gebhart/patrepeval huggingface dataset:
Purine nucleoside phosphorylase from human erythrocytes. 3. Inhibition by the inosine analog formycin B of the isolated enzyme and of nucleoside metabolism in intact erythrocytes and sarcoma 180 cells. (1968)

Formycin B, an analog of inosine, is a potent competitive inhibitor of purified erythrocytic purine nucleoside phosphorylase. The inhibition constant, Ki (1 x 10-4 M) is of the same order of magnitude as the Km for inosine (5 x 10-5 M). Formycin B also inhibits the degradation of nucleosides by intact and hemolyzed human erythrocytes and by Sarcoma 180 ascites cells.
Progress toward Characterization of the Group AStreptococcusMetagenome: Complete Genome Sequence of a Macrolide‐Resistant Serotype M6 Strain (2004)

We describe the genome sequence of a macrolide-resistant strain (MGAS10394) of serotype M6 group A Streptococcus (GAS). The genome is 1,900,156 bp in length, and 8 prophage-like elements or remnants compose 12.4% of the chromosome. A 8.3-kb prophage remnant encodes the SpeA4 variant of streptococcal pyrogenic exotoxin A. The genome of strain MGAS10394 contains a chimeric genetic element composed of prophage genes and a transposon encoding the mefA gene conferring macrolide resistance. This chimeric element also has a gene encoding a novel surface-exposed protein (designated "R6 protein"), with an LPKTG cell-anchor motif located at the carboxyterminus. Surface expression of this protein was confirmed by flow cytometry. Humans with GAS pharyngitis caused by serotype M6 strains had antibody against the R6 protein present in convalescent, but not acute, serum samples. Our studies add to the theme that GAS prophage-encoded extracellular proteins contribute to host-pathogen interactions in a strain-specific fashion.
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis (2010)

Monozygotic or 'identical' twins have been widely studied to dissect the relative contributions of genetics and environment in human diseases. In multiple sclerosis (MS), an autoimmune demyelinating disease and common cause of neurodegeneration and disability in young adults, disease discordance in monozygotic twins has been interpreted to indicate environmental importance in its pathogenesis. However, genetic and epigenetic differences between monozygotic twins have been described, challenging the accepted experimental model in disambiguating the effects of nature and nurture. Here we report the genome sequences of one MS-discordant monozygotic twin pair, and messenger RNA transcriptome and epigenome sequences of CD4(+) lymphocytes from three MS-discordant, monozygotic twin pairs. No reproducible differences were detected between co-twins among approximately 3.6 million single nucleotide polymorphisms (SNPs) or approximately 0.2 million insertion-deletion polymorphisms. Nor were any reproducible differences observed between siblings of the three twin pairs in HLA haplotypes, confirmed MS-susceptibility SNPs, copy number variations, mRNA and genomic SNP and insertion-deletion genotypes, or the expression of approximately 19,000 genes in CD4(+) T cells. Only 2 to 176 differences in the methylation of approximately 2 million CpG dinucleotides were detected between siblings of the three twin pairs, in contrast to approximately 800 methylation differences between T cells of unrelated individuals and several thousand differences between tissues or between normal and cancerous tissues. In the first systematic effort to estimate sequence variation among monozygotic co-twins, we did not find evidence for genetic, epigenetic or transcriptome differences that explained disease discordance. These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported.
SYNTHESIS, CRYSTAL-STRUCTURE AND LUMINESCENCE OF COORDINATION COMPOUND OF EUROPIUM P-METHYLBENZOATE WITH 2,2'-DIPYRIDINE (1995)

The coordination compound of europium p-methylbenzoate with 2,2 '-dipyridine was synthesized and characterized by elemental analysis and infrared spectrum. The crystal structure of the title compound, Eu-2(p-MBA)(6)(dipy)(2) (p-MBA: p-methylbenzoate, dipy: 2,2 '-dipyridine) was determined by the X ray diffraction analysis. It crystallizes in the monoclinic C2/c system with unit cell dimensions a=1.4086(6), b=1.9115(11), c=2.3077(16)nm; beta=96.60(4)degrees, V=6.1727nm(3) and Z=4. The metal atoms are octa-coordinated with the bidentates of p-methylbenzoate and 2,2 '-dipyridine. Since the title coordination compound Eu(p-MBA), dipy fluoresces very intensely under ultraviolet or visible light. Using Eu(III) ion as luminescent probe, the high-resolution laser excited excitation and luminescence spectra and time resolved spectra were recorded at 77K. The emission spectra indicate that two Eu(III) ion sites are present in the compound .
Strand displacement synthesis capability of Moloney murine leukemia virus reverse transcriptase (1994)

The accepted model of retroviral reverse transcription includes a circular DNA intermediate which requires strand displacement synthesis for linearization and creation of an integration-competent, long terminal repeat-flanked DNA product. We have used an in vitro model of this last step of reverse transcription to examine the role of the viral enzyme, reverse transcriptase (RT), in displacement synthesis. We show that Moloney murine leukemia virus RT possesses an activity which allows for displacement synthesis through a minimum of 1,334 bp of duplex DNA--an extent much greater than that required during in vivo reverse transcription and over 25-fold greater than has been previously demonstrated for a viral RT. RT does not function as a helicase in the classical sense but appears to closely couple duplex DNA melting with synthesis-driven translocation of the enzyme. In the absence of synthesis, the unwound region created by a primer-positioned RT appears to be no greater than 2 bp and does not advance along the template. Additionally, RT does not utilize ATP or any deoxynucleoside triphosphate not directly encoded by the template strand to catalyze processive duplex unwinding at a nick; nor does binding of the enzyme unwind duplex DNA in the absence of a 3' terminus. The approximate maximum chain elongation rate during strand displacement synthesis by Moloney murine leukemia virus RT falls between 0.73 and 1.5 nucleotides per s at 37 degrees C. The RNase H activity of RT does not appear to play a role in displacement synthesis; however, a 181-amino-acid C-terminal truncation of RT displays a dramatically reduced ability to catalyze synthesis through duplex DNA.
The short half-life of glucagon-like peptide-1 in plasma does not reflect its long-lasting beneficial effects (2002)

The incretin hormone glucagon-like peptide-1 (GLP-1) is capable of ameliorating glucose-dependent insulin secretion in subjects with diabetes. However, its very short half-life (1.5-5 min) in plasma represents a major limitation for its use in the clinical setting. The present study was designed to characterize the duration of the effect of GLP-1 in the Zucker diabetic fatty (ZDF) rat. ZDF rats were subjected to a 48 h infusion of human GLP-1 (30 pmol/kg per min), followed by an i.p. glucose tolerance test (IPGTT) (1 g/kg body weight), 2 h after removing the infusion pump. At 15 min from the beginning of the test, GLP-1-treated animals had lower plasma glucose levels (442+/-38 mg/dl) than saline-infused controls (583+/-63 mg/dl, P<0.01). This was reflected in the higher insulin levels attained in the GLP-1-treated animals (1999+/-163 vs 1250+/-51 pmol/l, GLP-1 vs saline respectively, P<0.01). Repetition of the IPGTT on day 3, 9 and 16 from the removal of the infusion pump revealed a surprising lasting 'memory' of the exposure to GLP-1. Indeed, the best insulin secretory response was observed approximately 1 week after discontinuation of the GLP-1 infusion, and lasted up to 3 weeks from the early exposure to GLP-1. Detection of fasting plasma levels of GLP-1 during the 3 weeks of the experiment showed a very rapid decline, consistent with the data reported by others. Our findings provide evidence for a long-lasting beneficial effect of GLP-1 that persists for weeks even when the circulating levels of GLP-1 are back to normal.
VHF, UHF and microwave frequency nanomechanical resonators (2005)

Nanomechanical resonators with fundamental mode resonance frequencies in the very-high frequency (VHF), ultra-high frequency (UHF) and microwave L-band ranges are fabricated from monocystalline silicon carbide (SiC) thin film material, and measured by magnetomotive transduction, combined with a balanced-bridge readout circuit. For resonators made from the same film, we measured the frequency dependence (thus geometry dependence) of the quality factor. We have seen a steady decrease of quality factor as the frequency goes up. This indicates the importance of clamping losses in this regime. To study this source of dissipation, a free-free beam SiC nanomechanical resonator has been co-fabricated on the same chip with a doubly clamped beam resonator operating at similar frequencies. Device testing has been performed to directly compare their characteristics and performance. It is observed that a significant improvement in quality factor is attained from the free-free beam design. In addition, from studies of resonators made from different chips with varying surface roughness, we found a strong correlation between surface roughness of the SiC thin film material and the quality factor of the resonators made from it. Furthermore, we experimentally studied the eddy current damping effect in the context of magnetomotive transduction. A high-aspect ratio SiC nanowire resonator is fabricated and tested for this study. Understanding the dissipation mechanisms, and thus improving the quality factor of these resonators, is important for implementing applications promised by these devices.
Exocellular polysaccharides from cyanobacteria and their possible applications (1998)

Cyanobacteria are photoautotrophic prokaryotes which include a large variety of species of widespread occurrence and with diverse morphological, physiological and biochemical properties. Many cyanobacteria are known to be able to synthesise outermost slimy investments and to release polysaccharidic material into the culture medium during cell growth. These released polysaccharides (RPSs), being easily recoverable from the culture medium, are attracting much interest in view of their possible uses in several industrial applications. In this paper, an overview of the current knowledge on both RPS-producing cyanobacterial strains (including the possible roles of the exopolysaccharides) and chemical characteristics of the cyanobacterial RPSs is given, with particular emphasis on RPS properties and possible industrial applications. On the whole, cyanobacterial RPSs are characterised by a great variety in both number (from two to 10) and type of constitutive monosaccharides (various arrangements of acidic and neutral sugars). Most polymers show an anionic nature due to the presence of uronic acids and/or other charged groups such as pyruvyl or sulfate. Polypeptide moieties as well as acetyl substituents have also sometimes been found, causing additional structural complexity. All the cyanobacterial RPSs so far tested showed a pseudoplastic behaviour, but with marked differences in both viscosity values and shear thinning. In terms of RPS production, the responses of cyanobacteria to changes of culture conditions appear strain-dependent. RPS productivities shown by some cyanobacteria are well comparable with those reported for other photosynthetic microorganisms proposed for polysaccharide production, but very low in comparison with those of heterotrophic microorganisms. Nevertheless, cyanobacteria may be regarded as a very abundant source of structurally diverse polysaccharides, some of which may possess unique properties for special applications, not fulfilled by the polymers currently available. However, much work has still to be done to bridge the wide gap existing between data on the biology of the RPS-producer strains and information concerning technological and other useful properties of the cyanobacterial RPS.
Carbonic anhydrase (Nce103p): an essential biosynthetic enzyme for growth of Saccharomyces cerevisiae at atmospheric carbon dioxide pressure (2005)

The NCE103 gene of the yeast Saccharomyces cerevisiae encodes a CA (carbonic anhydrase) that catalyses the interconversion of CO2 and bicarbonate. It has previously been reported that nce103 null mutants require elevated CO2 concentrations for growth in batch cultures. To discriminate between 'sparking' effects of CO2 and a CO2 requirement for steady-state fermentative growth, we switched glucose-limited anaerobic chemostat cultures of an nce103 null mutant from sparging with pure CO2 to sparging with nitrogen gas. This switch resulted in wash-out of the biomass, demonstrating that elevated CO2 concentrations are required even under conditions where CO2 is produced at high rates by fermentative sugar metabolism. Nutritional analysis of the nce103 null mutant demonstrated that growth on glucose under a non-CO2-enriched nitrogen atmosphere was possible when the culture medium was provided with L-aspartate, fatty acids, uracil and L-argininine. Thus the main physiological role of CA during growth of S. cerevisiae on glucose-ammonium salts media is the provision of inorganic carbon for the bicarbonate-dependent carboxylation reactions catalysed by pyruvate carboxylase, acetyl-CoA carboxylase and CPSase (carbamoyl-phosphate synthetase). To our knowledge, the present study represents the first full determination of the nutritional requirements of a CA-negative organism to date.
Cloning and tissue-specific functional characterization of the promoter of the rat diazepam binding inhibitor, a peptide with multiple biological actions. (1993)

Diazepam binding inhibitor (DBI) is a 10-kDa polypeptide that regulates mitochondrial steroidogenesis, glucose-induced insulin secretion, metabolism of acyl-CoA esters, and the action of gamma-aminobutyrate on GABAA receptors. To investigate the regulation of DBI gene expression, three positive clones were isolated from a rat genomic library. One of them contained a DBI genomic DNA fragment encompassing 4 kb of the 5' untranslated region, the first two exons, and part of the second intron of the DBI gene. Two other overlapping clones contained a processed DBI pseudogene. Several transcription initiation sites were detected by RNase protection and primer extension assays. Different tissues exhibited clear differences in the efficiencies of transcription startpoint usage. Transient expression experiments using DNA fragments of different length from the 5' untranslated region of the DBI gene showed that basal promoter activity required 146 bp of the proximal DBI sequence, whereas full activation was achieved with 423 bp of the 5' untranslated region. DNase I protection experiments with liver nuclear proteins demonstrated three protected regions at nt -387 to -333, -295 to -271, and -176 to -139 relative to the ATG initiation codon; in other tissues the pattern of protection was different. In gel shift assays the most proximal region (-176 to -139) was found to bind several general transcription factors as well as cell type-restricted nuclear proteins which may be related to specific regulatory patterns in different tissues. Thus, the DBI gene possesses some features of a housekeeping gene but also includes a variable regulation which appears to change with the function that it subserves in different cell types.
Optimization of the handover algorithm based on the position of the mobile terminals (2002)

Position location of mobile terminals is expected to be one of the key services for mobile network operators in the near future. A variety of services may be offered, such as emergency-call assistance, fleet management, location-based value added services, navigation, stolen vehicle monitoring, improved network management and differential billing. Currently, network suppliers and research institutes worldwide are trying to conclude on the integration of positioning techniques, that fulfils related FCC and ETSI localization requirements, without exaggerating network costs. Furthermore, the rapidly increasing number of mobile subscribers in addition to the introduction of new circuit/packet-based data services, will cause serious traffic overload in cellular networks. Handover procedures use the signaling resources of the network and this is one of the system's parameters that has to be optimized. We propose an intelligent algorithm that makes use of the user's location to simplify the procedure and results in a stable system, decreasing the signaling congestion and the call-drop probability.
The Isolation and Characterization of the Murine T Cell Antigen Receptor ζ Chain Gene (1989)

The T cell antigen receptor (TCR) is a multisubunit complex which has a dual function of antigen recognition and signal transduction. One of its invariant subunits, the zeta chain, has been shown to have a significant role in the expression and function of the TCR on the cell surface. The mouse and human zeta cDNAs share significant homologies to each other but are distinct from all of the previously characterized TCR components. We now report the isolation and structural analysis of the complete murine zeta gene. This gene spans at least 31 kilobases and divides into eight exons. The first exon, which is located at least 20 kilobases upstream from the second exon, codes for the 5'-untranslated region and most of the signal peptide. The second exon codes for the remainder of the signal peptide, the extracellular domain, the transmembrane domain, and the first three amino acids of the intracytoplasmic domain. Exons 3-7 encode the majority of the intracytoplasmic domain. The eight exon encodes the carboxyl-terminal 21 amino acids and the 3'-untranslated region. Four groups of mRNA initiation sites have been identified at approximately 140 base pairs upstream to the AUG codon. No TATA-like box has been detected. The gene is localized to the distal part of chromosome 1 in a linkage group highly conserved between man and mouse.
An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells (2009)

We have developed and tested a robust delivery method for the transport of proteins to the cytoplasm of mammalian cells without compromising the integrity of the cell membrane. This receptor-mediated delivery (RMD) technology utilizes a variant of substance P (SP), a neuropeptide that is rapidly internalized upon interaction with the neurokinin-1 receptor (NK1R). Cargos in the form of synthetic antibody fragments (sABs) were conjugated to the engineered SP variant (SPv) and efficiently internalized by NK1R-expressing cells. The sABs used here were generated to bind specific conformational forms of actin. The internalized proteins appear to escape the endosome and retain their binding activity within the cells as demonstrated by co-localization with the actin cytoskeleton. Further, since the NK1R is over-expressed in many cancers, SPv-mediated delivery provides a highly specific method for therapeutic utilization of affinity reagents targeting intracellular processes in diseased tissue.
Welcome to the neighborhood: epithelial cell‐derived cytokines license innate and adaptive immune responses at mucosal sites (2008)

There is compelling evidence that epithelial cells (ECs) at mucosal surfaces, beyond their role in creating a physical barrier, are integral components of innate and adaptive immunity. The capacity of these cells to license the functions of specific immune cell populations in the airway and gastrointestinal tract offers the prospect of novel therapeutic strategies to target multiple inflammatory diseases in which barrier immunity is dysregulated. In this review, we discuss the critical functions of EC-derived thymic stromal lymphopoietin (TSLP), interleukin-25 (IL-25), and IL-33 in the development and regulation of T-helper 2 (Th2) cytokine-dependent immune responses. We first highlight recent data that have provided new insights into the factors that control expression of this triad of cytokines and their receptors. In addition, we review their proinflammatory and immunoregulatory functions in models of mucosal infection and inflammation. Lastly, we discuss new findings indicating that despite their diverse structural features and differential expression of their receptors, TSLP, IL-25, and IL-33 cross-regulate one another and share overlapping properties that influence Th2 cytokine-dependent responses at mucosal sites.
The blood–brain-barrier in multiple sclerosis: Functional roles and therapeutic targeting (2007)

In most regions of the central nervous system (CNS), the composition of the neuronal microenvironment is maintained by virtue of particular blood-brain-barrier (BBB) characteristics, to which vascular endothelial cells (ECs) contribute an important role. Multiple sclerosis (MS) is an inflammatory demyelinating disease of the CNS, characterized at tissue level by multifocal perivascular infiltrates, predominantly of lymphocytes and macrophages. Thus, lymphocyte recruitment into the brain across ECs of the BBB represents a critical event in disease pathogenesis, which is highly restricted and carefully regulated. In recent years, different investigations have identified the crucial components involved in leukocyte migration, providing new insights into mechanisms modulating neuroinflammatory reactions. In this review, several topics relating to these events are discussed, namely: (1) cellular and molecular characteristics of the BBB regulating permeability, as well as signals inducing EC differentiation in the brain and specific cell properties; (2) pathogenic mechanisms guiding the migration of different leukocyte populations through the BBB in MS; and (3) current knowledge on how different MS therapies targeting leukocytes migration across the BBB function. Furthermore, because the BBB has proven to be an important retaining wall preventing drug passage into the CNS, novel strategies directed at successful delivery of large molecules for effective treatment of various inflammatory conditions of the brain, both currently available or still under development, are discussed.
Mechanism of Hepatic Insulin Resistance in Non-alcoholic Fatty Liver Disease (2004)

Short term high fat feeding in rats results specifically in hepatic fat accumulation and provides a model of non-alcoholic fatty liver disease in which to study the mechanism of hepatic insulin resistance. Short term fat feeding (FF) caused a approximately 3-fold increase in liver triglyceride and total fatty acyl-CoA content without any significant increase in visceral or skeletal muscle fat content. Suppression of endogenous glucose production (EGP) by insulin was diminished in the FF group, despite normal basal EGP and insulin-stimulated peripheral glucose disposal. Hepatic insulin resistance could be attributed to impaired insulin-stimulated IRS-1 and IRS-2 tyrosine phosphorylation. These changes were associated with activation of PKC-epsilon and JNK1. Ultimately, hepatic fat accumulation decreased insulin activation of glycogen synthase and increased gluconeogenesis. Treatment of the FF group with low dose 2,4-dinitrophenol to increase energy expenditure abrogated the development of fatty liver, hepatic insulin resistance, activation of PKC-epsilon and JNK1, and defects in insulin signaling. In conclusion, these data support the hypothesis hepatic steatosis leads to hepatic insulin resistance by stimulating gluconeogenesis and activating PKC-epsilon and JNK1, which may interfere with tyrosine phosphorylation of IRS-1 and IRS-2 and impair the ability of insulin to activate glycogen synthase.