gebhart/patrepeval huggingface dataset:
Specific interaction of anticodon loop residues with yeast phenylalanyl-tRNA synthetase (1982)

Thirteen different yeast tRNAPhe variants with single nucleotide changes in positions 34-37 in the anticodon region were prepared by an enzymatic procedure described previously. Aminoacylation kinetics using purified yeast phenylalanyl-tRNA synthetase revealed that the level of aminoacylation was very different for different sequences inserted. The low level of aminoacylation was the result of a steady state between a slow forward reaction rate and spontaneous deacylation of the product. Aminoacylation kinetics performed at higher synthetase concentrations revealed that substitution at position 34 in tRNAPhe decreased the Km nearly 10-fold but only had a small effect on Vmax. Similar substitutions at positions 35, 36, and 37 had a lesser effect. These data suggest a sequence-specific contact between the anticodon of yeast tRNAPhe and the cognate synthetase.
Structural requirements for Arabidopsisβ1,2‐xylosyltransferase activity and targeting to the Golgi (2003)

Characterization of a beta1,2-xylosyltransferase from Arabidopsis thaliana (AtXylT) was carried out by expression in Sf9 insect cells using a baculovirus vector system. Serial deletions at both the N- and C-terminal ends proved that integrity of a large domain located between amino acid 31 and the C-terminal lumenal region is required for AtXylT activity expression. The influence of N-glycosylation on AtXylT activity has been evaluated using either tunicamycin or mutagenesis of potential N-glycosylation sites. AtXylT is glycosylated on two of its three potential N-glycosylation sites (Asn51, Asn301, Asn478) and the occupancy of at least one of these two sites (Asn51 and Asn301) is necessary for AtXylT stability and activity. Contribution of the N-terminal part of AtXylT in targeting and intracellular distribution of this protein was studied by expression of variably truncated, GFP-tagged AtXylT forms in tobacco cells using confocal and electron microscopy. These studies have shown that the transmembrane domain of AtXylT and its short flanking amino acid sequences are sufficient to specifically localize a reporter protein to the medial Golgi cisternae in tobacco cells. This study is the first detailed characterization of a plant glycosyltransferase at the molecular level.
Regulation of pamp and adrenomedullin receptor expression in the rat adrenal zona glomerulosa (1998)

Two peptide hormones are produced from the precursor peptide pre-proadrenoemdullin, known to be expressed in rat zona glomerulosa cells. Receptors for both adrenomedullin and pro-adrenomedullin N-terminal 20 peptide (PAMP) have been identified in the rat adrenal cortex but there is no information to date about the regulation of expression of these receptors, and the significance of these peptides in the regulation of adrenocortical function. In the present study the effects of dietary sodium changes on PAMP and adrenomedullin receptor expression was investigated. Feeding rats a low sodium diet resulted in a decrease in both PAMP and adrenomedullin binding in the zona glomerulosa. Adrenomedullin specific binding was 378 fmol/mg protein in the controls and 89 fmol/mg protein following dietary sodium depletion. PAMP binding was 288 fmol/mg protein in controls and 110 fmol/mg protein in the low sodium group. These data do not support a role for these peptides in the response of the adrenal zona glomerulosa to sodium depletion. It is possible that these peptides may, like ACTH, have acute stimulatory, but long-term inhibitory actions on the zona glomerulosa.
Identification of Herpesvirus-Like DNA Sequences in AIDS-Sssociated Kaposi's Sarcoma (1994)

Representational difference analysis was used to isolate unique sequences present in more than 90 percent of Kaposi's sarcoma (KS) tissues obtained from patients with acquired immunodeficiency syndrome (AIDS). These sequences were not present in tissue DNA from non-AIDS patients, but were present in 15 percent of non-KS tissue DNA samples from AIDS patients. The sequences are homologous to, but distinct from, capsid and tegument protein genes of the Gammaherpesvirinae, herpesvirus saimiri and Epstein-Barr virus. These KS-associated herpesvirus-like (KSHV) sequences appear to define a new human herpesvirus.
Increased anxiety and synaptic plasticity in estrogen receptor β-deficient mice (2001)

Estrogens are powerful modulators of neuronal physiology and in humans may affect a broad range of functions, including reproductive, emotional, and cognitive behaviors. We studied the contribution of estrogen receptors (ERs) in modulation of emotional processes and analyzed the effects of deleting ERalpha or ERbeta in mice. Behavior consistent with increased anxiety was observed principally in ERbeta mutant females and was associated with a reduced threshold for the induction of synaptic plasticity in the basolateral amygdala. Local increase of 5-hydroxytryptamine 1a receptor expression in medial amygdala may contribute to these changes. Our data show that, particularly in females, there is an important role for ERbeta-mediated estrogen signaling in the processing of emotional behavior.
Error Correction Coding : Mathematical Methods and Algorithms (2005)

Preface. List of Program Files. List of Laboratory Exercises. List of Algorithms. List of Figures. List of Tables. List of Boxes. PART I: INTRODUCTION AND FOUNDATIONS. 1. A Context for Error Correcting Coding. PART II: BLOCK CODES. 2. Groups and Vector Spaces. 3. Linear Block Codes. 4. Cyclic Codes, Rings, and Polynomials. 5. Rudiments of Number Theory and Algebra. 6. BCH and Reed-Solomon Codes: Designer Cyclic Codes. 7. Alternate Decoding Algorithms for Reed-Solomon Codes. 8. Other Important Block Codes. 9. Bounds on Codes. 10. Bursty Channels, Interleavers, and Concatenation. 11. Soft-Decision Decoding Algorithms. PART III: CODES ON GRAPHS. 12. Convolution Codes. 13. Trefils Coded Modulation. PART IV: INTERATIVELY DECODED CODES. 14. Turbo Codes. 15. Low-Density Parity-Check Codes. 16. Decoding Algorithms on Graphs. PART V: SPACE-TIME CODING. 17. Fading Channels and Space-Time Coding. References. Index.
A reliable and accurate indoor localization method using phone inertial sensors (2012)

This paper addresses reliable and accurate indoor localization using inertial sensors commonly found on commodity smartphones. We believe indoor positioning is an important primitive that can enable many ubiquitous computing applications. To tackle the challenges of drifting in estimation, sensitivity to phone position, as well as variability in user walking profiles, we have developed algorithms for reliable detection of steps and heading directions, and accurate estimation and personalization of step length. We've built an end-to-end localization system integrating these modules and an indoor floor map, without the need for infrastructure assistance. We demonstrated for the first time a meter-level indoor positioning system that is infrastructure free, phone position independent, user adaptive, and easy to deploy. We have conducted extensive experiments on users with smartphone devices, with over 50 subjects walking over an aggregate distance of over 40 kilometers. Evaluation results showed our system can achieve a mean accuracy of 1.5m for the in-hand case and 2m for the in-pocket case in a 31m×15m testing area.
Total synthesis of rapamycin (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of rapamycinK. C. Nicolaou, T. K. Chakraborty, A. D. Piscopio, N. Minowa, and P. BertinatoCite this: J. Am. Chem. Soc. 1993, 115, 10, 4419–4420Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/ja00063a093https://doi.org/10.1021/ja00063a093research-articleACS PublicationsRequest reuse permissionsArticle Views4367Altmetric-Citations185LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
1,10-Phenanthroline and 2,2′-bipyridyl complexes of rhodium(III) (1972)

The preparation of cis-[Rh(aa)2Cl2]+(aa = 2,2′-bipyridyl or 1,10-phenanthroline) has been re-examined and shown to be catalytic. The preparation and characterisation of cis-[Rh(aa)2X2]n+(X = I–, CN–, H2O, and NH3) and cis-[Rh(aa)2ClY]m+(Y = H2O, NH3, pyridine, and NO2–) is described and the possible mechanisms of base hydrolysis and of substitution by cyanide and by iodide into cis-[Rh(aa)2Cl2]+ are discussed; the effect of dioxygen on these substitutions is also discussed. The resolution of cis-[M(aa)2Cl2]+(M = Rh or Ir) into optical isomers is described and their stability is discussed. A convenient catalytic preparation of [Rh(aa)3]3+ is given.
Structure of Tracheal Cytotoxin in Complex with a Heterodimeric Pattern-Recognition Receptor (2006)

Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.
Comparison of a miniature, ultrasonic, optical fibre hydrophone with PVDF hydrophone technology (2002)

A miniature optical fibre hydrophone has been developed for the measurement of ultrasound in the range 1-30 MHz. The acoustically sensitive element comprises a 23 /spl mu/m thick polymer film mounted at the end of an optical fibre. When illuminated by laser light launched into the fibre, the polymer film acts as a Fabry Perot interferometer. An incident acoustic wave modulates the optical thickness of the interferometer thereby producing a corresponding intensity modulation in the light reflected from the film. The system was characterised in terms of sensitivity, frequency response and directivity using a broadband (1-30 MHz) ultrasonic field produced by nonlinear propagation obtained by driving a 1 MHz PZT source with a high amplitude 1 MHz toneburst. PVDF needle and membrane reference hydrophones were used as comparisons. The minimum detectable acoustic pressure of the optical fibre hydrophone was found to be 10 kPa in a 25 MHz measurement bandwidth with a wideband response to 30 MHz. The -3dB beamwidth at 10 MHz was 60/spl deg/. Such performance is comparable to that achieved with PVDF hydrophone technology, with additional advantages of immunity to EMI, small physical size, a flexible probe-type configuration, robustness and potentially low cost. Among the applications that might benefit from these advantages are single-use applications such as the measurement of industrial CW fields in hostile environments and in vivo measurements of medical ultrasound exposure.
Photochemistry of the azoalkanes 2,3-diazabicyclo[2.2.1]hept-2-ene and spiro[cyclopropane-7,1'-[2,3]-diazabicyclo[2.2.1]hept-2-ene]: on the questions of one-bond vs. two-bond cleavage during the denitrogenation, cyclization vs. rearrangement of the 1,3-diradicals and double inversion (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of the azoalkanes 2,3-diazabicyclo[2.2.1]hept-2-ene and spiro[cyclopropane-7,1'-[2,3]-diazabicyclo[2.2.1]hept-2-ene]: on the questions of one-bond vs. two-bond cleavage during the denitrogenation, cyclization vs. rearrangement of the 1,3-diradicals and double inversionWaldemar Adam, Thomas Oppenlaender, and Gerald ZangCite this: J. Org. Chem. 1985, 50, 18, 3303–3312Publication Date (Print):September 1, 1985Publication History Published online1 May 2002Published inissue 1 September 1985https://pubs.acs.org/doi/10.1021/jo00218a012https://doi.org/10.1021/jo00218a012research-articleACS PublicationsRequest reuse permissionsArticle Views257Altmetric-Citations31LEARN 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
Constitutive expression of various chemokine genes in human T‐cell lines infected with human T‐cell leukemia virus type 1: Role of the viral transactivator Tax (1996)

We examined the genetic expression of 2 CXC chemokines (IL-8, IP-10), 5 CC chemokines (MCP-I, MIP-Iα, MIP-Iβ, RANTES, 1309) and I C chemokine (SCM-I/lymphotactin/ATAC) in various human T-cell lines. By Northern blot analysis, HTLV-I-positive T-cell lines were found to express a number of chemokine genes at variable levels and in different combinations. However, none of the chemokine genes was expressed in HTLV-I-negative T-cell lines. We further confirmed secretion of 3 chemokines (IL-8, MIP-Iα and RANTES) by some HTLV-I-positive T-cell lines. To examine the role of the HTLV-I-encoded transactivator Tax in the induction of these chemokine genes, we used JPX-9 and JPX-M, which were stably transformed with tax and non-functional tax, respectively, under the control of a metallothionein promoter. Induction of tax in JPX-9 with Cd2+ was accompanied by rapid induction of IL-8, IP-10, MIP-Iα, MIP-Iβ, 1309 and SCM-I as determined by reverse transcription PCR. No such induction was seen in JPX-M. We thus suggest that Tax is, at least in part, responsible for constitutive expression of certain chemokine genes in HTLV-I-infected T cells. Aberrant production of various chemokines by HTLV-I-infected T cells may impact on the pathophysiology of HTLV-I-associated diseases. © 1996 Wiley-Liss, Inc.
Regulation of Connective Tissue Growth Factor Activity in Cultured Rat Mesangial Cells and Its Expression in Experimental Diabetic Glomerulosclerosis (2000)

Connective tissue growth factor (CTGF) is a peptide secreted by cultured endothelial cells and fibroblasts when stimulated by transforming growth factor-beta (TGF-beta), and is overexpressed during fibrotic processes in coronary arteries and in skin. To determine whether CTGF is implicated in the pathogenesis of diabetic glomerulosclerosis, cultured rat mesangial cells (MC) as well as kidney cortex and microdissected glomeruli were examined from obese, diabetic db/db mice and their normal counterparts. Exposure of MC to recombinant human CTGF significantly increased fibronectin and collagen type I production. Furthermore, unstimulated MC expressed low levels of CTGF message and secreted minimal amounts of CTGF protein (36 to 38 kD) into the media. However, sodium heparin treatment resulted in a greater than fourfold increase in media-associated CTGF, suggesting that the majority of CTGF produced was cell- or matrix-bound. Exposure of MC to TGF-beta, increased glucose concentrations, or cyclic mechanical strain, all causal factors in diabetic glomerulosclerosis, markedly induced the expression of CTGF transcripts, while recombinant human CTGF was able to autoinduce its own expression. TGF-, and high glucose, but not mechanical strain, stimulated the concomitant secretion of CTGF protein, the former also inducing abundant quantities of a small molecular weight form of CTGF (18 kD) containing the heparin-binding domain. The induction of CTGF protein by a high glucose concentration was mediated by TGF-beta, since a TGF-beta-neutralizing antibody blocked this stimulation. In vivo studies using quantitative reverse transcription-PCR demonstrated that although CTGF transcripts were low in the glomeruli of control mice, expression was increased 28-fold after approximately 3.5 mo of diabetes. This change occurred early in the course of diabetic nephropathy when mesangial expansion was mild, and interstitial disease and proteinuria were absent. A substantially reduced elevation of CTGF mRNA (twofold) observed in whole kidney cortices indicated that the primary alteration of CTGF expression was in the glomerulus. These results suggest that CTGF upregulation is an important factor in the pathogenesis of mesangial matrix accumulation and progressive glomerulosclerosis, acting downstream of TGF-beta.
Treating inflammation in atherosclerotic cardiovascular disease: emerging therapies (2009)

Atherosclerosis constitutes the underlying disease to the clinical manifestations of myocardial infarction, stroke, and gangrene. Despite the success of statins, prevention of clinical events of atherosclerosis remains a major challenge in current-day cardiology. Research into the inflammatory nature of atherosclerosis has led to improved mechanistic understanding of its pathogenesis and to the identification of novel therapeutic targets discussed in this review. Recent genetic and epidemiological data document shared pathologies of chronic inflammatory diseases and atherosclerosis. Anti-inflammatory treatment regimens used in these diseases, including tumor necrosis factor-alpha blockade, IL-1 receptor antagonism, and leukotriene blockade may be beneficial also in patients with coronary artery disease. Enhancing inherent atheroprotective immunity by expansion of regulatory T cells may emerge as a future therapeutic strategy. Immunization strategies directed against atherosclerosis-related antigens such as epitopes within the low-density lipoprotein particle have been extensively studied in animal models and may enter the clinical stage. Success of these novel therapies will be critically dependent on the adequate identification of patients and choice of appropriate clinical endpoints.
Combined use of urinary UGP and serum CA 125 in the diagnosis of gynecological cancers. (1996)

UGP, the beta-core fragment of human chorionic gonadotropin has been proposed as a tumor marker for gynecological malignancies. This fragment may be detected in a single morning-specimen of urine using an enzyme immunoassay. In this study, the diagnostic usefulness of urine UGP and serum CA 125 measurement for gynecological neoplasias (149 cases) was evaluated using a control group of patients with benign gynecological diseases (69 cases) and healthy females (99 cases). Considering the neoplastic patients in comparison to patients with benign diseases, the best diagnostic efficiency (78%) was found to correspond to a cut-off level of 120 pmol/mol creatinine the sensitivity being 73% and the specificity 90%. With this cut-off, an efficiency of 82% for healthy controls was obtained. Since the menopausal condition increases UGP levels, and though no significant difference for UGP was found between healthy subjects and patients with benign diseases, we decided to consider the reference populations as a single group. Thus, we evaluated the UGP performance on the basis of menopausal status. When a specificity of 95% was fixed, the cut-off values were 120 and 180 pmol/mol creatinine for pre- and postmenopausal women respectively, the sensitivity being 73% and 64%. Finally the combined evaluation of UGP and CA 125 improved their individual clinical efficiency for the diagnosis of ovarian serous cystadenocarcinomas, assuring a sensitivity of 86% and a specificity of 89%.
Gain-of-Function Mutations of c- kit in Human Gastrointestinal Stromal Tumors (1998)

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors in the human digestive tract, but their molecular etiology and cellular origin are unknown. Sequencing of c-kit complementary DNA, which encodes a proto-oncogenic receptor tyrosine kinase (KIT), from five GISTs revealed mutations in the region between the transmembrane and tyrosine kinase domains. All of the corresponding mutant KIT proteins were constitutively activated without the KIT ligand, stem cell factor (SCF). Stable transfection of the mutant c-kit complementary DNAs induced malignant transformation of Ba/F3 murine lymphoid cells, suggesting that the mutations contribute to tumor development. GISTs may originate from the interstitial cells of Cajal (ICCs) because the development of ICCs is dependent on the SCF-KIT interaction and because, like GISTs, these cells express both KIT and CD34.
Association of programmed cell death-1 (PDCD-1) gene polymorphisms with rheumatoid arthritis in Iranian patients. (2012)

Our results indicate that among the polymorphisms which we evaluated only the PD1.1A allele in the promoter region of PDCD-1 gene is significantly associated with RA susceptibility in Iranian patients.
Derivation of Clinically Compliant MSCs from CD105+, CD24− Differentiated Human ESCs (2006)

Adult tissue-derived mesenchymal stem cells (MSCs) have demonstrated therapeutic efficacy in treating diseases or repairing damaged tissues through mechanisms thought to be mediated by either cell replacement or secretion of paracrine factors. Characterized, self-renewing human ESCs could potentially be an invariable source of consistently uniform MSCs for therapeutic applications. Here we describe a clinically relevant and reproducible manner of generating identical batches of hESC-derived MSC (hESC-MSC) cultures that circumvents exposure to virus, mouse cells, or serum. Trypsinization and propagation of HuES9 or H1 hESCs in feeder- and serum-free selection media generated three polyclonal, karyotypically stable, and phenotypically MSC-like cultures that do not express pluripotency-associated markers but displayed MSC-like surface antigens and gene expression profile. They differentiate into adipocytes, osteocytes, and chondrocytes in vitro. Gene expression and fluorescence-activated cell sorter analysis identified CD105 and CD24 as highly expressed antigens on hESC-MSCs and hESCs, respectively. CD105+, CD24- monoclonal isolates have a typical MSC gene expression profiles and were identical to each other with a highly correlated gene expression profile (r(2) > .90). We have developed a protocol to reproducibly generate clinically compliant and identical hESC-MSC cultures.