gebhart/patrepeval huggingface dataset:
G-CSF as immune regulator in T cells expressing the G-CSF receptor: implications for transplantation and autoimmune diseases (2003)

Results from experimental models, in vitro studies, and clinical data indicate that granulocyte colony-stimulating factor (G-CSF) stimulation alters T-cell function and induces Th2 immune responses. The immune modulatory effect of G-CSF on T cells results in an unexpected low incidence of acute graft-versus-host disease in peripheral stem cell transplantation. However, the underlying mechanism for the reduced reactivity and/or alloreactivity of T cells upon G-CSF treatment is still unknown. In contrast to the general belief that G-CSF acts exclusively on T cells via monocytes and dendritic cells, our results clearly show the expression of the G-CSF receptor in class I- and II- restricted T cells at the single-cell level both in vivo and in vitro. Kinetic studies demonstrate the induction and functional activity of the G-CSF receptor in T cells upon G-CSF exposure. Expression profiling of T cells from G-CSF-treated stem cell donors allowed identification of several immune modulatory genes, which are regulated upon G-CSF administration in vivo (eg, LFA1-alpha, ISGF3-gamma) and that are likely responsible for the reduced reactivity and/or alloreactivity. Most importantly, the induction of GATA-3, the master transcription factor for a Th2 immune response, could be demonstrated in T cells upon G-CSF treatment in vivo accompanied by an increase of spontaneous interleukin-4 secretion. Hence, G-CSF is a strong immune regulator of T cells and a promising therapeutic tool in acute graft-versus-host disease as well as in conditions associated with Th1/Th2 imbalance, such as bone marrow failure syndromes and autoimmune diseases.
Short intronic repeat sequences facilitate circular RNA production (2014)

Recent deep sequencing studies have revealed thousands of circular noncoding RNAs generated from protein-coding genes. These RNAs are produced when the precursor messenger RNA (pre-mRNA) splicing machinery "backsplices" and covalently joins, for example, the two ends of a single exon. However, the mechanism by which the spliceosome selects only certain exons to circularize is largely unknown. Using extensive mutagenesis of expression plasmids, we show that miniature introns containing the splice sites along with short (∼ 30- to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening exons to circularize in cells. The intronic repeats must base-pair to one another, thereby bringing the splice sites into close proximity to each other. More than simple thermodynamics is clearly at play, however, as not all repeats support circularization, and increasing the stability of the hairpin between the repeats can sometimes inhibit circular RNA biogenesis. The intronic repeats and exonic sequences must collaborate with one another, and a functional 3' end processing signal is required, suggesting that circularization may occur post-transcriptionally. These results suggest detailed and generalizable models that explain how the splicing machinery determines whether to produce a circular noncoding RNA or a linear mRNA.
In vitro-synthesized hepatitis delta virus RNA initiates genome replication in cultured cells (1990)

Monomers of the genomic strand of hepatitis delta virus RNA were transcribed in vitro and then delivered to NIH 3T3 fibroblasts by using a liposome fusion technique. After 7 days, genome replication was detected, but only in fibroblasts that stably expressed the delta antigen. Sequence analysis of the replicated products identified them as faithful copies of the hepatitis delta virus genome found in virions.
Nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses (1994)

The nucleotide sequence (9306 nucleotides) of cDNA clones of apple stem pitting virus (ASPV) obtained from a double-stranded RNA template, extracted from diseased plant tissue, was determined. The genome is composed of five open reading frames (ORFs) encoding putative proteins with M(r)s of 247083, 25147, 12832, 7429 and 43712, and has a poly(A) tail. Using two oligonucleotides designed from the ASPV sequence information a 1598 bp fragment from near the 3' terminus of the viral RNA, containing the coat protein of M(r) 43,766, was amplified from vein yellows (VY)-infected pear plants by PCR. The sequence determined showed eight nucleotide changes resulting in five amino acid substitutions compared with the sequence of ASPV. When compared to potex-, carla-, clostero- and capilloviruses, the ASPV genome organization appeared to be most closely related to that of potexviruses, but with a larger coat protein of M(r) 44K (ORF5). The predicted coat protein size was confirmed by immunoblot analysis. The results show that ASPV does not fall into subgroup A of the closteroviruses but that it probably belongs in an as yet undefined group of viruses. They also suggest that the virus associated with VY is a strain of ASPV.
Video orbits of the projective group a simple approach to featureless estimation of parameters (1997)

We present direct featureless methods for estimating the eight parameters of an "exact" projective (homographic) coordinate transformation to register pairs of images, together with the application of seamlessly combining a plurality of images of the same scene, resulting in a single image (or new image sequence) of greater resolution or spatial extent. The approach is "exact" for two cases of static scenes: (1) images taken from the same location of an arbitrary three-dimensional (3-D) scene, with a camera that is free to pan, tilt, rotate about its optical axis, and zoom, or (2) images of a flat scene taken from arbitrary locations. The featureless projective approach generalizes interframe camera motion estimation methods that have previously used a camera model (which lacks the degrees of freedom to "exactly" characterize such phenomena as camera pan and tilt) and/or which have relied upon finding points of correspondence between the image frames. The featureless projective approach, which operates directly on the image pixels, is shown to be superior in accuracy and the ability to enhance the resolution. The proposed methods work well on image data collected from both good-quality and poor-quality video under a wide variety of conditions (sunny, cloudy, day, night). These new fully automatic methods are also shown to be robust to deviations from the assumptions of static scene and no parallax.
A Bayesian framework for video affective representation (2009)

Emotions that are elicited in response to a video scene contain valuable information for multimedia tagging and indexing. The novelty of this paper is to introduce a Bayesian classification framework for affective video tagging that allows taking contextual information into account. A set of 21 full length movies was first segmented and informative content-based features were extracted from each shot and scene. Shots were then emotionally annotated, providing ground truth affect. The arousal of shots was computed using a linear regression on the content-based features. Bayesian classification based on the shots arousal and content-based features allowed tagging these scenes into three affective classes, namely calm, positive excited and negative excited. To improve classification accuracy, two contextual priors have been proposed: the movie genre prior, and the temporal dimension prior consisting of the probability of transition between emotions in consecutive scenes. The f1 classification measure of 54.9% that was obtained on three emotional classes with a nai¿ve Bayes classifier was improved to 63.4% after utilizing all the priors.
Progression of prostate cancer by synergy of AKT with genotropic and nongenotropic actions of the androgen receptor (2006)

Classic work by Huggins and Hodges demonstrated that human prostate cancer regresses dramatically during antihormonal therapy but recurs frequently with androgen independence. Perturbations in the androgen receptor (AR) and PTEN-AKT signaling axes are significantly correlated with the progression of prostate cancer. Genetic alterations of the AR cause receptor hypersensitivity, promiscuity, and androgen-independent receptor transactivation. Prostate cancers maintain an elevated AKT activity through the loss of PTEN function or the establishment of autocrine signaling by growth factors and cytokines. We used an in vivo prostate regeneration system to investigate the biological potency of the potential crosstalk between these two signal transduction pathways. We demonstrate a direct synergy between AKT and AR signaling that is sufficient to initiate and progress naïve adult murine prostatic epithelium to frank carcinoma and override the effect of androgen ablation. Both genotropic and nongenotropic signals mediated by AR are essential for this synergistic effect. However, phosphorylation of AR by AKT at Ser-213 and Ser-791 is not critical for this synergy. These results suggest that more efficient therapeutics for advanced prostate cancer may need to target simultaneously AR signaling and AKT or the growth factor receptor tyrosine kinases that activate AKT.
TEMPERATURE INCREASES OF ≥ 1°C WORSEN FUNCTIONAL NEUROLOGIC OUTCOME AND HISTOPATHOLOGY IN A CANINE MODEL OF COMPLETE CEREBRAL ISCHEMIA (1994)

Wass, C. T. M.D.; Lanier, W. L. M.D.; Hofer, R. E. M.D.; Scheithauer, B. W. M.D.; Andrews, A. G. D.V.M. Author Information
Viral Characterization by Direct Analysis of Capsid Proteins (1998)

Matrix-assisted laser desorption/ionization mass spectrometry has enabled viral coat proteins to be characterized directly from the virus. This analysis, demonstrated here with tobacco mosaic virus U2, a bacteriophage MS2, and equine encephalitis TRD, is achieved with a combination of organic acid, UV-absorbing matrix, and high-energy desorption with a nitrogen laser. The molecular weights of these proteins are determined with sufficient accuracy to allow differentiation among viral species and strains. The abundant hydrophobic MS2 coat protein was analyzed in aliquots of culture medium and of the tobacco mosaic virus coat protein in infected leaves. This method provides rapid detection of coat protein in the low-femtomole range, as estimated by titering plaque-forming units of MS2.
Genomic variation in Streptococcus mutans: deletions affecting the multiple pathways of β‐glucoside metabolism (2006)

The genome of Streptococcus mutans UA159 contains two phospho-beta-glucosidase genes, bglA and celA, which occur in operon-like arrangements along with genes for components of phosphotransferase transport systems and a third phospho-beta-glucosidase encoded by the arb gene, which does not have its own associated transport system but relies on uptake by the bgl or cel systems. Targeted inactivation of each of the phospho-beta-glucosidase genes revealed that bglA is involved in aesculin hydrolysis, celA is essential for utilisation of cellobiose, amygdalin, gentobiose and salicin, and arb is required for utilisation of arbutin. Inactivation of genes for the phosphotransferase systems revealed an overlap of specificity for transport of beta-glucosides and also indicated that further, unidentified transport systems exist. The cel and arb genes are subject to catabolite repression by glucose, but the regM gene is not essential for catabolite repression. Screening a collection of isolates of S. mutans revealed strains with deletions affecting the msm, bgl and/or cel operons. The phenotypes of these strains could largely be explained on the basis of the results obtained from the knockout mutants of S. mutans UA159 but also indicated the existence of other pathways apparently absent from UA159. The extensive genetic and phenotypic variation found in beta-glucoside metabolism indicates that there may be extensive heterogeneity in the species.
The Reticular Formation (2005)

This chapter contains sections titled: Introduction The Organization of the Reticular Formation Pathways of the Reticular Formation The Reticular Formation and Sleep Evolutionary Perspective on the Reticular Formation
The novel sphingosine 1-phosphate receptor AGR16 is coupled via pertussis toxin-sensitive and -insensitive G-proteins to multiple signalling pathways (1998)

In the present study, we determined the agonist specificity and the signalling mechanisms of a putative sphingosine 1-phosphate (S1P) receptor, AGR16. In CHO cells transiently transfected with an AGR16 expression vector, but not in cells transfected with an empty vector, the addition of a low concentration of S1P (1 nM) caused an increase in the intracellular free Ca2+ concentration ([Ca2+]i) by mobilization of Ca2+ from both intra- and extra-cellular pools. To determine the spectrum of agonists for AGR16, we employed K562 cells, which in the naive state do not respond at all to either S1P or structurally related lipids with an increase in [Ca2+]i. In K562 cells stably expressing AGR16, S1P and sphingosylphosphorylcholine (SPC) dose-dependently increased [Ca2+]i with half-maximal values of 3 nM and 100 nM respectively. In CHO cells stably expressing AGR16 (CHO-AGR16), but not in parental CHO cells, we observed specific binding of [32P]S1P, which was displaced by unlabelled S1P and SPC. In CHO-AGR16 cells, but not in parental CHO cells, S1P stimulated the production of inositol phosphates and Ca2+ mobilization which was only 30% inhibited by pertussis toxin (PTX), different from the case of the recently identified S1P receptor EDG1. Also in CHO-AGR16 cells, but not in CHO cells, S1P at higher concentrations activated mitogen-activated protein kinase (MAPK) in a PTX-sensitive and Ras-dependent manner. S1P also induced the activation of two stress-activated MAPKs, c-Jun N-terminal kinase and p38, in a manner that was totally insensitive to PTX. In CHO-AGR16 cells, S1P induced stress-fibre formation, with an increase in myosin light chain phosphorylation, in a PTX-insensitive and Rho-dependent manner. S1P also induced an increase in the cellular cAMP content in CHO-AGR16 cells, which contrasts sharply with the case of EDG1. These results establish that the S1P receptor AGR16 is coupled via both PTX-sensitive and -insensitive G-proteins to multiple effector pathways.
A Novel Muscle-Specific β1 Integrin Binding Protein (Mibp) That Modulates Myogenic Differentiation (1999)

Myogenesis is regulated by cell adhesion receptors, including integrins of the beta1 family. We report the identification of a novel muscle-specific beta1 integrin binding protein (MIBP). MIBP binds to the membrane-proximal cytoplasmic region shared by beta1A and beta1D integrins, and the binding occurs in vivo as well as in vitro. Furthermore, we show that MIBP is abundantly expressed by C2C12 myogenic cells before fusion, and the expression of MIBP is dramatically downregulated during subsequent differentiation. Finally, we show that overexpression of MIBP in C2C12 cells resulted in a suppression of fusion and terminal differentiation, suggesting that MIBP may play a key role in controlling the progression of muscle differentiation.
Cellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of Proteins (2014)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTCellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of ProteinsKathrin Lang* and Jason W. Chin*View Author Information Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom*E-mail: [email protected]*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 9, 4764–4806Publication Date (Web):March 21, 2014Publication History Received4 July 2013Published online21 March 2014Published inissue 14 May 2014https://pubs.acs.org/doi/10.1021/cr400355whttps://doi.org/10.1021/cr400355wreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views35561Altmetric-Citations835LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Azides,Fluorescence,Labeling,Monomers,Peptides and proteins Get e-Alerts
Branchial cleft anomaly, congenital heart disease, and biliary atresia: Goldenhar complex or Lambert syndrome? (2000)

The features of Goldenhar complex have been well-described and classically include branchial arch abnormalities, epibulbar dermoid and vertebral abnormalities. We have identified an infant with these features in association with complex congenital heart disease and intrahepatic biliary atresia. Although Lambert described an autosomal recessive disorder with an association of biliary atresia and branchial arch abnormalities, none of those cases had epibulbar dermoid. Diagnostic considerations in this case include inclusion of biliary atresia as a new feature in the expanding spectrum of the Goldenhar complex, versus Lambert syndrome with epibulbar dermoid.
ChemInform Abstract: CYCLIZATION IN THE PRESENCE OF FLUORIDE IONS. 2. 4,5‐PERFLUORO‐1,3‐DIOXOLANES (1983)

Abstract Die Umsetzung der Chloralkoxycarbonsäurehalogenide (I) mit Triethylam‐ moniumfluorid (II) liefert unter Ringschluß die "fluorierten Dioxolane (III).
Tissue- and development-specific expression of the human phenylalanine hydroxylase/chloramphenicol acetyltransferase fusion gene in transgenic mice. (1992)

Human phenylalanine hydroxylase (PAH) catalyzes the conversion of L-phenylalanine to L-tyrosine. Deficiency of this enzyme results in phenylketonuria, a common genetic disorder of amino acid metabolism that causes severe mental retardation. In primates, PAH is expressed specifically in the liver, while in rodents PAH activity is also present in kidney, although at a much lower level. A 9-kilobase genomic DNA fragment at the 5' end of the hPAH gene (hPAH) was fused to the bacterial chloramphenicol acetyltransferase (CAT) gene. The hPAH/CAT minigene was used to generate multiple transgenic mouse lines. In all expressing lines, CAT activity was detected predominantly in the liver and at much lower levels in the kidney. By immunohistochemical staining, CAT expression was localized to hepatocytes and renal epithelial cells, both of which also express the endogenous mouse PAH enzyme. Furthermore, both the transgene and the endogenous mouse PAH were activated at about the same stage of embryonic development in the mouse liver. These results suggest that the 9-kilobase DNA fragment flanking the 5' end of the human PAH gene contains all the necessary cis-acting elements to direct tissue- and developmental-specific expression in vivo.
Meta-analysis of Pap Test Accuracy (1995)

A literature search identified 62 studies published by August 1992 comparing Papanicolaou (Pap) test results with histology. Critical appraisal revealed that 82% of these had potential for verification bias and that only 37% stated that cytology and histology were independently assessed. Estimates of sensitivity and specificity ranged from 11 to 99% and 14 to 97%, respectively, and were highly negatively correlated (r = -0.63). Meta-analysis was used to combine data from 59 studies to estimate the accuracy of the Pap test using a summary receiver operating characteristic curve and to examine the effect of study quality. The summary receiver operating characteristic curve suggests that the Pap test may be unable to achieve concurrently high sensitivity and specificity. For example, specificity in the 90-95% range corresponds to sensitivity in the 20-35% range. Pap test accuracy was not associated with reported study characteristics or dimensions of quality. Future primary studies should pay more attention to methodologic standards for the conduct and reporting of diagnostic test evaluations.
Serum GH binding protein activities identifies the heterozygous carriers for Laron type dwarfism (1989)

Measurement of GH-binding protein activity and IGF-I was carried out in the sera of 13 patients with Laron type dwarfism, a syndrome caused by a lack of GH receptors which leads to impairment of IGF-I generation, and those of 16 of their close relatives. GH binding protein activity was measured by incubating 125I-hGH with 100 microliters serum in the presence and in the absence of excess unlabelled hGH, followed by separation of specifically bound 125I-hGH binding protein complexes from free 125I-hGH by gel filtration. The results are expressed as percent specific binding relative to an adult reference serum. IGF-I was determined by RIA after acid extraction on octadecylsilane silica columns. All Laron type dwarfism patients had no, or only negligible GH binding protein activity, which supports the evidence that serum GH binding protein corresponds to the extracellular domain of the membranal GH receptor. Eight of the 16 relatives had serum GH binding protein activity more than 2 SD below the mean for age, a finding considered to denote heterozygocity for their molecular defect disease. The significant correlation (p less than 0.001) between serum GH binding protein activity and IGF-I levels supports this conclusion. The ability to define heterozygotes of Laron type dwarfism will be helpful in genetic counselling.
Pulse-extended excimer laser annealing of lead zirconate titanate thin films (2000)

Abstract Excimer laser annealing is a promising method for the crystallisation of ferroelectric layers, such as PZT, in low thermal budget integrated device fabrication processes. A technique is described whereby the problem of very high surface temperatures in PZT is overcome by the use of temporal pulse extension, where the effective laser pulse length is increased from 24ns to 374ns. Modelled temperature profiles through a PZT thin film structure during laser irradiation illustrate the benefit of pulse extension due to enhanced heat propagation into the PZT. The modelling also shows that underlying silicon is not heated significantly even with pulse extension. Initial results show that PZT can be crystallised into the perovskite phase from the top downwards with minimal surface damage.