGF beta R, and TGF beta 1 but TGF beta/ was negative in most cases and TGF alpha, EGFR, Flt-1, Flk-1/KDR, TGF beta R-I, and TGF beta R-II were variably expressed. The most interesting possible auto/paracrine loops, as demonstrated on serial sections and by fluorescence double staining, were the TGF alpha/EGFR, TGF beta s/TGF beta R, VEGF/Flt-1, and the VEGF/Flk-1 combinations. In conclusion, growth factors, growth inhibiting factors, and their receptors are frequently expressed in invasive breast cancer. Indications for some possible auto- and paracrine loops have been found, which should encourage further study on the role of these factors in breast cancer proliferation and angiogenesis.
Differential Phosphorylation of the T Lymphocyte Costimulatory Receptor CD28 (1996)

Treatment of T lymphocytes with phorbol ester and anti-CD28 monoclonal antibody (mAb) can induce proliferation and interleukin 2 production by triggering still undefined intracellular signaling pathways. We have developed a deglycosylation procedure that allows the precise identification of a distinct CD28 protein band, facilitating the analysis of activation-dependent changes in the phosphorylation state of CD28. Phorbol 12-myristate 13-acetate (PMA) treatment induced the in vitro phosphorylation of CD28 on threonine as detected in immune complex kinase assays. This effect of PMA was (i) rapid, preceding a PMA-induced increase in CD28 surface expression; (ii) occurred using kinase buffer containing either manganese or magnesium; and (iii) was found in human peripheral T cells, Jurkat T cells, and in a Jurkat subclone, J.Cam1, that is deficient in Lck tyrosine kinase activity. In contrast, anti-CD28 monoclonal antibody stimulation led to in vitro phosphorylation of CD28 on tyrosine that was manganese-dependent and required Lck tyrosine kinase activity, as it was undetectable in J.Cam1 cells. Importantly, CD28 was phosphorylated on tyrosine in vivo as detected with anti-phosphotyrosine antibodies after stimulation with anti-CD28 monoclonal antibody. The in vivo tyrosine phosphorylation of CD28 was inhibited by PMA treatment and was absent in J.Cam1 cells. Thus, the CD28 coreceptor can trigger different intracellular signaling pathways, depending upon the nature of the initial costimulatory signal.
A Comparison of Balloon-Expandable-Stent Implantation with Balloon Angioplasty in Patients with Coronary Artery Disease (1994)

Over seven months of follow-up, the clinical and angiographic outcomes were better in patients who received a stent than in those who received standard coronary angioplasty. However, this benefit was achieved at the cost of a significantly higher risk of vascular complications at the access site and a longer hospital stay.
Epsilon Protein Kinase C Mediated Ischemic Tolerance Requires Activation of the Extracellular Regulated Kinase Pathway in the Organotypic Hippocampal Slice (2004)

Ischemic preconditioning (IPC) promotes brain tolerance against subsequent ischemic insults. Using the organotypic hippocampal slice culture, we conducted the present study to investigate (1) the role of adenosine A1 receptor (A1AR) activation in IPC induction, (2) whether epsilon protein kinase C (epsilonPKC) activation after IPC is mediated by the phosphoinositol pathway, and (3) whether epsilonPKC protection is mediated by the extracellular signal-regulated kinase (ERK) pathway. Our results demonstrate that activation of A1AR emulated IPC, whereas blockade of the A1AR during IPC diminished neuroprotection. The neuroprotection promoted by the A1AR was also reduced by the epsilonPKC antagonist. To determine whether epsilonPKC activation in IPC and A1AR preconditioning is mediated by activation of the phosphoinositol pathway, we incubated slices undergoing IPC or adenosine treatment with a phosphoinositol phospholipase C inhibitor. In both cases, preconditioning neuroprotection was significantly attenuated. To further characterize the subsequent signal transduction pathway that ensues after epsilonPKC activation, mitogen-activated protein kinase kinase was blocked during IPC and pharmacologic preconditioning (PPC) (with epsilonPKC, NMDA, or A1AR agonists). This treatment significantly attenuated IPC- and PPC-induced neuroprotection. In conclusion, we demonstrate that epsilonPKC activation after IPC/PPC is essential for neuroprotection against oxygen/glucose deprivation in organotypic slice cultures and that the ERK pathway is downstream to epsilonPKC.
Cytostatic and antiestrogenic effects of 2-(indol-3-ylmethyl)-3,3′-diindolylmethane, a major in vivo product of dietary indole-3-carbinol (1999)

Under acidic conditions, indole-3-carbinol (13C) is converted to a series of oligomeric products thought to be responsible for the biological effects of dietary 13C. Chromatographic separation of the crude acid mixture of 13C, guided by cell proliferation assay in human MCF-7 cells, resulted in the isolation of 2-(indol-3-ylmethyl)-3,3'-diindolylmethane (LTr-1) as a major antiproliferative component. LTr-1 inhibited the growth of both estrogen-dependent (MCF-7) and -independent (MDA-MB-231) breast cancer cells by approximately 60% at a non-lethal concentration of 25 microM. LTr-1 had no apparent effect on the proliferation of MCF-7 cells in the absence of estrogen. LTr-1 was a weak ligand for the estrogen receptor (ER) (IC50 70 microM) and efficiently inhibited the estradiol (E2)-induced binding of the ER to its cognate DNA responsive element. The antagonist effects of LTr-1 also were exhibited in assays of endogenous pS2 gene expression and in cells transiently transfected with an estrogen-responsive reporter construct (pERE-vit-CAT). LTr-1 activated both binding of the aryl hydrocarbon (Ah) receptor to its cognate DNA responsive element and expression of the Ah receptor-responsive gene CYP1A1. LTr-1 was a competitive inhibitor of CYP1A1-dependent ethoxyresorufin-O-deethylase (EROD) activity. In summary, these results demonstrated that LTr-1, a major in vivo product of I3C, could inhibit the proliferation of both estrogen-dependent and -independent breast tumor cells and that LTr-1 is an antagonist of estrogen receptor function and a weak agonist of Ah receptor function.
2‘-Chloro-2‘,3‘-dideoxy-3‘-fluoro-d-ribonucleosides:  Synthesis, Stereospecificity, Some Chemical Transformations, and Conformational Analysis (2003)

The synthesis of methyl 5-O-benzoyl-2-chloro-2,3-dideoxy-3-fluoro-beta-d-ribofuranoside (5) and its use as a glycosylating agent for persilylated thymine, N(6)-benzoyladenine, and N(4)-benzoylcytosine are described (Scheme 1). The 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides 10-12 synthesized were transformed to 2',3'-dideoxy-3'-fluoro-alpha- and -beta-d-erythro-pentofuranoside nucleosides of thymine (13a,b), adenine (14a,b), and cytidine (15a,b) by treatment with tributyltin hydride in the presence of alpha,alpha'-azobisisobutyronitrile (Scheme 2). Treatment of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides with 1 M MeONa/MeOH under reflux for 1-5 h afforded 2',3'-didehydro-2',3'-dideoxy-2'-chloro-d-pentofuranosyl nucleosides as the principal products (47-81%) of the reaction, along with recovered starting nucleoside (11-33%) (Scheme 3). Easy HF elimination was also observed in the case of the 2'-azido-2',3'-dideoxy-3'-fluoro-beta-d-ribofuranosides of thymine (17) and adenine (20) (Scheme 3). The role of conformational peculiarities of 2'-chloro-2',3'-dideoxy-3'-fluoro-d-ribonucleosides as well as of 17 and 20 in the observed exclusive elimination of HF is discussed. The conformational analysis of a rather broad palette of 2,3-dideoxy-3-fluoro-2-(X-substituted)-d-ribofuranosides was performed with the aid of the PSEUROT (version 6.3) program, using (i) the recently reparametrized Karplus-type relation (Chattopadhyaya and co-workers. J. Org. Chem. 1998, 63, 4967) and (ii) empirical bond angle correction terms suggested by us. The predictive power of the Brunck and Weinhold model (J. Am. Chem. Soc. 1979, 101, 1700) of the gauche effect between atoms and groups as a conformational driving force acting upon the pentofuranose ring is explored. Their model invokes maximum antiperiplanar sigma <--> sigma stabilization when the donating bond is the least polar one and the acceptor orbital is at the most polarized bond and is found at least as satisfactory, and in various specific cases more so than, as rationalizations on the basis of the preference of the gauche vs the trans conformation of two vicinal electronegative substituents (Wolfe. Acc. Chem. Res. 1972, 5, 102).
Discrete Signal Reconstruction by Sum of Absolute Values (2015)

In this letter, we consider a problem of reconstructing an unknown discrete signal taking values in a finite alphabet from incomplete linear measurements. The difficulty of this problem is that the computational complexity of the reconstruction is exponential as it is. To overcome this difficulty, we extend the idea of compressed sensing, and propose to solve the problem by minimizing the sum of weighted absolute values. We assume that the probability distribution defined on an alphabet is known, and formulate the reconstruction problem as linear programming. Examples are shown to illustrate that the proposed method is effective.
Simultaneous acquisition of T1ρand T2quantification in knee cartilage: Repeatability and diurnal variation (2013)

A sequence that combines T1ρ and T2 quantification with scan time less than 10 minutes and is robust to B0 and B1 inhomogeneity was developed with excellent repeatability. For a cohort with low-level daily activity, although no significant diurnal variation of cartilage MR relaxation times was observed, the afternoon scans had inferior repeatability compared to morning scans.
Catalytic Enantioselective Diels-Alder Reactions: Methods, Mechanistic Fundamentals, Pathways, and Applications (2002)

One hundred years after the birth of Kurt Alder and seventy-five years after the discovery of his famous reaction, one of the most important and fascinating transformations in chemistry, research on that process continues to surprise, excite, delight, and inform the chemical community. This article is based on presentations given first at the University of Cologne, Germany (Kurt Alder lecture, 1992), then at the Roger Adams Award Symposium (1993), and later at the Bürgenstock Conference of 2001, and describes research by our group on the development and understanding of enantioselective versions of the Diels-Alder reactions. The elements of this review include (1) development of new chiral Lewis acid catalysts for highly enantioselective (>25:1) [4+2] cycloadditions; (2) the fine mechanistic details and pre-transition-state assemblies of these reactions; (3) the fundamental understanding of catalytic activity and enantioselectivity for highly enantioselective Diels-Alder processes; and (4) applications to the synthesis of complex molecules. The range and power of the Diels-Alder reaction have steadily increased over seven decades. The end of this remarkable development is not in sight, a high compliment to this field of Science and to its great inventor.
A review on worldwide essential software resources in pharmacy (2011)

Softwares are the collection of computer programs and related data that provide the instructions telling a computer what to do and thereby help to process the data as wanted. These programs are designed to address general and special purpose applications. Softwares used in pharmaceutical sciences cover wide subject areas such as pharmacology, pharmaceutical chemistry, pharmaceutics, pharmacognosy, pharmaceutical biotechnology, etc. Softwares used in pharmacology are mainly related to minimize the efforts needed in determining pharmacokinetic principles of particular drug in individuals, pathways of drug, and consequently, its adverse reactions. Applications of softwares in pharmaceutical chemistry are to elucidate various physiological properties of drugs and to predict activity values for new compounds within certain limits. They may be enormous assistance to those trying to generate the large databases from massive efforts in drug research. However, softwares used in pharmaceutics help for predicting the dissolution rate, biopharmaceutical characterization, accurate and precise stability profile, etc. of formulated dosage form. Softwares used in pharmacognosy give information on herb activity, interactions, mechanisms of action and supporting data underlying the use of herb for health. Wide applications of software in pharmaceutical biotechnology help to increase the predictability of results, identify genes, elucidate protein structure, identify genome responsible for expression of particular characteristics, etc. Hence, in the present article, we have enlisted the subject wise different software names, websites and their features used in the milieu of pharmacy.
CD22, A B LYMPHOCYTE–SPECIFIC ADHESION MOLECULE THAT REGULATES ANTIGEN RECEPTOR SIGNALING* (1997)

The development of B lymphocytes is a highly regulated process that depends in part on lineage-specific cell surface molecules. In addition, transmembrane signals generated through the B cell antigen receptor and other surface molecules regulate B cell responses to foreign antigens. Recent studies reveal CD22 to be a functionally significant receptor during these processes. CD22 is first expressed in the cytoplasm of pro-B and pre-B cells, and on the surface as B cells mature to become IgD+. CD22 is a member of the Ig superfamily that serves as an adhesion receptor for sialic acid-bearing ligands expressed on erythrocytes and all leukocyte classes. In addition to its potential role as a mediator of intercellular interactions, signal transduction through CD22 can activate B cells and modulate antigen receptor signaling in vitro. CD22 signaling is mediated via interactions with a number of kinases and phosphatases that bind the cytoplasmic domain through phosphorylated tyrosine residues located within consensus TAM and TIM motifs. The phenotype of CD22-deficient mice suggests that CD22 is primarily involved in the generation of mature B cells within the bone marrow, blood, and marginal zones of lymphoid tissues. Most notable in CD22-deficient mice is a significant diminution of surface Ig levels in these B cell subpopulations, which suggests that CD22 functions in vivo to adjust the signaling threshold of cell surface antigen receptors. A further understanding of CD22 function is required and may reveal roles for CD22 in disease susceptibility or the development of autoimmunity.
Mesenchymal Stem Cells and Idiopathic Pulmonary Fibrosis. Potential for Clinical Testing (2013)

Idiopathic pulmonary fibrosis (IPF) is a progressive, debilitating, and fatal lung disease characterized by interstitial fibrosis with decreasing lung volumes and hypoxemic respiratory failure. The prognosis for patients with IPF is poor and the quest to find effective therapies has been unsuccessful. Despite several clinical trials over the past decade, there are no U.S. Food and Drug Administration-approved treatments for patients with IPF and thus no standard of care. In terms of pathogenesis, IPF is characterized by alveolar epithelial cell injury and activation with interstitial inflammation, fibroblast proliferation with extracellular matrix collagen deposition, and loss of lung function. Because mesenchymal stem cells (MSCs) home to sites of injury, inhibit inflammation, and contribute to epithelial tissue repair, their use has been suggested as a therapy for the treatment of IPF. MSCs have potential as a novel therapeutic agent in multiple diseases and they have been safely administered in a number of clinical trials. Some, but not all, preclinical studies in animal models of lung fibrosis suggest that MSCs might be effective in the treatment of IPF. Given the safety and ease of MSC administration in other patient populations, the results in preclinical animal models of IPF, and the major need for novel therapeutic options in this devastating disease, we propose that carefully designed clinical trials of MSCs for the treatment of patients with IPF are appropriate. Establishing safety in the setting of IPF is the first priority in early clinical trials followed by clinical and biological measures of efficacy.
Cyclic amidine analogues of taurine and homotaurine: synthesis and effects on rat skeletal muscle. (1994)

A series of amidinosulfonic acids IIIa-f, analogs of taurine and homotaurine, was synthesized by reacting 2-aminoethane or 3-aminopropane sulfonic acid with lactim ethers Ia-c and then cyclized to sultams IVa-c and Vd-f. The effects of some selected amidinosulfonic acids III on membrane ionic conductances of rat skeletal muscle are described.
A Distributed Architecture for Adaptive and Intelligent Learning Managament Systems (2003)

This paper presents KnowledgeTree, an architecture for adaptive eLearning based on distributed re-usable intelligent learning activities. The goal of KnowledgeTree is to bridge the gap between the modern approach to Web-based education based on learning management systems and powerful but underused intelligent tutoring and adaptive hypermedia technologies. This architecture attempts to address both the component-based development of adaptive systems and the teacher-level reusability.
The E3L gene of vaccinia virus encodes an inhibitor of the interferon-induced, double-stranded RNA-dependent protein kinase. (1992)

A vaccinia virus-encoded double-stranded RNA-binding protein, p25, has been previously implicated in inhibition of the interferon-induced, double-stranded RNA-activated protein kinase. In this study, we have identified the vaccinia viral gene (WR strain) that encodes p25. Amino acid sequence analysis of a chymotryptic fragment of p25 revealed a close match to the vaccinia virus (Copenhagen strain) E3L gene. The WR strain E3L gene was cloned and expressed either in COS-1 cells or in rabbit reticulocyte lysates in vitro. A M(r) 25,000 polypeptide that could bind to poly(rI).poly(rC)-agarose and that reacted with p25-specific antiserum was produced in each case. In addition, COS cells expressing E3L gene products inhibited activation of the double-stranded RNA-activated protein kinase in extracts from interferon-treated cells. Removal of E3L-encoded products by adsorption with anti-p25 antiserum resulted in loss of kinase inhibitory activity. These results demonstrate that the vaccinia virus E3L gene encodes p25 and that the products of the E3L gene have kinase inhibitory activity. Comparison of the deduced amino acid sequence of the E3L gene products with the protein sequence data base revealed a region closely related to the human interferon-induced, double-stranded RNA-activated protein kinase.
A 50 GHz direct injection locked oscillator topology as low power frequency divider in 0.13 μm CMOS (2004)

An injection locked oscillator topology is presented, based on MOS-switches directly coupled to the LC-tank of well-known LC-oscillators. The direct injection locking scheme features a very low input capacitance and high frequency capability. The functionality of the direct locking is verified through two test circuits in 0.13 /spl mu/m standard CMOS. With a power consumption of 3 mW, one oscillator divides 50 GHz by two with a locking range of 80 MHz. Also at a power consumption of 3 mW, the second oscillator with a lower Q tank divides 42 GHz by two with a locking range of 1.5 GHz.
The Functions of Nitric Oxide-Mediated Signaling and Changes in Gene Expression During the Hypersensitive Response (2003)

Nitric oxide (NO) is a highly reactive molecule that rapidly diffuses and permeates cell membranes. In animals, NO is implicated in a number of diverse physiological processes, such as neurotransmission, vascular smooth muscle relaxation, and platelet inhibition. It may have beneficial effects, e.g., as a messenger in immune responses, but it is also potentially toxic when the antioxidant system is overwhelmed and reactive oxygen intermediates (ROI) accumulate. During the last few years, NO has been detected in several plant species, and an increasing number of reports on its function have implicated NO as an important effector in plant growth, development, and defense. The broad chemistry of NO involves an array of interrelated redox forms with different chemical reactivities and numerous potential biological targets in plants. NO signaling functions depend on its reactivity. ROI are key modulators of NO in triggering cell death, but the nature of the mechanisms by which this occurs in plants is different from those commonly observed in animals. This review focuses on the signaling functions of NO, when channeled through the cell death pathway by ROI.