gebhart/patrepeval huggingface dataset:
Human T-cell leukemia virus type II Rex binding and activity require an intact splice donor site and a specific RNA secondary structure (1991)

The human T-cell leukemia virus type II (HTLV-II) regulatory protein Rex augments cytoplasmic levels of unspliced gag-pol mRNA by acting through a Rex-responsive element (RxRE) in the long terminal repeat. Purified Rex protein binds to long terminal repeat mRNA. Here, using an immunobinding assay to measure the binding of Rex protein to mutated RxRE RNAs, we show that efficient Rex binding requires a stem-bulge-loop RNA secondary structure (nucleotides [nt] 465 to 500) and specific sequences both within the stem-bulge (nt 470 to 476) and within a conserved upstream splice donor site (nt 449 to 455). Rex function in a transient transfection expression system correlates with Rex protein-RxRE RNA binding. The ability of HTLV-II Rex to interact directly with the HTLV-II splice donor site suggests that HTLV-II Rex may increase expression of unspliced gag-pol mRNA, in part, by inhibiting splicing.
Diastereoselective Cobalt-Catalyzed Aldol and Michael Cycloreductions (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDiastereoselective Cobalt-Catalyzed Aldol and Michael CycloreductionsTae-Gon Baik, Ana Liza Luis, Long-Cheng Wang, and Michael J. KrischeView Author Information University of Texas at Austin Department of Chemistry and Biochemistry Austin, Texas 78712 Cite this: J. Am. Chem. Soc. 2001, 123, 21, 5112–5113Publication Date (Web):May 3, 2001Publication History Received28 November 2000Published online3 May 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/ja0040971https://doi.org/10.1021/ja0040971rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views2580Altmetric-Citations111LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Aldehydes,Aldol reactions,Cyclization,Enolates,Enones Get e-Alerts
High-Throughput Synthesis of Graphene by Intercalation−Exfoliation of Graphite Oxide and Study of Ionic Screening in Graphene Transistor (2009)

We report a high-throughput method of generating graphene monolayer (>90% yield) from weakly oxidized, poorly dispersed graphite oxide (GO) aggregates. These large-sized GO aggregates consist of multilayer graphite flakes which are oxidized on the outer layers, while the inner layers consist of pristine or mildly oxidized graphene sheets. Intercalation-exfoliation of these GO aggregates by tetrabutylammonium cations yields large-sized conductive graphene sheets (mean sheet area of 330 +/- 10 microm(2)) with high monolayer yield. Thin-film field-effect transistors made from these graphene sheets exhibit high mobility upon nullifying Coulomb scattering by ionic screening. Ionic screening versus chemical doping effects of different ions such as chloride and fluoride on these graphene films were investigated with a combination of in situ Raman spectroscopy and transport measurement.
Laboratory Evaluation of Laparoscopic Vascular Clamps Using a Load-Cell Device—Are All Clamps the Same? (2008)

Vascular clamps have varying occlusive forces according to clamp type, manufacturer, jaw and teeth characteristics, jaw clamping position and duration of use. However, across all clamps the jaw force was greatest at the proximal position. This is most important when applying laparoscopic bulldog clamps. In contrast, all handheld vascular clamps generated higher force than intracorporeal bulldog clamps. At 1 notch the handheld vascular clamps provided supraphysiological occlusion force regardless of position or manufacturer.
Pharmaceutical Inhalation Aerosol Technology (2003)

This thoroughly revised and expanded reference provides authoritative discussions on the physiologic, pharmacologic, metabolic, molecular, cellular and physicochemical factors, influencing the efficacy and utilization of pharmaceutical aerosol. It analyzes the latest science and developments in the generation, administration and characterization of
Severe iron deficiency anemia in transgenic mice expressing liver hepcidin (2002)

We recently reported the hemochromatosis-like phenotype observed in our Usf2 knockout mice. In these mice, as in murine models of hemochromatosis and patients with hereditary hemochromatosis, iron accumulates in parenchymal cells (in particular, liver and pancreas), whereas the reticuloendothelial system is spared from this iron loading. We suggested that this phenotypic trait could be attributed to the absence, in the Usf2 knockout mice, of a secreted liver-specific peptide, hepcidin. We conjectured that the reverse situation, namely overexpression of hepcidin, might result in phenotypic traits of iron deficiency. This question was addressed by generating transgenic mice expressing hepcidin under the control of the liver-specific transthyretin promoter. We found that the majority of the transgenic mice were born with a pale skin and died within a few hours after birth. These transgenic animals had decreased body iron levels and presented severe microcytic hypochromic anemia. So far, three mosaic transgenic animals have survived. They were unequivocally identified by physical features, including reduced body size, pallor, hairless and crumpled skin. These pleiotropic effects were found to be associated with erythrocyte abnormalities, with marked anisocytosis, poikylocytosis and hypochromia, which are features characteristic of iron-deficiency anemia. These results strongly support the proposed role of hepcidin as a putative iron-regulatory hormone. The animal models devoid of hepcidin (the Usf2 knockout mice) or overexpressing the peptide (the transgenic mice presented in this paper) represent valuable tools for investigating iron homeostasis in vivo and for deciphering the molecular mechanisms of hepcidin action.
Differential expression and processing of two cell associated forms of the kit-ligand: KL-1 and KL-2. (1992)

The c-kit ligand, KL, and its receptor, the proto-oncogene c-kit are encoded, respectively, at the steel (Sl) and white spotting (W) loci of the mouse. Both Sl and W mutations affect cellular targets in melanogenesis, gametogenesis, and hematopoiesis during development and in adult life. Although identified as a soluble protein, the predicted amino acid sequence of KL indicates that it is an integral transmembrane protein. We have investigated the relationship between the soluble and the cell associated forms of KL and the regulation of their expression. We show that the soluble form of KL is generated by efficient proteolytic cleavage from a transmembrane precursor, KL-1. An alternatively spliced version of KL-1, KL-2, in which the major proteolytic cleavage site is removed by splicing, is shown to produce a soluble biologically active form of KL as well, although with somewhat diminished efficiency. The protein kinase C inducer phorbol 12-myristate 13-acetate and the calcium ionophore A23187 were shown to induce the cleavage of both KL-1 and KL-2 at similar rates, suggesting that this process can be regulated differentially. Furthermore, proteolytic processing of both the KL-1 and KL-2 transmembrane protein products was shown to occur on the cell surface. The relative abundance of KL-1 and KL-2 is controlled in a tissue-specific manner. Sld, a viable steel allele, is shown to encode a biologically active secreted mutant KL protein. These results indicate an important function for both the soluble and the cell associate form of KL. The respective roles of the soluble and cell associated forms of KL in the proliferative and migratory functions of c-kit are discussed.
Acetylcholine receptor-aggregating activity of agrin isoforms and mapping of the active site. (1995)

Agrin is a basal lamina protein that induces aggregation of acetylcholine receptors (AChRs) and other molecules at the developing neuromuscular junction. Alternative splicing of chick agrin mRNA at two sites, A and B, gives rise to eight possible isoforms of which five are expressed in vivo. Motor neurons express high levels of isoforms with inserts at sites A and B, muscle cells synthesize isoforms that lack amino acids at the B-site. To obtain further insights into the mechanism of agrin-induced AChR aggregation, we have determined the EC50 (effective concentration to induce half-maximal AChR clustering) of each agrin isoform and of truncation mutants. On chick myotubes, EC50 of the COOH-terminal, 95-kD fragment of agrinA4B8 was approximately 35 pM, of agrinA4B19 approximately 110 pM and of agrinA4B11 approximately 5 nM. While some AChR clusters were observed with 64 nM of agrinA4B0, no activity was detected for agrinA0B0. Recombinant full-length chick agrin and a 100-kD fragment of ray agrin showed similar EC50 values. A 45-kD, COOH-terminal fragment of agrinA4B8 retained high activity (EC50 approximately equal to 130 pM) and a 21-kD fragment was still active, but required higher concentrations (EC50 approximately equal to 13 nM). Unlike the 45-kD fragment, the 21-kD fragment neither bound to heparin nor did heparin inhibit its capability to induce AChR aggregation. These data show quantitatively that agrinA4B8 and agrinA4B19, expressed in motor neurons, are most active, while no activity is detected in agrinA0B0, the dominant isoform synthesized by muscle cells. Furthermore, our results show that a fragment comprising site B8 and the most COOH-terminal G-like domain is sufficient for this activity, and that agrin domains required for binding to heparin and those for AChR aggregation are distinct from each other.
Immunogenic Gal alpha 1----3Gal carbohydrate epitopes are present on pathogenic American Trypanosoma and Leishmania . (1989)

Anti-Gal is a natural antibody present in unusually high concentrations in human sera. It constitutes as much as 1% of circulating IgG and displays a distinct specificity for the Gal alpha 1----3Gal carbohydrate epitope. In the present study, we have found in the sera of patients with Chagas' disease and Leishmania infection anti-Gal titers 10- and 16-fold higher than that of healthy or bacteria-infected individuals. This increase in anti-Gal titer seemed to be the result of a specific immune response toward parasitic Gal alpha 1----3Gal epitopes. Binding studies of affinity chromatography-purified anti-Gal antibodies to Trypanosoma cruzi and American Leishmania parasites indeed demonstrated the presence of Gal alpha 1----3Gal epitopes on these parasites. This finding was supported by the observed binding to the parasites of two additional Gal alpha 1----3Gal recognizing molecules: the mAb Gal-13, and the lectin, Bandeiraea simplicifolia I B4. Furthermore, the binding of both anti-Gal antibody and of the B. simplicifolia I B4 lectin could be inhibited by galactose, and not glucose. In addition, removal of the terminal alpha-galactosyl residues from the parasites by pretreatment with alpha-galactosidase, or the oxidation of the binding epitopes by periodate prevented the subsequent binding of both the antibody and the lectin. A crude leishmanial lipid extract readily bound these three reagents, suggesting that at least part of these epitopes are of a glycolipid nature. These Gal alpha 1----3Gal epitopes may thus serve as an antigenic source for the excess production of anti-Gal. In view of the naturally high level of anti-Gal in humans and its binding to T. cruzi and Leishmania, it is argued that these antibodies may contribute to the natural defense against the invasion of such parasites.
TheFugu rubripes tyrosinase gene promoter targets transgene expression to pigment cells in the mouse (2000)

The regulation of the mouse tyrosinase gene expression is controlled by a highly conserved element at -100 bp, the M-box, and an enhancer at -12 kb. In most vertebrates, the length of intergenic sequences makes it difficult to analyze the whole gene and the complete regulatory region. We took advantage of the compact Fugu genome to identify regulatory regions involved in pigment cell-specific expression. We isolated the Fugu tyrosinase gene, and identified putative cis-acting regulatory elements within the promoter. We then asked whether the Fugu promoter sequence functions in mouse pigment cells. We showed that E11.5 transgenic embryos bearing 6 kb or 3 kb of Fugu tyrosinase 5' sequence fused to the reporter gene lacZ revealed melanoblast and RPE-specific expression. This is the first evidence that the tyrosinase promoter is active at midgestation in melanoblasts, long before the onset of pigmentation.
Multi-organ reactivity of a monoclonal natural autoantibody that promotes remyelination in a mouse model of multiple sclerosis. (1996)

A contemporary view of autoimmunity suggests that self-reactivity is a normal phenomenon, in contrast to the classical association between autoimmunity and immunopathology. We have previously demonstrated that monoclonal antibody SCH94.03, a natural autoantibody with polyreactivity towards several purified protein and hapten antigens, promotes central nervous system remyelination when passively transferred to SJL/J mice chronically infected with Theiler's murine encephalomyelitis virus, an established experimental model of multiple sclerosis. In this study we characterized the autoreactivity of SCH94.03 with endogenous mouse tissue using immunoperoxide and multiple-color immunofluorescence staining techniques on frozen tissue sections. Within the nervous system, SCH94.03 labeled fibrous astrocytes, ependymal cells, ganglion satellite cells, and a sub-population of microglia, oligodendrocytes, and peripheral nervous system neurons. Outside the nervous system, SCH94.03 labeled gastrointestinal tract smooth muscle and luminal epithelium, erythrocytes, and interdigitating dendritic cells in peripheral lymphoid organs. These data indicate that SCH94.03 is a multi-organ reactive autoantibody and support the hypothesis that autoantibodies can have a beneficial rather than a pathogenic function in central nervous system demyelinating diseases.
Red Shift of Photoluminescence and Absorption in Dilute GaAsN Alloy Layers (1992)

We present the first report on the optical properties of dilute GaAS 1- x N x alloys (0&lt; x &lt;0.015). The layers have been grown by plasma-assisted metalorganic chemical vapor deposition (MOCVD). The grown layers show a systematic red shift of the band-edge luminescence with increasing N content. The assignement of the photoluminescence to band-edge transitions and not to isolated N-N pair emission is verified by the characteristics of the optical absorption.
Apoptosis signal ceramide c6 synergizes anti-tumor effects of paclitaxel oxaliplatin & cisplatin on growth of pancreatic cancer in SCID mice (2006)

13135 Background: Ceramide (C6) is an analog of endogenous ceramides, which are a major signaling pathway for apoptosis in cells undergoing stress, exposure to chemotherapy. Current report documents in vivo anti tumor effects combining C 6 with oxaliplatin &amp; cisplatin on L3.6 human pancreatic adenocarcinoma implanted in the SCID mouse. Correlative histologic studies provide additional mechanistic insights. Methods: SCID/Beige/ Taconicmale mice were inoculated subcutaneously (S.C.) w/2×10 6 L3.6 pancreatic cells. Chemotherapy doses were based on clinical &amp; in vitro data. Treatment began 4 days post tumor implant with 3 weekly 3×/wk) intraperitoneal (IP) injections of Paclitaxel (P) 3.0 m/kg, oxaliplatin (OX) 2.5 mg/kg, cisplatin (CP) 2.5 mg/kg, with/without ceramide 10 mg/kg. Mice were observed for 6 weeks &amp; were autopsied when near death, or at 6 week level. (All controls died by 3 rd week). Data recovered included maximum tumor volume, tumor weight, body weight &amp; survival. Histopathology studies were carried out in a separate group of 40 mice treated by the same drug dose levels &amp; autopsied at 4 hours &amp; 24 hours. Tumors were bi-valved &amp; fixed in buffered formalin or frozen in hexane/acetone bath. Major focus was effects on tumor necrosis, apoptosis, mitotic index &amp; Apoptosis (caspase 3 expression) index. Results: Combination w/C 6 ceramide augmented the tumor reduction obtained by chemotherapy alone by 57% (while preserving body weight), &amp; increased 6 wk survival from 0% (Chemotherapy alone) to 60% w/combined therapy. Mean survival was increased from 25 to 37 days. Preliminary short term immunohisto chemical studies showed enhancement of apoptotic index by increased and caspase 3 expression at 4 &amp; 24 hr by ceramide combinations. Conclusion: Combination therapy w/C 6 Ceramide significantly enhanced anti tumor response to Paclitaxel, Oxaliplatin &amp; Cisplatin in SCID Mice bearing L3.6 pancreatic tumor implants. Early development of enhanced apoptosis by caspase 3 expressions was shown in preliminary short term exposure experiments. No significant financial relationships to disclose.
Stereoselective Conjugate Addition Reactions of α,β-Unsaturated tert-Butyl Esters with Aryllithium Reagents (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTStereoselective Conjugate Addition Reactions of α,β-Unsaturated tert-Butyl Esters with Aryllithium Reagents†Lisa F. Frey, Richard D. Tillyer, Alain-Sebastien Caille, David M. Tschaen, Ulf-H. Dolling, Edward J. J. Grabowski, and Paul J. ReiderView Author Information Department of Process Research, Merck Research Laboratories, Merck & Co., Inc., Rahway, New Jersey 07065 Cite this: J. Org. Chem. 1998, 63, 9, 3120–3124Publication Date (Web):April 9, 1998Publication History Received16 September 1997Revised3 March 1998Published online9 April 1998Published inissue 1 May 1998https://doi.org/10.1021/jo971723cCopyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views554Altmetric-Citations32LEARN 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 InReddit Read OnlinePDF (138 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chemical reactions,Organic compounds,Reagents,Solvents,Stereoselectivity Get e-Alerts
u-shaped encodes a zinc finger protein that regulates the proneural genesachaete and scute during the formation of bristles in Drosophila (1997)

The pattern of the large sensory bristles on the notum of Drosophila arises as a consequence of the expression of the achaete and scute genes. The gene u-shaped encodes a novel zinc finger that acts as a transregulator of achaete and scute in the dorsal region of the notum. Viable hypomorphic u-shaped mutants display additional dorsocentral and scutellar bristles that result from overexpression of achaete and scute. In contrast, overexpression of u-shaped causes a loss of achaete-scute expression and consequently a loss of dorsal bristles. The effects on the dorsocentral bristles appear to be mediated through the enhancer sequences that regulate achaete and scute at this site. The effects of u-shaped mutants are similar to those of a class of dominant alleles of the gene pannier with which they display allele-specific interactions, suggesting that the products of both genes cooperate in the regulation of achaete and scute. A study of the sites at which the dorsocentral bristles arise in mosaic u-shaped nota, suggests that the levels of the u-shaped protein are crucial for the precise positioning of the precursors of these bristles.
Model for Polymerase Access to the Overlapped L Gene of Respiratory Syncytial Virus (1999)

The last two genes of respiratory syncytial virus (RSV), M2 and L, overlap by 68 nucleotides, an arrangement which has counterparts in a number of nonsegmented negative-strand RNA viruses. Thus, the gene-end (GE) signal of M2 lies downstream of the L gene-start (GS) signal, separated by 45 nucleotides. Since RSV transcription ostensibly is sequential and unidirectional from a single promoter within the 3' leader region, it was unclear how the polymerase accesses the L GS signal. Furthermore, it was previously shown that 90% of transcripts which are initiated at the L GS signal are polyadenylated and terminated at the M2 GE signal, yielding a short, truncated L mRNA as the major transcription product of the L gene. Despite these apparent down-regulatory features, we show that the accumulation of full-length L mRNA during RSV infection is only sixfold less than that of its upstream neighbor, M2. We used cDNA-encoded genome analogs in an intracellular transcription assay to investigate the mechanism of transcription of the overlapped genes. Expression of L was found to be dependent on sequential transcription from the 3' end of the genome. Apart from the L GS signal, the only other strict requirement for initiation at L was the M2 GE signal. This implies that the polymerase accesses the L GS signal only following arrival at the M2 GE signal. Thus, polymerase which terminates at the M2 GE signal presumably scans upstream to initiate at the L GS signal. This also would provide a mechanism whereby polymerase which terminates prematurely during transcription of L could recycle from the M2 GE signal to the L GS signal, thereby accounting for the unexpectedly high level of synthesis of full-length L mRNA. The sequence and spacing between the two signals were not critical. Furthermore, the polymerase also was capable of efficiently transcribing from an L GS signal placed downstream of the M2 GE signal, implying that the overlapping arrangement is not obligatory. When copies of the L GS signal were placed concurrently upstream and downstream of the M2 GE signal, both were utilized. This finding indicates that a polymerase situated at a GE signal is capable of scanning for a GS signal in either the upstream or downstream direction and thereafter initiating transcription.