gebhart/patrepeval huggingface dataset:
Mutation is required to activate the p53 gene for cooperation with the ras oncogene and transformation (1989)

Previous experiments have brought into question which amino acid sequence of the p53 oncogene product should be considered wild type and whether the normal protein is capable of cooperating with the ras oncogene to transform cells in culture. To address these questions, a series of p53 cDNA-genomic hybrid clones have been compared for the ability to cooperate with the ras oncogene in transformation assays. From these experiments, it has become clear that the amino acid alanine at position 135, in either the genomic clone or the cDNA clone, failed to produce a p53 protein that cooperated with the ras oncogene and transformed cells. Replacing alanine with valine at this position in either the genomic or the cDNA clone activated for transformation in this assay. Using restriction enzyme polymorphisms in the p53 gene, it was shown that normal mouse DNA encodes alanine at position 135 in the p53 protein. Thus, mutation is required to activate the p53 protein for cooperation with the ras oncogene. After cotransfection with the activated ras gene, the genomic p53 DNA clone always produced more transformed cell foci (1.7-fold) than similar cDNA clones and these foci were more readily cloned (3.6-fold) into permanent cell lines. A series of deletion mutants of the genomic p53 clone were employed to show that the presence of intron 4 in the p53 gene was sufficient to provide much enhanced clonability of transformed foci from culture dishes. The presence of introns in the p53 gene constructions also resulted in elevated levels of p53 protein in the p53-plus-ras-transformed cell lines. Thus, qualitative changes in the p53 protein are required to activate p53 for transformation with the oncogene ras. Quantitative improvements of transformation frequencies are associated with the higher expression levels of altered p53 protein that are provided by having one of the p53 introns in the transforming plasmid.
MR imaging of articular cartilage: current status and future directions. (1994)

Advances in surgical and pharmacologic techniques for treating and preventing chondral abnormalities are creating a demand for an accurate, noninvasive imaging method to evaluate articular cartilage. The most promising technique is MR imaging, but its exact role in this evaluation remains undefined. This article reviews the MR appearance of normal and abnormal articular cartilage and the various pulse sequences that can be used to evaluate chondral lesions. It also briefly discusses possible future directions for MR imaging of articular cartilage.
The influence of tunneling on the relation between tritium and deuterium isotope effects. The exchange of 2-nitropropane-2-t (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe influence of tunneling on the relation between tritium and deuterium isotope effects. The exchange of 2-nitropropane-2-tEdward S. Lewis and John K. RobinsonCite this: J. Am. Chem. Soc. 1968, 90, 16, 4337–4344Publication Date (Print):July 1, 1968Publication History Published online1 May 2002Published inissue 1 July 1968https://pubs.acs.org/doi/10.1021/ja01018a025https://doi.org/10.1021/ja01018a025research-articleACS PublicationsRequest reuse permissionsArticle Views103Altmetric-Citations42LEARN 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
Structure of Recombinant Human Renin, a Target for Cardiovascular-Active Drugs, at 2.5 Å Resolution (1989)

The x-ray crystal structure of recombinant human renin has been determined. Molecular dynamics techniques that included crystallographic data as a restraint were used to improve an initial model based on porcine pepsinogen. The present agreement factor for data from 8.0 to 2.5 angstroms (A) is 0.236. Some of the surface loops are poorly determined, and these disordered regions border a 30 A wide solvent channel. Comparison of renin with other aspartyl proteinases shows that, although the structural cores and active sites are highly conserved, surface residues, some of which are critical for specificity, vary greatly (up to 10A). Knowledge of the actual structure, as opposed to the use of models based on related enzymes, should facilitate the design of renin inhibitors.
Rapamycin Attenuates Load-Induced Cardiac Hypertrophy in Mice (2003)

mTOR or its target(s) seems to play an important role in load-induced cardiac hypertrophy. Because systemic administration of rapamycin has been used successfully for the treatment of transplant rejection in clinical practice, it may be a useful therapeutic modality to suppress cardiac hypertrophy in patients.
Characterization and Quantitation of NF-κB Nuclear Translocation Induced by Interleukin-1 and Tumor Necrosis Factor-α (1998)

A new quantitative cytometric technique, termed the ArrayScanTM, is described and used to measure NF-kappaB nuclear translocation induced by interleukin (IL)-1 and tumor necrosis factor-alpha (TNFalpha). The amount of p65 staining is measured in both the nuclei defined by Hoechst 33342 labeling and in the surrounding cytoplasmic area within a preselected number of cells/well in 96-well plates. Using this technique in synchronously activated human chondrocytes or HeLa cells, NF-kappaB was found to move to the nucleus with a half-time of 7-8 min for HeLa and 12-13 min for chondrocytes, a rate in each case about 4-5 min slower than that of Ikappa Balpha degradation. IL-1 receptor antagonist and anti-TypeI IL-1 receptor antiserum on the one hand and anti-TNFalpha and monoclonal anti-TNF receptor 1 antibodies on the other hand could be shown to respectively inhibit IL-1 and TNFalpha stimulation in both cell types. In contrast, a polyclonal anti-TNF receptor 1 antiserum exhibited both a 50% agonism and a 50% antagonism to a TNFalpha stimulation in a dose-dependent fashion, indicating that subtle functional responses to complex agonist and antagonist stimuli could be measured. The effects of different proteasome inhibitors to prevent Ikappa Balpha degradation and subsequent NF-kappaB translocation could also be discriminated; Leu-Leu-Leu aldehyde was only a partial inhibitor with an IC50 of 2 microM, while clastolactacystin beta-lactone was a complete inhibitor with an IC50 of 10 microM. The nonselective kinase inhibitor K252a completely inhibited both IL-1 and TNFalpha stimulation in both cell types with an IC50 of 0.4 microM. This concentration, determined after a 20-min stimulation, was shown to be comparable with that obtained for inhibition of IL-6 production induced by a 100-fold lower IL-1 and TNFalpha concentration measured after 17 h of stimulation. These results suggest that the ArrayScanTM technology provides a rapid, sensitive, quantitative technique for measuring early events in the signal transduction of NF-kappaB.
High-Performance Semiconducting Polythiophenes for Organic Thin-Film Transistors (2004)

Conjugated polymers have been widely studied as potential semiconductor materials for organic thin-film transistors (TFTs). However, they have provided functionally poor transistor properties when the TFTs are fabricated in air. We have developed a class of liquid crystalline regioregular polythiophenes, PQTs, that possess sufficient air stability to enable achievement of excellent TFT properties under ambient conditions. These polythiophenes exhibit unique self-assembly ability and form highly structured thin films when deposited from solution under appropriate conditions. TFTs fabricated in air with PQT channel layers have provided high field-effect mobility to 0.14 cm2 V-1 s-1 and high current modulation to over 107, together with other desirable transistor properties. These high-performance polythiophenes will therefore help bring the long-standing concept of low-cost organic/polymer transistor circuits closer to commercial reality.
Phase behaviour of alkyl glycerol ether surfactants (1998)

In this paper the phase behaviour and physical properties of a series of alkyl (C-6, C-8, C-12 and iso-C-8) monoglycerol ethers and 2-hydroxyalkyl (C-6, C-8, C-12) monoglycerol ethers are presented ...
Evolutionary Shape Control During Colloidal Quantum‐Dot Growth (2007)

Size-dependent optical properties of semiconductor nanocrystals are of great interest because of the myriad of phenomena stemming from them. The preparation of more complex colloidal shapes will facilitate the systematic study of shape-dependent phenomena. It is shown that a strategy to obtain systematically more complex nanocrystal structures is to exert a sequence of shape-directing steps during the colloidal growth. Using experiments based on multiple reagent injections we show how changes in the type of surfactant introduced during growth of CdSe nanocrystals promotes shape evolution. On this basis, we propose a means to achieve a further generation of shape design in nanometer-sized colloids by using a series of growth steps, each one building from the previous conditions of shape as well as surface-specific reactivity. To understand the shape formation and stability in nanocrystalline colloids, and particularly the importance of surface ligands, we introduce an analogy with the thermodynamics of droplets.
Gain-of-function mutations of PPM1D/Wip1 impair the p53-dependent G1 checkpoint (2013)

The DNA damage response (DDR) pathway and its core component tumor suppressor p53 block cell cycle progression after genotoxic stress and represent an intrinsic barrier preventing cancer development. The serine/threonine phosphatase PPM1D/Wip1 inactivates p53 and promotes termination of the DDR pathway. Wip1 has been suggested to act as an oncogene in a subset of tumors that retain wild-type p53. In this paper, we have identified novel gain-of-function mutations in exon 6 of PPM1D that result in expression of C-terminally truncated Wip1. Remarkably, mutations in PPM1D are present not only in the tumors but also in other tissues of breast and colorectal cancer patients, indicating that they arise early in development or affect the germline. We show that mutations in PPM1D affect the DDR pathway and propose that they could predispose to cancer.
Molecular Cloning and Functional Expression of Glutamate Receptor Subunit Genes (1990)

Three closely related genes, GluR1, GluR2, and GluR3, encode receptor subunits for the excitatory neurotransmitter glutamate. The proteins encoded by the individual genes form homomeric ion channels in Xenopus oocytes that are sensitive to glutamatergic agonists such as kainate and quisqualate but not to N-methyl-D-aspartate, indicating that binding sites for kainate and quisqualate exist on single receptor polypeptides. In addition, kainate-evoked conductances are potentiated in oocytes expressing two or more of the cloned receptor subunits. Electrophysiological responses obtained with certain subunit combinations show agonist profiles and current-voltage relations that are similar to those obtained in vivo. Finally, in situ hybridization histochemistry reveals that these genes are transcribed in shared neuroanatomical loci. Thus, as with gamma-aminobutyric acid, glycine, and nicotinic acetylcholine receptors, native kainate-quisqualate-sensitive glutamate receptors form a family of heteromeric proteins.
Effect of Carbon-4 and Carbon-5 Volatile Fatty Acids on Digestion of Plant Cell Wall In Vitro (1985)

Abstract When mixed ruminal bacteria were incubated in an artificial medium with isolated plant cell walls, cell wall digestion and ammonia utilization were increased by low concentrations ( M ) of carbon-4 and carbon-5vol.tile fatty acids (isobutyric, isovaleric, valeric, and 2-methylbutyric). Carbon-4 and carbon-5 acid supplementation also increased cell wall digestion of intact forages. No pattern was observed between protein content of the feed and response to carbon-4 and carbon-5vol.tile fatty acids. Only the branch-chain acids (isovaleric, isobutyric, and 2-methylbutyric) stimulated bacterial growth and plant cell wall digestion. No synergisms were observed among the branched-chain acids, and they could replace each other. Valeric acid, a straight chain compound, was without effect, and phenylpropionic and phenylacetic acids likewise did not improve digestibility. The peptide source, Trypticase, enhanced cell wall digestion more than carbon-4 and carbon-5vol.tile fatty acids alone, and this observation suggested that fiber digesting bacteria may be stimulated directly by amino acids or peptides.
C‐type natriuretic peptide activates a non‐selective cation current in acutely isolated rat cardiac fibroblasts via natriuretic peptide C receptor‐mediated signalling (2007)

In the heart, fibroblasts play an essential role in the deposition of the extracellular matrix and they also secrete a number of hormonal factors. Although natriuretic peptides, including C-type natriuretic peptide (CNP) and brain natriuretic peptide, have antifibrotic effects on cardiac fibroblasts, the effects of CNP on fibroblast electrophysiology have not been examined. In this study, acutely isolated ventricular fibroblasts from the adult rat were used to measure the effects of CNP (2 x 10(-8) M) under whole-cell voltage-clamp conditions. CNP, as well as the natriuretic peptide C receptor (NPR-C) agonist cANF (2 x 10(-8) M), significantly increased an outwardly rectifying non-selective cation current (NSCC). This current has a reversal potential near 0 mV. Activation of this NSCC by cANF was abolished by pre-treating fibroblasts with pertussis toxin, indicating the involvement of G(i) proteins. The cANF-activated NSCC was inhibited by the compounds Gd(3+), SKF 96365 and 2-aminoethoxydiphenyl borate. Quantitative RT-PCR analysis of mRNA from rat ventricular fibroblasts revealed the expression of several transient receptor potential (TRP) channel transcripts. Additional electrophysiological analysis showed that U73122, a phospholipase C antagonist, inhibited the cANF-activated NSCC. Furthermore, the effects of CNP and cANF were mimicked by the diacylglycerol analogue 1-oleoyl-2-acetyl-sn-glycerol (OAG), independently of protein kinase C activity. These are defining characteristics of specific TRPC channels. More detailed molecular analysis confirmed the expression of full-length TRPC2, TRPC3 and TRPC5 transcripts. These data indicate that CNP, acting via the NPR-C receptor, activates a NSCC that is at least partially carried by TRPC channels in cardiac fibroblasts.
Combined Cell Culture Enzyme-Linked Immunosorbent Assay for Quantification of Poliovirus Neutralization- Relevant Antibodies (2000)

A combined cell culture enzyme-linked immunosorbent assay (CCC-ELISA) was developed for measuring the neutralizing antipoliovirus antibodies in human sera. The binding of different concentrations of each of the three poliovirus types to BGM cells in the presence and absence of a constant dilution from each test and reference serum was measured in the CCC-ELISA. The titers of the viruses neutralized by each serum were measured with the titration curves and used for interpretation of neutralizing titers to the three poliovirus types. Analysis of human sera revealed that the sensitivity and specificity of the CCC-ELISA and the microneutralization assay were comparable. The CCC-ELISA is nonsubjective, rapid, and highly reproducible. Furthermore, the CCC-ELISA could potentially be used as a seroepidemiologic tool for assessment of the humoral response to the cell culture infectious viruses.
Longitudinal Data Analysis for Discrete and Continuous Outcomes (1986)

Longitudinal data sets are comprised of repeated observations of an outcome and a set of covariates for each of many subjects. One objective of statistical analysis is to describe the marginal expectation of the outcome variable as a function of the covariates while accounting for the correlation among the repeated observations for a given subject. This paper proposes a unifying approach to such analysis for a variety of discrete and continuous outcomes. A class of generalized estimating equations (GEEs) for the regression parameters is proposed. The equations are extensions of those used in quasi-likelihood (Wedderburn, 1974, Biometrika 61, 439-447) methods. The GEEs have solutions which are consistent and asymptotically Gaussian even when the time dependence is misspecified as we often expect. A consistent variance estimate is presented. We illustrate the use of the GEE approach with longitudinal data from a study of the effect of mothers' stress on children's morbidity.
Microprocessor reliability performance as a function of die location for a 0.25 μ, five layer metal CMOS logic process (2003)

In this paper, we present the results of multiple correlations between reliability (infant mortality and other reliability metrics) and yield on a die level basis for an advanced microprocessor fabricated using a 0.25 /spl mu/m, five layer metal CMOS logic process. Traceability information was programmed into each unit; infant mortality of edge die verses center die, effects of unusual sort yield signatures on infant mortality, alternating row effects, and the sources of variability of burn-in failures were investigated. The model with reliability defect density proportional to yield defect density was found to be in excellent agreement with experimental data over a wide range of yield values. The x-y die position yield was found to be an excellent predictor of infant mortality. The variation in infant mortality from wafer to wafer was found to be twice the lot to lot variation, consistent with the large number of single wafer processing tools used on advanced fabrication processes. As the traceability information is part of the standard manufacturing flow, this analysis was performed using a very large 1 million unit sample size. Die near the edge of the wafer were found to have worse reliability than those near the center; certain die locations were particularly poor. Unusual yield signatures at wafer sort often showed the same map of failures in burn-in. The level of resolution possible from a die level analysis also allowed us to identify specific tools and interactions between tools in the fabrication process which were responsible for reliability failures.
Combinatorial Libraries (1993)

Combinatorial antibody libraries, in which PCR amplified immunoglobulin light and heavy chain DNA are randomly recombined irrespective of their pairing in vivo into a vector and subsequently expressed in E. coli, have quickly become a very productive tool to generate monoclonal antibodies from various species. It has been drastically improved by utilizing phage display technologies in the selection process of specific antibodies. A brief summary of current techniques, critical published experiments showing the versatility of these systems with emphasis on human antibodies and discussions on chain preference, affinity maturation and the advent of semisynthetic and non-immune libraries will be presented.
Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence. (1992)

Single and multiple Xaa----Ala substitutions were constructed in the alpha-helix comprising residues 39-50 in bacteriophage T4 lysozyme. The variant with alanines at 10 consecutive positions (A40-49) folds normally and has activity essentially the same as wild type, although it is less stable. The crystal structure of this polyalanine mutant displays no significant change in the main-chain atoms of the helix when compared with the wild-type structure. The individual substitutions of the solvent-exposed residues Asn-40, Ser-44, and Glu-45 with alanine tend to increase the thermostability of the protein, whereas replacements of the buried or partially buried residues Lys-43 and Leu-46 are destabilizing. The melting temperature of the lysozyme in which Lys-43 and Leu-46 are retained and positions 40, 44, 45, 47, and 48 are substituted with alanine (i.e., A40-42/44-45/47-49) is increased by 3.1 degrees C relative to wild type at pH 3.0, but reduced by 1.6 degrees C at pH 6.7. In the case of the charged amino acids Glu-45 and Lys-48, the changes in melting temperature indicate that the putative salt bridge between these two residues contributes essentially nothing to the stability of the protein. The results clearly demonstrate that there is considerable redundancy in the sequence information in the polypeptide chain; not every amino acid is essential for folding. Also, further evidence is provided that the replacement of fully solvent-exposed residues within alpha-helices with alanines may be a general way to increase protein stability. The general approach may permit a simplification of the protein folding problem by retaining only amino acids proven to be essential for folding and replacing the remainder with alanine.
Multiplex PCR for identifying mycobacterial isolates. (1995)

This method may facilitate rapid and convenient identification of most clinical isolates of mycobacteria by PCR and gel electrophoresis. Further evaluation is warranted.
Assignment of Transforming Growth Factor β1 and β3 and a Third New Ligand to the Type I Receptor ALK-1 (1999)

Germ line mutations in one of two distinct genes, endoglin or ALK-1, cause hereditary hemorrhagic telangiectasia (HHT), an autosomal dominant disorder of localized angiodysplasia. Both genes encode endothelial cell receptors for the transforming growth factor beta (TGF-beta) ligand superfamily. Endoglin has homology to the type III receptor, betaglycan, although its exact role in TGF-beta signaling is unclear. Activin receptor-like kinase 1 (ALK-1) has homology to the type I receptor family, but its ligand and corresponding type II receptor are unknown. In order to identify the ligand and type II receptor for ALK-1 and to investigate the role of endoglin in ALK-1 signaling, we devised a chimeric receptor signaling assay by exchanging the kinase domain of ALK-1 with either the TGF-beta type I receptor or the activin type IB receptor, both of which can activate an inducible PAI-1 promoter. We show that TGF-beta1 and TGF-beta3, as well as a third unknown ligand present in serum, can activate chimeric ALK-1. HHT-associated missense mutations in the ALK-1 extracellular domain abrogate signaling. The ALK-1/ligand interaction is mediated by the type II TGF-beta receptor for TGF-beta and most likely through the activin type II or type IIB receptors for the serum ligand. Endoglin is a bifunctional receptor partner since it can bind to ALK-1 as well as to type I TGF-beta receptor. These data suggest that HHT pathogenesis involves disruption of a complex network of positive and negative angiogenic factors, involving TGF-beta, a new unknown ligand, and their corresponding receptors.