gebhart/patrepeval huggingface dataset:
Angiostatin and matrix metalloprotease expression following ischemic acute renal failure (2004)

Ischemic injury to the kidney results in blood vessel loss and predisposition to chronic renal disease. Angiostatin is a proteolytic cleavage product of plasminogen that inhibits angiogenesis, promotes apoptosis of endothelial cells, and disrupts capillary integrity. A combination of lysine-Sepharose enrichment followed by Western blotting was used to study the expression of angiostatin in response to the induction of ischemic renal injury. No angiostatin products were readily detectable in kidneys of sham-operated control rats. In contrast, both 38- and 50-kDa forms of angiostatin were dramatically enhanced in the first 3 days following 45-min ischemia-reperfusion injury. Renal angiostatin levels declined but remained detectable at late time points postrecovery (8-35 days postischemia). Angiostatin-like immunoreactivity was also elevated in the plasma and in urine for up to 35 days following injury. Lysine-Sepharose extracts of either kidney or urine inhibited vascular endothelial cell growth factor-induced proliferation of human aortic endothelial cells in vitro; an effect that was blocked by coincubation with an angiostatin antibody. RT-PCR verified that mRNA of the parent protein plasminogen was produced in the liver, but it was not present in either sham-operated or postischemic kidney. Matrix metalloproteinase (MMP)-2 and MMP-9, which may mediate angiostatin generation, were enhanced in postischemic kidney tissue and were localized to the renal tubules, interstitial cells, and the tubulo-interstitial space. These data indicate the possible local synthesis of angiostatin following acute renal failure (ARF) and suggest a possible role for MMPs in this activity. Renal angiostatin generation following ARF may modulate renal capillary density postischemia and thereby influence chronic renal function.
N-terminal amino acid sequences of the polyoma middle-size T antigen are important for protein kinase activity and cell transformation. (1984)

We constructed deletion mutations which removed N-terminal coding sequences of various lengths from a cloned polyoma middle-size T antigen (MT antigen) gene. We introduced the MT antigen genes into a simian virus 40 expression vector so that they were expressed at high levels under the control of the simian virus 40 late promoter in COS-1 cells. The deletion mutant genes synthesized truncated MT antigens whose size was consistent with the deletion of either 70 or 106 amino acids from N termini, owing to initiation of translation at internal methionine codons in the MT antigen-coding region. The truncated MT antigens were found in cell membrane fractions but failed to show MT antigen-associated protein kinase activity. The cloned deletion mutant DNAs failed to transform rat F2408 or mouse NIH 3T3 cells. Therefore, N-terminal amino acid sequences of the polyoma MT antigen, as well as C-terminal sequences, are important for protein kinase activity and cell transformation.
Rapid Up-regulation of IκBβ and Abrogation of NF-κB Activity in Peritoneal Macrophages Stimulated with Lipopolysaccharide (1997)

Lipopolysaccharide (LPS) administration to mice elicited the activation of nuclear factor kappaB (NF-kappaB) in several tissues including liver and macrophages. Maximal activation was observed 1 h after treatment but declined at 3 and 6 h. The levels of IkappaBalpha and IkappaBbeta were analyzed during this period in an attempt to correlate NF-kappaB activity with IkappaB resynthesis. Degradation of IkappaBalpha was very rapid and was followed by recovery 1 h after LPS administration. IkappaBbeta degradation, which has been associated with persistent NF-kappaB activation, was complete at 1 h. However, a rapid recovery of IkappaBbeta in these tissues was observed at 3 h in parallel with the abrogation of NF-kappaB activity. Immunolocalization of newly synthesized IkappaBbeta by confocal microscopy revealed its preferential accumulation in the cytosol. Analysis of IkappaBbeta by Western blot using high resolution polyacrylamide gel electrophoresis showed the presence of two bands in cytosolic extracts of LPS-treated macrophages at 3 h, but only one band with the same mobility as the control was detected at 6 h. Moreover, treatment of extracts of resynthesized IkappaBbeta with alkaline phosphatase resulted in the accumulation of the protein of slightly higher electrophoretic mobility, indicating the prevalence of a rapid phosphorylation of the newly synthesized IkappaBbeta. At the mRNA level, up-regulation of IkappaBbeta was observed in macrophages stimulated for 1 h with LPS. When the effect of pro-inflammatory cytokines was investigated, tumor necrosis factor alpha, but not interleukin-1 or interferon-gamma, promoted an important degradation of IkappaBbeta followed by an increase in the mRNA at 1 h. These results suggest the existence of LPS- and tumor necrosis factor alpha- specific pathways involved in a rapid IkappaBbeta degradation and resynthesis and might explain the transient period of activation of NF-kappaB in these tissues upon stimulation with these factors. This rapid control of NF-kappaB function may contribute to the attenuation of the inflammatory response of these cells.
Electromagnetically coupled circular-patch antenna consisting of multilayered configuration (1996)

A new multilayered circular-patch antenna fed by an electromagnetic coupling method is proposed. This antenna realizes good impedance matching to a feed line. From experimental results, one observes that the bandwidth is 3.05%, which is 1.4 times wider than that of a conventional circular-patch antenna of the same parameters. The resonant frequency of the proposed circular-patch antenna fed by the proximity method was 1.13 times higher than that of the conventionally fed patch. The bandwidth of the proposed circular-patch antenna fed by the aperture-coupled method was 1.98%, and this bandwidth was 1.2 times wider than that of a conventional circular-patch antenna.
A COMPREHENSIVE MODEL OF MUTATIONS AFFECTING FITNESS AND INFERENCES FOR ARABIDOPSIS THALIANA (2002)

As the ultimate source of genetic variation, spontaneous mutation is essential to evolutionary change. Theoretical studies over several decades have revealed the dependence of evolutionary consequences of mutation on specific mutational properties, including genomic mutation rates, U, and the effects of newly arising mutations on individual fitness, s. The recent resurgence of empirical effort to infer these properties for diverse organisms has not achieved consensus. Estimates, which have been obtained by methods that assume mutations are unidirectional in their effects on fitness, are imprecise. Both because a general approach must allow for occurrence of fitness-enhancing mutations, even if these are rare, and because recent evidence demands it, we present a new method for inferring mutational parameters. For the distribution of mutational effects, we retain Keightley's assumption of the gamma distribution, to take advantage of the flexibility of its shape. Because the conventional gamma is one sided, restricting it to unidirectional effects, we include an additional parameter, rho, as an amount it is displaced from zero. Estimation is accomplished by Markov chain Monte Carlo maximum likelihood. Through a limited set of simulations, we verify the accuracy of this approach. We apply it to analyze data on two reproductive fitness components from a 17-generation mutation-accumulation study of a Columbia accession of Arabidopsis thaliana in which 40 lines sampled in three generations were assayed simultaneously. For these traits, U approximately/= 0.1-0.2, with distributions of mutational effects broadly spanning zero, such that roughly half the mutations reduce reproductive fitness. One evolutionary consequence of these results is lower extinction risks of small populations of A. thaliana than expected from the process of mutational meltdown. A comprehensive view of the evolutionary consequences of mutation will depend on quantitatively accounting for fitness-enhancing, as well as fitness-reducing, mutations.
A Novel Synthesis of Sulfones via the 0.0-Diethylphosphorotellurite Ion-Assisted Coupling of Arenesulfonyl Chlorides with Active Halides (1990)

Abstract Arenesulfonyl chlorides undergo a facile onepot coupling reaction with active halides assisted by sodium 0.0-diethylphosphorotellurite to give the corresponding sulfones in excellent yieldo
Prethymic CD34+ progenitors capable of developing into T cells are not committed to the T cell lineage (1997)

Progenitor cells that seed the fetal thymus are derived from the fetal liver and the bone marrow. These cells migrate through the fetal blood to the thymus. In this work, we address which peripheral progenitor cells have the potential to become T cells and whether these progenitor cells are already committed to the T cell lineage. All CD34+CD38- precursor cells, regardless of their origin, are able to develop into T cells in a hybrid human/mouse fetal thymic organ culture. Previously, we found that the more differentiated CD34+CD38+ progenitor cells from fetal liver cannot develop into T cells. In this work, we show that CD34+CD38+ cells from fetal bone marrow and cord blood are capable of T cell development. In spite of the T cell-developing potential, we did not detect rearrangements of TCR-delta or TCR-beta loci in any of the CD34+ peripheral precursors. CD34+ fetal bone marrow cell subpopulations express pre-TCR-alpha. However, we could not detect expression of pT alpha or of recombination-activating gene 1 in CD34+ cord blood cells. Since cord blood CD34+ cells should contain the direct progenitors of the CD34+ thymocytes, our data do not support the notion that in humans commitment to the T cell lineage occurs before the cells migrate into the thymus.
Significance of GTP Hydrolysis in Ypt1p-regulated Endoplasmic Reticulum to Golgi Transport Revealed by the Analysis of Two Novel Ypt1-GAPs (2002)

We here report on the identification and detailed biochemical characterization of two novel GTPase-activating proteins, Gyp5p and Gyp8p, whose efficient substrate is Ypt1p, a Ypt/Rab-GTPase essential for endoplasmic reticulum-to-Golgi trafficking in yeast. Gyp5p accelerated the intrinsic GTPase activity of Ypt1p 4.2 x 10(4)-fold and, surprisingly, the 40-fold reduced GTP hydrolysis rate of Ypt1(Q67L)p 1.5 x 10(4)-fold. At steady state, the two newly discovered GTPase-activating proteins (GAPs) as well as the previously described Gyp1p, which also uses Ypt1p as the preferred substrate, display different subcellular localization. To add to an understanding of the significance of Ypt1p-bound GTP hydrolysis in vivo, yeast strains expressing the GTPase-deficient Ypt1(Q67L)p and having different Ypt1-GAP genes deleted were created. Depending on the genetic background, different mutants exhibited growth defects at low temperature and, already at permissive temperature, various morphological alterations resembling autophagy. Transport of proteins was not significantly impaired. Growth defects of Ypt1(Q67L)-expressing cells could be suppressed on high expression of all three Ypt1-GAPs. We propose that permanently active Ypt1p leads to increased vesicle fusion, which might induce previously unnoticed autophagic degradation of exaggerated membrane-enclosed structures. The data indicate that hydrolysis of Ypt1p-bound GTP is a prerequisite for a balanced vesicle flow between endoplasmic reticulum and Golgi compartments.
Improved hot-carrier reliability of SOI transistors by deuterium passivation of defects at oxide/silicon interfaces (2002)

The effect of deuterium on hot-carrier reliability of fully processed 0.18 /spl mu/m silicon-on-insulator (SOI) devices is investigated. The improvement of device lifetime by a factor of 30 is achieved by passivating the interface defects with deuterium instead of hydrogen. The hydrogen/deuterium isotope effect (/spl gamma/), defined as the ratio of generation interface traps of a hydrogenated device to that of a deuterated one, shows strong dependence on the gate stress voltages (V/sub gs/). Increasing V/sub gs/ results in the decrease of /spl gamma/. These results suggest that the breaking of Si-H(D) bonds by channel electrons through the vibrational heating mechanism may play an important role in the degradation of deep submicron SOI devices.
Demonstration of the Proarrhythmic Preconditioning of Single Premature Extrastimuli by Use of the Magnitude, Phase, and Distribution of Repolarization Alternans (1999)

A single S(2) increases RPA magnitude, reverses its phase, and redistributes it later in repolarization in patients with the substrates for VT. These effects become more pronounced with shorter coupling intervals. These results suggest that it is possible to track the dynamic proarrhythmic preconditioning of single premature depolarizations.
In vitro assays fail to predict in vivo effects of regulatory polymorphisms (2007)

A typical paradigm in the investigation of complex human disease is to assess the effects of cis-regulatory polymorphisms implicated in association studies on transcription in cellular expression systems. Evidence from in vitro transfection studies is often assumed to be sufficient evidence for the in vivo functional importance of a polymorphism in the context of human disease, even though many confounding effects (e.g. temporal regulation, tissue specificity, genetic background) are not considered. In this study, we evaluate this assumption directly by examining the translation of in vitro results on allele-specific expression to an in vivo system using four genes that have been well documented through reporter assays to have promoter polymorphisms affecting transcription level: monoamine oxidase A (MAOA), neuropeptide Y (NPY), endothelial nitric oxide synthase (NOS3), and prodynorphin (PDYN). In our study, MAOA was found to have large allelic imbalances, which indicates that there is in vivo variation in the expression of this gene. However, the imbalances observed were not correlated with genotype at the putatively functional polymorphism. PDYN, NOS3 and NPY did not have large allelic imbalances. Overall, there was no statistically significant effect of these polymorphisms on expression level as measured by imbalance ratios in any of these genes. These results suggest that the functional effects of a polymorphism on gene expression may be more complicated and context dependent than is often assumed and also imply that the use of cell-based expression studies to support the role of such polymorphisms in disease etiology should be treated with caution.
Urinary excretion of N-acetyl-beta-D-glucosaminidase in proteinuric states. (1992)

Urinary excretion of N-acetyl-beta-D-glucosaminidase (NAG) was studied in 22 children with proteinuria and a normal glomerular filtration rate. Twelve patients had minimal change nephrotic syndrome (MCNS), 10 children suffered from different types of glomerulonephritis (GN) without tubulointerstitial renal disease. Sixty-six random urine samples were analyzed for protein, creatinine and NAG. There was a strong positive correlation between proteinuria and urinary NAG activity (r = 0.79, p = 0.0001). The raised NAG activities in proteinuric states turned to normal during remission of the disease. Patients with MCNS and GN did not differ significantly and had nearly identical correlation curves. Our results seem to indicate that functional changes in the renal tubular cells probably caused by protein resorption are responsible for this association. Raised NAG activities in proteinuria reflect the activity of the disease but cannot distinguish patients with MCNS and GN.
The chemistry of Eremophila spp. XVI. New serrulatanes from Eremophila spp. (1981)

Three new serrulatane diterpenes have been isolated from Eremophila species. Evidence is presented for the structure of (15S)-7,8,16-trihydroxyserrulatan-19-oic acid, isolated as its methyl ester from E. drummondii , serrulat-14-ene-7,8,20-trio1 from E. linearis Chinnock and for (2S)-serrulat-14-ene- 2,7,8,20-tetraol from E. granitica .
Stereochemistry of lysine formation by meso-diaminopimelate decarboxylase from wheat germ: use of proton-carbon-13 NMR shift correlation to detect stereospecific deuterium labeling (1985)

The stereochemical course of the wheat germ meso-diaminopimelate (DAP) decarboxylase reaction is compared to that of the decarboxylase isolated from Bacillus sphaericus, which has been reported to proceed with an unusual inversion of configuration [Asada, Y., Tanizawa, K., Sawada, S., Suzuki, T., Misono, H., & Soda, K. (1981) Biochemistry 20, 6881-6886]. Reaction of each enzyme with either unlabeled diaminopimelic acid in D2O or [2,6-2H2]diaminopimelic acid in H2O gave stereospecifically deuterium-labeled lysine samples that were derivatized with (-)-camphanoyl chloride and diazomethane. Analysis by two-dimensional 1H-13C heteronuclear NMR shift correlation spectroscopy with 2H decoupling confirmed the stereochemistry of the B. sphaericus enzyme reaction and showed that the eukaryotic wheat germ meso-DAP decarboxylase also operates with inversion of configuration. This suggests similar mechanisms for the prokaryotic and eukaryotic enzymes and contrasts the retention mode observed with other pyridoxal phosphate dependent alpha-decarboxylases.
Sandwich ELISAs for soluble immunoglobulin superfamily receptor translocation-associated 2 (IRTA2)/FcRH5 (CD307) proteins in human sera (2006)

These ELISAs may be useful for monitoring soluble IRTA2/FcRH5 in HCL and other B-cell malignancies.
Chemical synthesis of oligonucleotides (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical synthesis of oligonucleotidesV. Amarnath and A. D. BroomCite this: Chem. Rev. 1977, 77, 2, 183–217Publication Date (Print):April 1, 1977Publication History Published online1 May 2002Published inissue 1 April 1977https://pubs.acs.org/doi/10.1021/cr60306a002https://doi.org/10.1021/cr60306a002research-articleACS PublicationsRequest reuse permissionsArticle Views1668Altmetric-Citations159LEARN 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
[DNA microarray reveals changes in gene expression of endothelial cells under shear stress]. (2004)

cDNA microarray technology is used as a powerful tool for rapid, comprehensive, and quantitative analysis of gene profiles of cultured human umbilical vein endothelial cells(HUVECs) in the normal static group and the shear stressed (4.20 dyne/cm2, 2 h) group. The total RNA from normal static cultured HUVECs was labeled by Cy3-dCTP, and total RNA of HUVECs from the paired shear stressed experiment was labeled by Cy5-dCTP. The expression ratios reported are the average from the two separate experiments. After bioinformatics analysis, we identified a total of 108 genes (approximately 0.026%) revealing differential expression. Of these 53 genes expressions were up-regulated, the most enhanced ones being human homolog of yeast IPP isomerase, human low density lipoprotein receptor gene, Squalene epoxidase gene, 7-dehydrocholesterol reductase, and 55 were down-regulated, the most decreased ones being heat shock 70 kD protein 1, TCB gene encoding cytosolic thyroid hormone-binding protein in HUVECs exposed to low shear stress. These results indicate that the cDNA microarray technique is effective in screening the differentially expressed genes in endothelial cells induced by various experimental conditions and the data may serve as stimuli to further researches.
Multiple redox regulation in NF-kappaB transcription factor activation. (1997)

The well-known Rel/NF-kappaB family of vertebrate transcription factors comprises a number of structurally related, interacting proteins that bind DNA as dimers and whose activity is regulated by subcellular location. This family includes many members (p50, p52, RelA, RelB, c-Rel, ...), most of which can form DNA-binding homo- or hetero-dimers. All Rel proteins contain a highly conserved domain of approximately 300 amino-acids, called the Rel homology domain (RH), which contains sequences necessary for the formation of dimers, nuclear localization, DNA binding and IkappaB binding. Nuclear expression and consequent biological action of the eukaryotic NF-kappaB transcription factor complex are tightly regulated through its cytoplasmic retention by ankyrin-rich inhibitory proteins known as IkappaB. The IkappaB proteins include a group of related proteins that interact with Rel dimers and regulate their activities. The interaction of a given IkappaB protein with a Rel complex can affect the Rel complex in distinct ways. In the best characterized example, IkappaB-alpha interacts with a p50/RelA (NF-kappaB) heterodimer to retain the complex in the cytoplasm and inhibit its DNA-binding activity. The NF-kappaB/IkappaB-alpha complex is located in the cytoplasm of most resting cells, but can be rapidly induced to enter the cell nucleus. Upon receiving a variety of signals, many of which are probably mediated by the generation of reactive oxygen species (ROS), IkappaB-alpha undergoes phosphorylation at serine residues by a ubiquitin-dependent protein kinase, is then ubiquitinated at nearby lysine residues and finally degraded by the proteasome, probably while still complexed with NF-kappaB. Removal of IkappaB-alpha uncovers the nuclear localization signals on subunits of NF-kappaB, allowing the complex to enter the nucleus, bind to DNA and affect gene expression. Like proinflammatory cytokines (e.g. IL-1, TNF), various ROS (peroxides, singlet oxygen, ...) as well as UV (C to A) light are capable of mediating NF-kappaB nuclear translocation, while the sensor molecules which are sensitive to these agents and trigger IkappaB-alpha proteolysis are still unidentified. We also show that a ROS-independent mechanism is activated by IL-1beta in epithelial cells and seems to involve the acidic sphingomyelinase/ceramide transduction pathway.
Plasma needle forin vivomedical treatment: recent developments and perspectives (2006)

In this paper we describe the hitherto unravelled facts on the interactions of a cold atm. plasma with living cells and tissues. A specially designed source, plasma needle, is a low-power discharge, which operates under the threshold of tissue damage. When applied properly, the needle does not cause fatal cell injury which would result in cell death (necrosis). Instead, it allows precise and localized cell removal by means of the so-called cell detachment. In addn., plasma can be used for bacterial disinfection. Because of mild treatment conditions, plasma disinfection can be performed in vivo, e.g. on wounds and dental cavities. Presently, one strives to obtain a better control of the operating device. Therefore, plasma has been characterized using a variety of diagnostics, and a smart system has been designed for the positioning of the device with respect to the treated surface.