gebhart/patrepeval huggingface dataset:
Structural Studies of Ribonuclease. XVII. A Reactive Carboxyl Group in Ribonuclease* (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural Studies of Ribonuclease. XVII. A Reactive Carboxyl Group in Ribonuclease*John P. Riehm and Harold A. ScheragaCite this: Biochemistry 1965, 4, 4, 772–782Publication Date (Print):April 1, 1965Publication History Published online1 May 2002Published inissue 1 April 1965https://doi.org/10.1021/bi00880a023RIGHTS & PERMISSIONSArticle Views117Altmetric-Citations50LEARN 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 PDF (878 KB) Get e-Alertsclose Get e-Alerts
Cutting Edge: Identification of an Alternative GATA-3 Promoter Directing Tissue-Specific Gene Expression in Mouse and Human (2002)

The GATA family of transcription factors regulates development of multiple tissues. Several GATA factors have two promoters directing distinct tissue-specific expression. Although GATA-3 acts in both neuronal and thymocyte development, no alternative promoter usage has been reported. We examined various cell types and tissues for potential alternative GATA-3 transcripts and identified an alternative transcript directed by a promoter located 10 kb upstream of the recognized promoter. Sequences within this promoter and alternative first exon are highly conserved between mouse and human genomes. This new promoter is expressed selectively in the brain but is essentially undetectable in the thymus. In contrast, the recognized promoter is selectively expressed in the thymus but not in the brain. We also observed a gradual increase in expression from this new promoter during Th2 development. These results indicate that similar to other GATA factors, the GATA-3 gene can be controlled by two promoters that may direct lineage- and tissue-specific expression.
Lactate elicits vascular endothelial growth factor from macrophages: a possible alternative to hypoxia (2000)

Macrophages respond to various stimuli to produce angiogenic factors but few mechanistic details are known. We examined the effects of hypoxia, lactate and nicotinamide on the expression of vascular endothelial growth factor by cultured macrophages. These agents were chosen because they down-regulate polyadenosine diphosphoribose levels. Following exposure, conditioned media were analyzed for vascular endothelial growth factor protein. Nicotinamide adenine dinucleotide, polyadenosine diphosphoribose, and vascular endothelial growth factor mRNA were measured in the cellular fraction. Angiogenic capacity of the conditioned media was tested in rabbit corneas and Matrigel implants. All three agents, hypoxia, lactate and nicotinamide, elicited significantly increased levels of vascular endothelial growth factor mRNA and vascular endothelial growth factor in the conditioned media, and these levels were paralleled by their angiogenic activity. Polyadenosine diphosphoribose in the cellular fraction was correspondingly depressed. Anti-vascular endothelial growth factor antibody inhibited most of the angiogenic response whereas anti-basic fibroblast growth factor antibody had little effect. We propose that redox changes associated with the alteration of cellular nicotinamide adenine dinucleotide and polyadenosine diphosphoribose are involved in lactate-mediated VEGF expression.
Induced Pluripotent Stem Cell Generation Using a Single Lentiviral Stem Cell Cassette (2008)

Induced pluripotent stem (iPS) cells can be generated using retroviral vectors expressing Oct4, Klf4, Sox2, and cMyc. Most prior studies have required multiple retroviral vectors for reprogramming, resulting in high numbers of genomic integrations in iPS cells and limiting their use for therapeutic applications. Here we describe the use of a single lentiviral vector expressing a "stem cell cassette" composed of the four transcription factors and a combination of 2A peptide and internal ribosome entry site technology, generating iPS cells from postnatal fibroblasts. iPS cells generated in this manner display embryonic stem cell-like morphology, express stem cell markers, and exhibit in vivo pluripotency, as evidenced by their ability to differentiate in teratoma assays and their robust contribution to mouse chimeras. Combining all factors into a single transcript achieves the most efficient reprogramming system to date and allows derivation of iPS cells with a single viral integration. The use of a single lentiviral vector for reprogramming represents a powerful laboratory tool and a significant step toward the application of iPS technology for clinical purposes.
Proliferation of mutators in A cell population (1997)

A Lac- strain of Escherichia coli that reverts by the addition of a G to a G-G-G-G-G-G sequence was used to study the proliferation of mutators in a bacterial culture. Selection for the Lac+ phenotype, which is greatly stimulated in mismatch repair-deficient strains, results in an increase in the percentage of mutators in the selected population from less than 1 per 100,000 cells to 1 per 200 cells. All the mutators detected were deficient in the mismatch repair system. Mutagenesis results in a similar increase in the percentage of mutators. Mutagenesis combined with a single selection can result in a population of more than 50% mutators when a sample of several thousand cells is grown out and selected. Mutagenesis combined with two or more successive selections can generate a population that is 100% mutator. These experiments are discussed in relation to ideas that an early step in carcinogenesis is the creation of a mutator phenotype.
Tunable spatial heterodyne spectroscopy (TSHS): a new technique for broadband visible interferometry (2010)

In the study of faint, extended sources at high resolving power, interferometry offers significant etendue advantages relative to conventional dispersive grating spectrometers. A Spatial Heterodyne Spectrometer (SHS) is a compact format two-beam interferometer that produces wavenumber dependent 2-D Fizeau fringe pattern from which an input spectrum can be obtained via a Fourier transform. The sampled bandpass of SHS is limited by the highest spatial frequency that can be sampled by the detector, which is typically less than 10 nm. This limitation has made these instruments useful primarily for studies of single emission line features or molecular bands. To date there have been few broadband implementations. We describe here continuing progress toward development of a broadband tunable SHS (TSHS) that is based on an all-reflective format where a single grating operates simultaneously as a beam-splitter, dispersive element, and beam combiner. The narrow spectral coverage of the TSHS is moved to different tuning wavenumbers by adjusting the angle of the pilot mirrors that guide the interfering beams through the optical path, thus slewing the acceptance band over a much broader spectral range. Our present effort involves a breadboard laboratory prototype of a secondgeneration TSHS in which we address several technical limitations of an earlier version. In particular the new design reduces wavefront distortions on the pilot mirrors, solves problems with magnification and focus of the fringe localization plane onto the detector, and addresses the variability in sensitivity and resolving power limitations of using a single grating over a large bandpass.
Stable Non-Gaussian Random Processes (2017)

This book serves as a standard reference, making this area accessible not only to researchers in probability and statistics, but also to graduate students and practitioners. The book assumes only a first-year graduate course in probability. Each chapter begins with a brief overview and concludes with a wide range of exercises at varying levels of difficulty. The authors supply detailed hints for the more challenging problems, and cover many advances made in recent years.
Composite Chitosan/Nano-Hydroxyapatite Scaffolds Induce Osteocalcin Production by Osteoblasts In Vitro and Support Bone Formation In Vivo (2009)

There is a significant clinical need to develop alternatives to autografts and allografts for bone grafting procedures. Porous, biodegradable scaffolds based on the biopolymer chitosan have been investigated as bone graft substitutes, and the addition of calcium phosphate to these scaffolds has been shown to improve the mechanical properties of the scaffold and may increase osteoconductivity. In this study, in vitro mineralization was examined for osteoblasts seeded in a porous scaffold composed of fused chitosan/nano-hydroxyapatite microspheres. Human fetal osteoblasts were cultured on composite and chitosan scaffolds for 21 days. On days 1, 4, 7, 14, and 21, total dsDNA, alkaline phosphatase, type I collagen, and osteocalcin production were measured. Total cellularity (measured by dsDNA), alkaline phosphatase, and type I collagen production were similar between the two scaffold groups. However, osteocalcin production occurred significantly earlier (day 7 vs. day 21) and was more than three times greater (0.0022 vs. 0.0068 ng/mL/ng DNA) on day 21 when osteoblasts were cultured on composite scaffolds. Osteocalcin is a marker of late osteoblastic differentiation and mineralized bone matrix formation. Therefore, the increase in osteocalcin production seen when cells were cultured on composite scaffolds may indicate that these scaffolds were superior to chitosan-only scaffolds in facilitating osteoblast mineralization. Composite scaffolds were also shown to be biocompatible and osteoconductive in a preliminary critical size rat calvarial defect study. These results demonstrate the potential of composite chitosan/nano-hydroxyapatite scaffolds to be used in bone tissue engineering.
Indium-111-labeled leukocytes for the localization of abscesses: preparation, analysis, tissue distribution, and comparison with gallium-67 citrate in dogs. (1977)

Leukocytes have been labeled with indium-111-8-hydroxyquinoline complex. Seventy-five to 85 per cent of the initial activity has been obtained in the complex form of which 75 to 95 per cent is incorportaed with leukocytes. The polymophonuclear leukocytes are predominantly labeled, and the label has been found stable for at least 27 hours after invivo administration. The radioactivity clears from the circulating blood with a half time of 8 to 9-hours and accumulates in normal liver and spleen and in experimentally induced abscesses. The cells which have been labeled and damaged by heat concentrate mainly in the lungs. The in vivo distribution of the indium-111 labeled cells has been compared with the gallium-67 administered as citrate. The abscess to blood ratios of the indium-111 activity varied between 35 to 117, compared to 1.2 to 8 of the gallium-67. The abscess to liver, spleen, and kidney ratios are several fold higher with indium-111 leukocytes than with gallium=67 citrate. These results plus the suitable physical characteristics of indium-111 make the labeled leukocytes a better agent for the localization of abscesses.
On the Structure of Al2O3 and Photoelectron Spectra of Al2O2- and Al2O3- (1999)

Ab initio and density functional theory (DFT) calculations with the 6-311+G(2df) basis set have been performed on Al2O3, Al2O2, and their corresponding negative ions. A triplet ground state is predicted for the Al2O3 molecule and a doublet ground state for Al2O3-. Both Al2O3 and its negative ion have a C2v structure, which is a distorted form of the structure proposed in a recent report on negative ion photoelectron spectroscopy (PES) of AlxOy- (x = 1−2, y = 1−5) [J. Chem. Phys. 1997, 106, 1309]. Al2O2 and its negative ion have a planar (D2h) rhombic structure. The adiabatic electron affinity calculated at the CCSD(T) level is 3.28 eV for Al2O3 and 1.81 eV for Al2O2 compared to the experimental values of 3.71 and 1.88 eV, respectively. The singlet−triplet (S−T) gap of 0.49 eV observed for Al2O2 in the PES experiment compares quite well with our computed value of 0.47 eV. Adiabatic electron detachment energies (AEDE) of the anions calculated at the CCSD(T) level and B3LYP harmonic vibrational frequencies (including isotopic frequency shifts) of the lowest energy structures of the neutral molecules are provided for future experimental studies on these species.
Mitochondrial fatty acid oxidation defects—remaining challenges (2008)

Mitochondrial fatty acid oxidation defects have been recognized since the early 1970s. The discovery rate has been rather constant, with 3-4 'new' disorders identified every decade and with the most recent example, ACAD9 deficiency, reported in 2007. In this presentation we will focus on three of the 'old' defects: medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, riboflavin responsive multiple acyl-CoA dehydrogenation (RR-MAD) deficiency, and short-chain acyl-CoA dehydrogenase (SCAD) deficiency. These disorders have been discussed in many publications and at countless conference presentations, and many questions relating to them have been answered. However, continuing clinical and pathophysiological research has raised many further questions, and new ideas and methodologies may be required to answer these. We will discuss these challenges. For MCAD deficiency the key question is why 80% of symptomatic patients are homozygous for the prevalent ACADM gene variation c.985A > G whereas this is found in only approximately 50% of newborns with a positive screen. For RR-MAD deficiency, the challenge is to find the connection between variations in the ETFDH gene and the observed deficiency of a number of different mitochondrial dehydrogenases as well as deficiency of FAD and coenzyme Q(10). With SCAD deficiency, the challenge is to elucidate whether ACADS gene variations are disease-associated, especially when combined with other genetic/cellular/environmental factors, which may act synergistically.
Fc Receptors (1991)

Recent advances in the structural analysis of the genes and proteins for immunoglobulin Fc domain receptors have provided a molecular characterization of this complex family. The wide cellular distribution of these receptors and their functional heterogeneity are reflected in the diversity of molecules which bind antibody and immune complexes. The detailed analysis of the IgG and IgE Fc receptors has indicated that these molecules have evolved from a common precursor through gene duplication. Similarities among these receptors, in both structure and function have emerged. Thus, the Fc receptors provide an example of a class of molecules in which conserved domains are combined with divergent sequences to yield a diversity of function.
Site-selective derivatization of oligoethylenimines using five-membered-ring protection method (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSite-selective derivatization of oligoethylenimines using five-membered-ring protection methodTakeo Araki, Yasuo Kubo, Shinji Gohbara, Tatsuya Fujimoto, Akio Notsu, Masaru Nakahara, Toshihisa Isono, Noriko Masuda, and Kazumi FukumotoCite this: Macromolecules 1988, 21, 7, 1995–2001Publication Date (Print):July 1, 1988Publication History Published online1 May 2002Published inissue 1 July 1988https://pubs.acs.org/doi/10.1021/ma00185a018https://doi.org/10.1021/ma00185a018research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations10LEARN 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
Nuclear Induction in Inhomogeneous Fields (1955)

The mathematical methods developed by Jaynes are applied to the study of nuclear resonance in inhomogeneous magnetic fields. It is shown that a description of delayed-signal phenomena such as spin echoes is greatly simplified by the use of the spinor representation involving 2\ifmmode\times\else\texttimes\fi{}2 transformation matrices. The original results of Hahn on spin echoes are rederived in simplified fashion and more complicated situations are discussed, including large numbers of pulses, exact time dependence in extremely inhomogeneous fields, and continuous pulse trains. Several previously unreported types of delayed-signal phenomena are discussed and illustrated experimentally by oscilloscope traces. The apparatus used to study nuclear induction in very inhomogeneous fields is briefly discussed.
Differing modulation of protein kinase C by bryostatin 1 and phorbol esters in JB6 mouse epidermal cells. (1988)

Bryostatin 1 (Bryo), a macrocyclic lactone, stimulates some but not all of the biologic effects which are induced by phorbol esters (PEs). In vitro, it competes with PEs for binding to whole cells and activates the calcium/phospholipid-dependent protein kinase, PK-C. To examine whether Bryo, like PEs, is able to stimulate the nonadherent growth of cells, we used the mouse epidermal cell line JB6, which is stimulated by PEs to grow in soft agar. Like PEs, Bryo stimulates both the adherent and nonadherent growth of these cells, but Bryo (0.001-1 microM) is less active than equivalent concentrations of PEs. To attempt to explain the biologic differences between these two agents, we examined the modulation of PK-C by both PEs and Bryo. In a phosphotransferase assay using partially purified PK-C from JB6 cells, Bryo (1-0.001 microM) stimulated less phosphorylation of histone substrate than did PMA. Also, when whole cells were treated with equal concentrations of Bryo or PMA, Bryo stimulated a decreased loss of PK-C from the cytosol. Using purified isozymes of PK-C from rat brain, Bryo demonstrated identical competition to PMA for binding to forms alpha and gamma but decreased binding to form beta. Hydroxylapatite chromatography of JB6 cytosol demonstrated that these cells contain largely peak 2, or beta-PK-C. Although Bryo more weakly activates PK-C from JB6 cells, prolonged exposure of JB6 cells to either 1.0 or 0.01 microM Bryo caused a more rapid loss of immunologically detectable PK-C than did similar concentrations of PEs. We conclude that Bryo is capable of stimulating both the nonadherent and the adherent growth of JB6 cells in a similar fashion to phorbol esters. The differences in biologic effects of Bryo and PMA may be partially explained by Bryo's modulation of PK-C.
Effects of JAK3 Inhibition with CP-690,550 on Immune Cell Populations and Their Functions in Nonhuman Primate Recipients of Kidney Allografts (2005)

Potent in vitro and in vivo immunomodulatory effects of the JAK3 inhibitor CP-690,550 likely contribute to its efficacy in the prevention of organ allograft rejection.
Effects of medium chain fatty acids (MCFA), myristic acid, and oleic acid on serum lipoproteins in healthy subjects (1997)

In this study we investigated the effects on lipoproteins of medium chain fatty acids (MCFA) and myristic acid relative to those of oleic acid. Thirty-seven women and 23 men consumed a 3-wk run-in diet enriched in oleic acid followed by a 6-wk test diet rich in MCFA (n = 21), myristic (n = 20), or oleic acid (n = 19). Experimental fats were incorporated into solid foods. Total fat intake was 40 En% fat. The dietary compositions were the same except for 10 En%, which was provided by MCFA, myristic, or oleic acids, respectively. With the myristic acid diet, low density lipoprotein (LDL) cholesterol was 0.37 mmol/L higher compared with the oleic acid diet (P = 0.0064 for difference in changes). The MCFA diet increased LDL cholesterol, though not significantly, with 0.23 mmol/L relative to the oleic acid diet (P = 0.0752). Compared with the oleic acid diet, HDL cholesterol concentrations increased with the myristic acid diet by 0.10 mmol/L (P = 0.0273) but not with the MCFA diet. The MCFA diet slightly elevated triacylglycerol concentrations, but responses did not significantly differ between the diets. The MCFA diet significantly decreased the apoA-I to apoB ratio compared with both other diets (P < 0.02). We conclude that MCFA raise LDL cholesterol concentrations slightly and affect the apoA-I to apoB ratio unfavorably compared with oleic acid. Myristic acid is hypercholesterolemic, although less than predicted earlier, and raises both LDL and HDL cholesterol concentrations compared with oleic acid.
Probing weakly polar interactions in cytochrome c (1993)

Theoretical, statistical, and model studies suggest that proteins are stabilized by weakly polar attractions between sulfur atoms and properly oriented aromatic rings. The two sulfur-containing amino acids, methionine and cysteine, occur frequently among functional alleles in random mutant libraries of Saccharomyces cerevisiae iso-1-cytochrome c genes at positions that form a weakly polar aromatic-aromatic interaction, the wild-type protein. To determine if a weakly polar sulfur-aromatic interaction replaced the aromatic-aromatic interaction, the structure and stability of two variants were examined. Phenylalanine 10, which interacts with tyrosine 97, was replaced by methionine and cysteine. The cysteine was modified to form the methionine and cysteine analog, S-methyl cysteine (CysSMe). Proton NMR studies indicate that changing Phe 10 to Met or CysSMe affects only local structure and that the structures of sulfur-containing variants are nearly identical. Analysis of chemical shifts and nuclear Overhauser effect data indicates that both sulfur-containing side chains are in position to form a weakly polar interaction with Tyr 97. The F10M and F10CSMe variants are 2-3 kcal mol-1 less stable than iso-1-cytochrome c at 300 K. Comparison of the stabilities of the F10M and F10CSMe variants allows evaluation of the potential weakly polar interaction between the additional sulfur atom of F10CSMe and the aromatic moiety of Tyr 97. The F10CSMe;C102T variant is 0.7 +/- 0.3 kcal mol-1 more stable than the F10M;C102T protein. The increased stability is explained by the difference in hydrophobicity of the sulfur-containing side chains. We conclude that any weakly polar interaction between the additional sulfur and the aromatic ring is too weak to detect or is masked by destabilizing contributions to the free energy of denaturation.